Next Article in Journal
Sentinel or Disperser? The Role of White Storks (Ciconia ciconia) in the Spread of Antibiotic-Resistant Bacteria
Previous Article in Journal
Microbiological Analysis of Traditional Sausage in Prishtina, Republic of Kosovo, During Production and Storage
 
 
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Review

The Prevalence of ESKAPE Pathogens and Their Drug Resistance Profiles in Aquatic Environments Around the World

by
Tunde Olarinde Olaniyan
1,
Ana Verónica Martínez-Vázquez
1,
Cesar Marcial Escobedo-Bonilla
2,
Cristina López-Rodríguez
3,
Patricia Huerta-Luévano
3,
Oziel Castrejón-Sánchez
3,
Wendy Lizeth de la Cruz-Flores
4,
Manuel J. Cedeño-Castillo
4,
Erick de Jesús de Luna-Santillana
1,
Maria Antonia Cruz-Hernández
1,
Gildardo Rivera
1 and
Virgilio Bocanegra-García
1,*
1
Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
2
CIIDIR Sinaloa, Instituto Politécnico Nacional, Guasave 81101, Mexico
3
Campus Reynosa, Universidad del Valle de México, Reynosa 88769, Mexico
4
Campus de Medicina, Universidad México Americana del Norte, Reynosa 88640, Mexico
*
Author to whom correspondence should be addressed.
Microbiol. Res. 2025, 16(9), 201; https://doi.org/10.3390/microbiolres16090201
Submission received: 25 June 2025 / Revised: 31 August 2025 / Accepted: 2 September 2025 / Published: 4 September 2025

Abstract

Antimicrobial-resistant bacteria (ARB) in the ESKAPE group include Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. These pathogens continue to pose a global threat to human health. Urban and non-urban rivers affected by anthropogenic activities such as farming can act as reservoirs for ARB. The influx of wastewater from animal farms and irrigation processes can affect the normal microbiota in surrounding waterbodies. New bacteria, such as those in the ESKAPE family, may be introduced into these waterbodies, since most ESKAPE pathogens are domiciled in humans and animals. There is a dearth of information on the persistence of ESKAPE isolates and their associated health hazards in non-nosocomial settings. Therefore, this review aimed to collect data on the global distribution of ESKAPE pathogens in aquatic systems. PubMed and Google Scholar were searched for articles published from 2009 to 2025. A total of 76 studies published in peer-reviewed journals were included. Data were collected from 21 papers for E. faecium/faecalis, 12 for S. aureus, 15 for K. pneumoniae, 11 for A. baumannii, 8 for P. aeruginosa, and 9 for Enterobacter spp. The findings in this review will increase public health awareness on the significance of ESKAPE pathogens in aquatic systems.

1. Introduction

Antibiotic-resistant bacterial (ARB) pathogens are considered a serious global health hazard by the World Health Organization [1] and the U.S. Centers for Disease Control and Prevention [2]. This is based on widespread patterns of resistance, impacts on animal and plant health, and the cost of treatment [1]. A major contributor to antimicrobial resistance (AMR) is the intensive and widespread use of antibiotics globally, leading to an increasing public health hazard [3,4]. To minimize risk and address the challenges associated with AMR, the WHO has identified certain bacteria as key contributors to resistance and classified them into three priority groups: critical, high, and medium. The critical priority group includes carbapenem-resistant Acinetobacter baumannii, as well as carbapenem-resistant and third-generation cephalosporin-resistant Klebsiella pneumoniae and Enterobacter spp., while the high-priority group includes carbapenem-resistant Pseudomonas aeruginosa and Enterococcus faecium and Staphylococcus aureus, resistant to vancomycin and methicillin, respectively [5,6].
AMR poses a significant challenge globally, affecting nations irrespective of their geographic location or economic status [1]. Antibiotic-resistant microbes are thought to be the cause of over 2 million infections and at least 29,000 fatalities per year in the United States [7,8]. In Thailand and the United States, the anticipated total cost of combating resistance to five pathogenic bacteria (S. aureus, Escherichia coli, K. pneumoniae, A. baumannii, and P. aeruginosa) was approximately USD 0.5 billion and USD 2.9 billion, respectively [9]. AMR infections are responsible for more than 33,000 annual deaths and 874,000 disability-adjusted life years (DALYs) in countries in the European Union (EU) and European Economic Area (EEA) in Europe, and result in USD 1.5 billion in direct and indirect costs [10,11]. Switzerland (a non-EEA member) estimated 276 associated deaths and 7400 DALYs from over 7000 infections [12]. Compared with individual EU and EEA countries, Switzerland’s 2015 estimate (87.8 DALYs per 100,000) was higher than that of Austria (77.2), Germany (64.3), and economically comparable countries, such as Luxembourg (70.9) and Denmark (52.3), but lower than that of Italy (448.4) and France (220.7) [10,12]. The deaths caused by AMR in sub-Saharan Africa were estimated at 23.5 deaths per 100,000 people in 2019, the highest in the region [13]. It is predicted that AMR will cause approximately 10 million deaths annually worldwide by 2050 if no preventative measures are implemented to control it [14].
According to standardized international terminology developed by the European Centre for Disease Prevention and Control (ECDC) and the U.S. CDC, multidrug-resistant (MDR) bacteria are characterized by non-susceptibility to at least one agent in three or more antimicrobial categories, and extensively drug-resistant (XDR) bacteria are defined as bacterial isolates susceptible to only one or two categories of antimicrobial agents [15,16].
The high incidence of resistance among the ESKAPE pathogens is associated with the diversity of the resistance mechanisms that these bacteria utilize [17]. These mechanisms include drug inactivation, modification of the target site, antibiotic elimination mediated by efflux pumps, reduced absorption of drugs, and the development of biofilms [17]. A significant number of resistance genes are located on mobile genetic elements (plasmids, transposons, and integrative conjugative elements), which enable the swift spread of resistance characteristics among ESKAPE pathogens. This hastens the dissemination of resistance mechanisms both within and among species through horizontal gene transfer (HGT) [18,19]. Recent studies have found that A. baumannii is becoming the hardest ESKAPE pathogen to treat with regular antibiotics because it quickly picks up and spreads resistance genes, mainly through mobile genetic elements such as plasmids, resistance islands, and insertion sequences [20]. Biofilms generated by A. baumannii help it develop resistance to several drugs [20]. Another study reported carbapenem-resistant A. baumannii resistance to most antibiotics except colistin[6].
Healthcare-associated infections are predominantly caused by ESKAPE pathogens [17]. These organisms have contributed to the increasing incidence of treatment failures and high death rates, and increased the cost of healthcare [18,21]. As important as the ESKAPE bacteria seem to be, most studies have focused on hospital or clinically associated strains, whereas environmentally associated pressures may also be responsible for the development of resistant behaviors in ESKAPE pathogens. Rivers, being critical sources of water for drinking, agriculture (livestock production and irrigation), and recreational activities, can become reservoirs for these ESKAPE pathogens, posing risks to public health and the environment at large. Some studies have reported the presence of ESKAPE pathogens in the environment, with 576 research studies published in PubMed reporting on individual ESKAPE members in surface water between 2000 and 2025 (Figure 1).
According to Figure 1, Pseudomonas aeruginosa was the most commonly identified ESKAPE pathogen in surface water, as reported in articles on PubMed between 2000 and 2025. It was followed closely by S. aureus and Enterobacter species. Articles on K. pneumoniae also showed that it was common in the environment, while articles on E. faecium and A. baumannii were published less often. The graph shows an increase in PubMed publications on ESKAPE bacteria in surface waters from 2010, with the trend continuing to increase after 2020. The years with the highest publication activity were 2023 and 2024, during which more research articles were published on K. pneumoniae and Enterobacter spp. Reports on P. aeruginosa and S. aureus were also found. The increase in reports of these ESKAPE pathogens in surface water, particularly from 2020 to 2024, may be attributed to the European Union’s implementation of the “One Health” approach in 2017 to address AMR [22]. The discovery of widely distributed ESKAPE bacteria within the environment by Savin et al. (2020) is also a possibility [23]. Even though articles on A. baumannii were rare, they did appear from time to time, with a notable increase in 2024. The increase could be due to new outbreaks of drug-resistant A. baumannii infections or health alerts around the world. The data in Figure 1 indicate an increasing environmental burden of ARB in surface waterbodies, which may pose potential risks to public health through environmental exposure, recreational activities, and the water–food–animal interface. Therefore, this review evaluated the prevalence of ESKAPE pathogens and analyzed their current AMR and virulence profiles, with a focus on recent global trends in significant aquatic environments.

2. Materials and Methods

2.1. Study Design

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed to ensure a systematic and transparent approach to identification, screening, eligibility, and inclusion of studies focused on individual ESKAPE bacteria and those examining multiple bacterial species, including ESKAPE members, in rivers.

2.2. Search Strategy

PubMed and Google Scholar articles with complete information on investigated rivers, sampling sites, sample collection, targeted antibiotic resistance genes, individual ESKAPE pathogens, and the effects on the environment and public health were searched to collect relevant information. The search was restricted to articles published between 2000 and 2025, with a focus on those from 2009 to 2025. to collect relevant information.

2.3. Study Selection

To achieve a comprehensive coverage in this review, both general and specific keywords and phrases were applied using the Boolean research method on PubMed and Google Scholar databases [24]. The search strategy used keywords and Boolean operators such as (“Prevalence” OR “Occurrence” OR “Diversity”) AND (“ESKAPE pathogens” OR “E. faecium” OR “S. aureus” OR “K. pneumoniae” OR “A. baumannii “ OR “P. aeruginosa” OR “Enterobacter spp.”) AND (“river water” OR “dams” OR “streams” OR “springs” OR “lake water” OR “beach”) AND (“antibiotic resistance” OR “contamination” OR “environmental impact”) AND (“Africa” OR “Asia” OR “Europe” OR “North America” OR “South America” OR “Australia”). This Boolean combination is designed to retrieve scholarly articles that are of high quality, credible, use scientifically valid methods, are peer-reviewed, data-driven, and suitable for informed scientific analysis.

2.4. Quality Assessment of the Studies

Titles were initially reviewed to assess the relevance of the selected articles. Next, all article abstracts were screened, and full-text articles were retrieved and evaluated to identify those relevant to this review. Studies on bacterial diversity; occurrence or prevalence of antimicrobial resistance and/or virulence; multidrug or environmental surveillance; and molecular characterization, whole-genome sequencing (WGS), comparative genomics, and quantitative risk assessment of bacteria in aquatic systems were included. Articles in the selection that reported on all or individual ESKAPE pathogens were considered relevant. All articles reviewed for this study are listed in the Scopus and JCR databases.

2.5. Data Collection and Analysis

Data on individual ESKAPE pathogens in aquatic systems were compiled using Microsoft Excel® (Microsoft Corporation, Redmond, WA, USA). We extracted relevant information from the articles; this included the year of study, the country of origin, the type of aquatic environment, the presence of antibiotic resistance genes (ARGs), virulence genes (VGs), multidrug resistance (MDR), genetic lineages (ST/CC), and the genomic analysis conducted. The variables were descriptively compared using tables.

3. Results

3.1. Eligibility of Assessment Outcomes

A total of 76 articles that reported the prevalence of individual ESKAPE pathogens in aquatic systems, and/or ARGs, VGs, MDR, ST/CC, and genomic analysis were used in this review. Studies reporting on more than one ESKAPE pathogen were consolidated and presented as a single article in the analysis.

3.2. Characteristics and Quality of the Study

The geographical distribution of ESKAPE pathogens in waterbodies in different continents and the total number of articles used are presented in Table 1. From a continental perspective, America has the highest number of studies on individual ESKAPE pathogens (23), followed by Asia (20), Europe (19), Africa (13), and Oceania (1). The most studied organism is E. faecium/faecalis (n = 21), followed by K. pneumoniae (n = 15), S. aureus (n = 12), A. baumannii (n = 11), Enterobacter spp. (n = 9), and P. aeruginosa (n = 8).
According to data gathered from the studies included, the ESKAPE bacterial isolates identified across various studies included E. faecium (682), E. faecalis (1397), S. aureus (373), K. pneumoniae (89), A. baumannii (628), P. aeruginosa (719), and Enterobacter spp. (39) from one hundred and nine (109) aquatic systems, including rivers, springs, dams, beaches, streams, and lakes across 29 countries worldwide. Dams and beaches were studied because they are important components of water environments used for recreational activities such as fishing and swimming. The countries with the largest number of studies are South Africa (n = 10), followed by Brazil (n = 9), India (n = 7), USA (n = 6), Spain (n = 5), Mexico (n = 3), China (4), Japan (n = 3), Portugal (n = 3), Austria (n = 3), Italy (n = 2), Germany (n = 2), Switzerland (n = 2), Canada (n = 2), Bangladesh (n = 2), Australia (n = 1), Chile (n = 1), Bolivia (n = 1), Ecuador (n = 1), Philippines (n = 1), France (n = 1), Poland (n = 1), Croatia (n = 1), Iran (n = 1), Iraq (n = 1), Taiwan (n = 1), Algeria (n = 1), Tunisia (n = 1), and Isreal (n = 1). The global prevalence and indicators of pathogenicity of individual ESKAPE pathogens in different waterbodies, based on data from the 76 studies, are presented in Table 2, Table 3, Table 4, Table 5, Table 6 and Table 7. In each table, the articles are arranged chronologically, starting with the most recent.
Table 2 presents a diverse range of E. faecium/faecalis isolates from studies published between 2011 and 2025, with the majority of studies originating from Europe. A total of 28 waterbodies, including rivers (n = 21), streams (n = 4), lakes (1), beaches (1), and dams (1), were sampled across the 21 selected papers. Thirteen of the studies reported the presence of important ARGss. Reports on vanA (6/21), which confers resistance to vancomycin, were the most common, followed closely by its functional analog, vanB (4/21). Some studies also found tetracycline {tetA (1), tetB, tetM (4), tetL (3)}, aminoglycosides {aac(6′)-Ii (4), ant(6)-Ia(2), aph (3′)-III (1), aph(3′)-III (1), and erythromycin {ermB (3) and ermC (1)}. Nine studies reported the recovery of virulence factors in E. faecium/faecalis. A total of 12 studies reported MDR E. faecium, while eight studies reported MDR E. faecalis.
Table 3 presents the diversity of S. aureus isolates from studies published between 2009 and 2023. The waterbodies in which S. aureus was identified included rivers (9), beaches (8), streams (1), dams (1), springs (1), and lakes (1). A total of 12 studies reported MRSA; among these, six studies reported mecA-MRSA. Additionally, six studies identified blaZ in either MRSA, MSSA, or both. Five studies reported VGs in this pathogen. Eight studies reported MDR in MRSA/MSSA. Seven studies also conducted molecular typing to determine the genetic relatedness of the identified S. aureus isolates.
The diversity of K. pneumoniae isolates identified in studies published between 2015 and 2024 is shown in Table 4. The waterbodies reporting the presence of K. pneumoniae were rivers (18), dams (2), streams (1), and lakes (2). ARGs were reported in all 15 studies in this review. Eight studies reported the co-occurrence of Extended-spectrum beta-lactamases (ESBLs) and carbapenemase, while five studies reported ESBLs alone, and only one study focused on carbapenemase alone. Furthermore, eight studies discovered VGs in some of their isolates. Of the 15 studies analyzed in this review, 12 reported the presence of MDR K. pneumoniae. The presence of K. pneumoniae ST11 was reported in Austria, China, and Brazil.
The distribution of A. baumannii in 14 rivers from 2016 to 2024 is presented in Table 5. The pathogen was most prevalent in Africa. The studies show similar resistance patterns to K. pneumoniae, with two studies showing the co-occurrence of ESBL and carbapenemases, and four studies reporting the presence of carbapenemases. Only two studies reported the detection of VGs. Additionally, eight studies reported the presence of MDR A. baumannii, while two studies isolated both MDR and XDR A. baumannii.
The distribution of P. aeruginosa in different aquatic systems from 2011 to 2024 is presented in Table 6. A total of 14 waterbodies—rivers (n = 11), streams (n = 1), lakes (1), and dams (1)—were reported in the 10 selected papers. Co-occurrence of ESBL and carbapenemases was reported in one study. Two studies also identified aminoglycosides in rivers, and two studies reported similar VGs such as exoT/Y.
Table 7 presents the diversity of Enterobacter spp. isolates based on studies published between 2011 and 2024. The waterbodies in which Enterobacter spp. were identified included 13 rivers and a lake. Eleven studies reported different Enterobacter spp. (E. cloacae, E. hormaechei, E. asburiae, E. kobei, E. tabaci, E. xiangfangensis, E. aerogenes, E. cancerogenus, and E. amnigenus). Five studies reported the presence of carbapenemases, including blaFRI−4 and blaFRI−8. None of the studies identified VGs in Enterobacter spp.; however, eight studies reported MDR in Enterobacter spp.

4. Discussion

This study aimed to conduct a systematic review of data on the occurrence of ESKAPE pathogens in aquatic environments between 2009 and 2025. We focused on the presence of ARGs, VGs, MDR, genetic lineages, and geographic distribution (country and continent). This selection is crucial in understanding the presence and behavior of ESKAPE pathogens in water systems. ARGs, VGs, and MDR in ESKAPE pathogens are very significant because they enable these bacteria to evade antibiotic treatment and cause severe infections, which leads to more illness, death, and healthcare costs around the world [18,101]. However, few studies have analyzed ESKAPE pathogens in water systems; therefore, examining data on each pathogen individually provides valuable insights into their environmental occurrence and pathogenicity.

4.1. Enterococcus faecium/faecalis

E. faecium and E. faecalis are among the most common species of enterococci isolated from surface water [44,102,103]. Both are part of the human gut microbiome and are often regarded as indicators of fecal pollution in water samples [104,105,106]. Cho et al. (2020) [31] identified some MDR E. faecium harboring common genes (tetL, tetM, ermB, ermC), an intrinsic gene (ant(6)-Ia), and unusual genes (tetO, lnuB) in surface water in the Upper Oconee Watershed in Georgia, USA. The bacteria showed resistance to as many as five classes of antimicrobials; E. faecalis was also identified in the same waterbody. An important finding from their study is the resistance to some newly developed and rare antimicrobial agents, such as daptomycin and tigecycline, in these bacteria [31]. A related observation was reported, where several MDR E. faecium were recovered from rivers and beaches in Minas Gerais, Rio de Janeiro, and São Paulo, in the southeastern region of Brazil. Most E. faecium reported in their study harbored the ermB gene (known for conferring resistance to macrolides, lincosamides, and streptogramins) and three essential virulent genes: gelE, esp, and ace [29]. The ermB gene was also reported by Giebułtowicz et al. in MDR E. faecium and E. faecalis isolated from the sewage-impacted Vistula River in Poland, as well as by Mukwevho et al. in the Palmiet River stream near informal settlements in Durban and Pietermaritzburg, South Africa [25,35]. Another study found relatively low expression of multiple antibiotic resistance and virulence factors (including gelatinase, β-hemolysin, and bacteriocin) in E. faecalis and E. faecium in the upper Passaic River in Morris County, New Jersey. This observation suggests a potentially low public health risk [42].
In addition, vancomycin-resistant E. faecium/faecalis (VREs) have been isolated from rivers and other related waterbodies. In Brazil and Portugal, E. faecalis harboring the vanA gene was recovered from the Tiete and Pinheiros Rivers in Brazil and the Ave River in Portugal. The detection of vanA-containing enterococci indicates that rivers serve as an important reservoir of ARB and genes that can be disseminated across human pathogens [36,39]. Biggel and his colleagues detected E. faecium sequence type 133 (ST133) harboring a vanA gene cluster on transposon Tn1546 in the Aare, Rhein, and Rhone Rivers in Switzerland. They concluded that the detection of the VRE clone ST133 in various water sampling sites across Switzerland suggests the local dominance of this lineage [30]. VanB-gene-harboring VREs have also been isolated from the Alhama River along the Ebro basin in the North of Spain and the South of France, showing the presence of extensive MDR and high-priority pathogens in different aquatic environments [32]. Similarly, Lata et al. identified E. faecalis carrying the vanB gene in River Gomti in India. They also found that VRE. faecalis isolates in this river exhibited high resistance (22–100%) and carried multiple virulence markers, including gelatinase (gelE), collagen-binding protein (ace), and endocarditis-associated antigen (efaA) [37]. The presence of virulence factors such as gelE, ace, and efaA suggests an increased potential for these bacteria to cause severe infections, including endocarditis and biofilm-associated infections [37,107].
VRE strains harboring both vanA and vanB genes were identified in several studies. For example, Matlou et al. (2019) [34], and Rathnayake et al. (2012) [43] isolated E. faecalis and E. faecium isolates carrying vanA and vanB genes from diverse aquatic environments, including dams and rivers in Rustenburg, Potchefstroom, Taung, and Coligny in the Northwest Province of South Africa, and the Coomera River in Southeast Queensland, Australia. Matlou et al. (2019) [34] highlighted the prevalence of VREs with antibiotic resistance and virulence traits in water sources used by humans; and Rathnayake et al. (2012) [43] showed that clinical isolates of E. faecalis and E. faecium have higher antibiotic resistance and virulence traits compared with environmental isolates. Ekwanzala et al. (2020) also isolated VRE harboring vanA, vanC, vanN, vanL, and vanG gene clusters in the E. faecalis and E. faecium genomes in Apies River in South Africa [33]. This could lead to increased complexity of resistance mechanisms, resulting in more complications from the treatment of infections.
The presence of E. faecalis resistant to penicillin, gentamicin, fluoroquinolones, and kanamycin, has been reported in rivers in Mexico, India, and Iran [27,40,45]. E. faecalis isolated from the Mololoa River, in the municipality of Tepic, Nayarit, Mexico, also showed resistance to cadmium and chromium. The recovery of MDR and heavy-metal-resistant E. faecalis from the Mololoa River in Mexico indicates a high level of contamination in this waterbody. The authors concluded that the Mololoa River provides a model for studying the genetic diversity of bacteria affecting human health [45]. In addition to the antibiotics reported above, E. faecium/faecalis resistant to rifampicin were also identified in the Ganga, Yamuna, and Sangam rivers in India. The authors believe that detailed data on the resistance patterns of these pathogens would enhance understanding of treatment options for enterococcal infections in humans [27]. The resistance of these bacteria to commonly used antibiotics, such as tetracycline, and less frequently utilized antibiotics, such as chloramphenicol, was evaluated in some strains of E. faecium/faecalis from the Babolrud River and coastal waters of Babolsar in Iran. The presence of antibiotic-resistant Enterococcus spp. in coastal waters poses a potential health risk to swimmers [40]. Furthermore, unlike in India, Mexico, and Iran, the report from Monte Cotugno Lake, Italy, identified E. faecium as the dominant species exhibiting different virulence factors such as gelE, agg, efaAfm, gelE+efaA, and agg+efaA [41].
E. faecium with two copies of the poxtA gene was identified in the Salibnello estuary in the Abruzzo region of Italy. The poxtA gene is known to confer resistance toward linezolid in bacteria. Genes conferring resistance to phenicols (fexB), tetracyclines (tet(M) and tet(L)), macrolides, lincosamides, and quinupristin streptogramins group B (msr(C)) were also identified. Additionally, streptogramin group B (ermB), lincosamides (lnuB), and lincosamides and dalfopristin streptogramin group A (lsaE) were also found. Furthermore, genes that confer resistance toward aminoglycosides (aph3′-III, aac6′-Ii, ant6-Ia, and aac6′-aph2″) were also identified using whole genome analysis [28].
Table 2 summarizes the occurrence of E. faecium and E. faecalis in major waterbodies worldwide. We analyzed studies published between 2011 and 2024 and identified E. faecium and E. faecalis in twenty-four rivers across thirteen different countries, with E. faecalis as the dominant species across the studied rivers. E. faecium and E. faecalis were prevalent in Canada’s South Nation River and the USA’s Passaic River. Conversely, only E. faecium was found in the Ebro basin River in France, and only E. faecalis was found in the river in Veracruz, Mexico. A small fraction of the isolates from these rivers were found to be MDR.
We found that vanA and vanB continue to be widespread, while ermB remains a major resistance mechanism in these waterbodies. The prevalence of tetM may be linked to agricultural practices near some of the sampled rivers. The detection of poxtA in one river in 2022 suggests that such resistance genes can emerge and potentially become more widespread in environmental isolates [28].

4.2. Staphylococcus aureus

Hospital-associated methicillin-resistant S. aureus was first isolated in the hospital environment in the 1960s, and community-associated MRSA infections appeared in the 1990s, with no associated risk factors [108,109]. S. aureus is not a common bacterium in surface water; hence, its recovery from surface water may be an indication of recent anthropogenic contamination. Since humans are the primary reservoir of S. aureus, recreational activities such as swimming may contribute to the spread of Staphylococci in the aquatic environments [110].
A strain of MRSA, known as USA300, is known for causing various infections, such as those affecting the skin and soft tissues (SSTIs), and is associated with severe complications in infections acquired both in the community and healthcare settings [111,112]. Gerken et al. (2021) [47] documented the presence of methicillin-susceptible S. aureus (MSSA), MRSA isolates of USA300 ST8 SCCmec IVa CA-MRSA with the Panton-Valentine leukocidin (PVL) toxin, and other MRSA isolates in Lehia, Richardson’s, Honoliʻi, Pohoiki, Kealoha, Onekahakaha beach parks, Wailuku River Estuary, anchialine pools, and sand in locations with limited human activity on the Hawaiʻi Island. Similarly, Lepuschitz and his group reported the first draft genome sequence of the MRSA USA300 isolate obtained from a surface water sample from the River Mur in the province of Carinthia, southern Austria. They observed the presence of CA-MRSA USA300, characterized by relevant features such as sequence type 8 (ST8), spa type t008, staphylococcal cassette chromosome mec element type IV (SCCmec IV), PVL, and the arginine catabolic mobile element (ACME) cluster. Their findings also suggested a potential health risk associated with the detection of the CA-MRSA USA300 isolate in aquatic environments, which is closely associated with clinical isolates [113].
The mecA gene plays a key role in the resistance of S. aureus to methicillin by producing a penicillin-binding protein, PBP2a, which exhibits low binding affinity for β-lactam antibiotics, thereby rendering it ineffective [114,115]. Similarly, blaZ encodes beta-lactamase, an enzyme that hydrolyzes beta-lactam antibiotics, making them ineffective for the treatment regimen [115,116]. mecA and blaZ genes work synergistically; for example, regulatory factors linked to blaZ help mecA acquisition stay stable and make antibiotic resistance more visible in the phenotype [117]. An investigation revealed the simultaneous presence of these genes and other genes in a river that receives water from the Bon Accord dam located at the Tshwane University of Technology (TUT) research farm in Honingnestkranz, Pretoria North, South Africa. Ramaite et al. [49] identified S. aureus ARGs (mecA, ermA, and blaZ), enterotoxins (sec and seq genes), and STs (ST80, ST728, ST1931, ST2030, ST3247, and ST5440) associated with clonal complex 80 (CC80) in environmental samples. They cautioned about the potential for the widespread dissemination of ARGs and virulent bacterial strains due to the combination of these ARGs and enterotoxins found in livestock-associated MRSA. Similarly, Ramessar & Olaniran [50] identified ARGs (blaZ, ermC, aac(6′)/aph(2′’), msrA, and tetK) and VGs such as hla, hld, lukS/FPV, and sea in the upstream and downstream points of receiving rivers of two wastewater treatment plants (WWTPs) in the Durban area, South Africa. Their findings suggested that the treated effluent might pose a threat to the environment and human health. The association between ARGs and virulence factors could complicate the treatment of infections caused by S. aureus, necessitating broader strategies for their management. In addition, Levin-Edens et al. [56] identified 22 MRSA isolates carrying the mecA gene, with a predominant prevalence of SCCmec type IV, of which 17 showed MDR harboring tet(K), erm(C), msr(A), and aadD ARGs. These isolates were found on popular recreational beaches in marine waters, freshwater, and lakes on the west side of Lake Washington. They suggested that the MRSA strains might be linked to humans and animals based on MLST typing, which could have significant implications for individuals visiting recreational beaches in colder climates. Akanbi et al. [52] identified blaZ, mecA, ermB, rpoB, and tetM ARGs in some S. aureus isolates collected from 10 beaches in the Eastern Cape Province of South Africa. They observed a higher frequency of these genes in beach water than in sand isolates; moreover, they confirmed the presence of the femA gene in all mecA-positive isolates, indicating functional methicillin resistance.
The mecC gene is a variant of the mecA gene, which is responsible for methicillin resistance in Staphylococci. It encodes a distinct penicillin-binding protein (PBP2c) with a lo w affinity for beta-lactam antibiotics, contributing to the methicillin resistance characteristic [118]. Some studies have reported the co-occurrence of these genes in bacterial isolates from rivers. For example, mecC-MRSA isolates were detected in river water that runs through a game estate in Spain; these isolates were closely related to isolates of ST425 mecC-MRSA found in wild animals. These isolates were resistant to benzylpenicillin and cefoxitin and carried the resistance genes mecC and blaZLGA251, highlighting the potential role of water in the dissemination of mecC-MRSA [54]. In a similar study, Silva et al. [119] also identified three MRSA, resistant to penicillin and cefoxitin, and harboring the blaZ-SCCmecIX characteristic of mecC-MRSA strains, in the Douro River Basin in Portugal.
The presence of MDR S. aureus in river environments poses significant public health risks, particularly in areas impacted by anthropogenic activities. For instance, 65% of S. aureus isolates in a study from Brazil were resistant to at least three classes of antibiotics, with the highest resistance to trimethoprim–sulfamethoxazole and clindamycin and gentamicin; these isolates were obtained from the Extrema River Spring in central Brazil, a river known to be the target dumping ground of pharmaceutical products from surrounding industries [46]. The implication of the study’s observation is that the release of pharmaceutical waste into surrounding waterbodies can trigger the development of AMR in resident bacteria. In a similar study, Soge et al. identified five MDR MRSA-SCCmec type I, which carried the ermA gene and were PVL-negative. These characteristics are commonly associated with hospital MRSA rather than US CA-MRSA isolates from public beaches in Washington State, USA, which were not near hospitals [57]. Analysis of water from the Ganga River in India (a river extensively used as a drinking water source and for religious bathing and cleaning purposes) found a high prevalence of MRSA isolates primarily resistant to erythromycin, augmentin, tetracycline and streptomycin in the lower region of the riverbanks of due to extensive anthropologic activities in the state of Uttarakhand, India [55]. Furthermore, Skariyachan et al. (2015) [53] reported that the preliminary antimicrobial testing of all S. aureus isolates recovered from River Cauvery, a significant drinking water source in Karnataka, India, showed MDR to the present generation of antibiotics.
This review documented the presence of a few S. aureus isolates in natural aquatic environments from 2009 to 2023, as shown in Table 3. We focused on beaches and rivers as habitats for S. aureus due to the similarity in anthropogenic activities, such as human and recreational interactions, that contribute to its dissemination in these environments. The prevalence of MRSA and MSSA was notable in developing countries like India and South Africa [50,55]. It is worth noting that only a small proportion of the MRSA and MSSA strains reviewed in this study were MDR. In addition, at least one of the three erm genes associated with macrolide resistance (ermA, ermB, or ermC) was recovered from most parts of the river, suggesting that macrolide resistance is common in river water, likely due to human activity, agriculture, and environmental factors. Some sequence types (STs) and clonal complexes (CCs), such as ST8 (CC8), ST5, ST398, and ST80 (CC80), which are considered dangerous due to their association with MRSA, virulence factors, and global dissemination, were identified [47,56,119].

4.3. Klebsiella pneumoniae

K. pneumoniae has been increasingly recovered in aquatic environments, particularly in rivers, lakes, and estuaries [120,121,122]. K. pneumoniae in the aquatic ecosystem could disrupt the ecosystem via interactions with other bacteria and competition for nutrients. In a bid to compete, K. pneumoniae could secrete toxic substances that can eliminate other microbial populations from the environment [123].
Research has indicated that MDR K. pneumoniae, which carries the blaKPC-2 gene alongside other crucial resistance genes, is not only present in clinical environments but can also be found in natural water sources. For example, Nascimento et al. documented resistance to carbapenems (blaKPC-2), beta-lactams (blaSHV-11), fluoroquinolones (oqxA and oqxB), trimethoprim (dfrA30), tetracycline (tetA), and fosfomycin (fosA) by a strain of K. pneumoniae isolated from Ibirapuera Lake in São Paulo, Brazil. WGS analysis confirmed that this strain belonged to the high-risk hospital-associated clone ST11/CC258, showing that the blaKPC-2 gene was contained on a conjugative IncN plasmid found within a Tn4401b, which means it can potentially spread this resistance to other bacteria [68]. In a related study from Croatia, a KPC-producing K. pneumoniae was isolated from the Krapina River, situated 300 m downstream of the sewage outlet from the Zabok General Hospital. Four isolates from the river shared characteristics (carbapenem and MDR, plus the blaKPC-2 gene associated with an IncFII plasmid) with a clinical isolate marked “ST258” from a nearby hospital. This discovery indicated that the K. pneumoniae isolates from the river likely have a clinical origin, with the KPC-producing K. pneumoniae ST258 being able to survive in river water for extended periods, highlighting their potential to spread ARGs within the natural bacterial population [66]. Recent findings in China by Zou et al. also included the detection of four carbapenem-resistant K. pneumoniae strains carrying blaKPC-2 and blaNDM in the Dongluo, Quanfu, and Shunhe rivers of Jinan City, China. Among these, two carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) clones of ST11-KL64 were retrieved from the Dongluo River, suggesting transmission between hospital and urban aquatic environments, given the relative abundance of blaKPC and blaNDM genes [61]. Additionally, Piedra-Carrasco et al. identified carbapenemase-producing K. pneumoniae (KPC-2) carrying carbapenemase-encoding plasmid genes (vagCD and parAB) and expressing low levels of virulence-associated factors in the Llobregat River, Catalunya, Spain, proposing these isolates as low-risk pathogens [70]. The emergence of KPC-producing strains raises concern due to their resistance to carbapenems, which are often the antibiotics of last resort for treating severe bacterial infections [124].
Several studies have reported the presence of significant carbapenemases and other antimicrobial resistance genes in rivers, raising concerns for public health [67,71]. In Austria, Lepuschitz et al. identified three ESBL-producing strains and two carbapenem-resistant strains in samples from various rivers (Inn, Drau, Glan, Traun, and Danube). They discovered the first case of K. pneumoniae strains positive for blaVIM-1 in an Austrian river, emphasizing their alarming presence due to the limited treatment options available for this antimicrobial-resistant strain [67]. Finally, Tafoukt et al. described the first identification of three K. pneumoniae isolates carrying OXA-48 carbapenemase with different STs from Soummam River, Algeria, emphasizing the importance of monitoring and controlling such water environments to prevent gene dissemination [71].
MDR K. pneumoniae and hypervirulent K. pneumoniae are normally classified in distinct groups, with MDR strains being prevalent in healthcare settings and hypervirulent strains being associated with severe community-acquired infections [125,126]. In 2020, Furlan et al. identified three MDR and hypervirulent K. pneumoniae isolates—EW158, EW160, and EW185—in Sertãozinho Stream, Moquem Stream (Euclides Morelli Lake), and Monjolinho River, respectively, in several cities of São Paulo State, Brazil [65].
Donato et al. reported an MDR frequency of 10% for K. pneumoniae among 59 environmental isolates collected from dams and various points spanning from the upper to the lower parts of the Lerma River basin in Mexico. WGS of two isolates revealed the presence of significant ARGs, including common genes (aac(6′)-Ib-cr, fosA, sul2, blaTEM-1B, blaCTX-M-15, oqxA, oqxB), intrinsic genes (fosA, blaSHV-11), and unusual genes (aac(3)-IIa, strA, strB, dfrA14, QnrS1, QnrB66, tet(A), blaOXA-1, blaOXA-232, catB4), as well as virulence genes such as standard genes (fimH) and dangerous genes (ppdD, dam). The study emphasized that the detection of MDR strains in areas where such strains were previously absent can cause significant environmental and public health concern [62]. Similarly, Lobato et al. reported the first evidence of blaBKC-1-producing K. pneumoniae belonging to the high-risk ST11/CC258 clone with an extensive drug-resistant phenotype in Guajará Bay (intersection of the Guamá and Acará rivers), Brazil. They also identified the presence of common genes (blaCTX-M-15, blaSHV-11, aph (3′)-VIa, aac(6′)-Ib-cr, qnrE1, qnrB19, catB3, and sul1), intrinsic genes (fosA6), rare genes (rsmA, emrR, crp, arr-3, and aac(3)-IIa), and various virulence-related genes in the same river [63]. Sahoo et al. (2023) [60] reported the first case of a K. pneumoniae isolate expressing a rare gene, blaNDM-5, common resistance determinants (blaCTX-M and blaTEM), an intrinsic gene (blaSHV), as well as the virulence factors fimH, mrkD, and entB (standard virulence genes) and irp-1 and ybtS (dangerous virulence genes) in samples collected from the Kathajodi River in Odisha, India. The study suggested that this strain originated from infected people or healthcare facilities [60].
Studies from Northern Portugal and China reported the isolation of ESBL K. pneumoniae harboring blaSHV from samples collected from the Douro River Basin and Qinhuai River, respectively [58,59]. Another study on the Tigris River in Iraq found that 87.5% of the 40 K. pneumoniae isolates carried the blaCTX-M gene, indicating a significant prevalence of ESBL-producing strains [72]. In Africa, Hassen et al. (2020) identified two K. pneumoniae isolates with a predominance of blaCTX-M-15, blaSHV, and high genetic diversity in river water from the Rouriche River, Tunis City, Tunisia [64].
Tigecycline is a last-resort antibiotic used for treating MDR infections, particularly when microorganisms have already developed resistance to carbapenems and/or colistin [127]. However, the rising cases of tigecycline resistance in Enterobacterales strains are raising concerns regarding the efficacy of this antimicrobial agent [127,128]. Hladicz et al. identified two tigecycline-resistant K. pneumoniae isolates in the River Mur, Austria; the two belonged to different, unrelated MLST types—ST2392 and ST2394—and both exhibited resistance to tetracycline and tigecycline. They postulated that river water may contain substances such as mutagenic agents that can cause mutations, leading to overexpression of the efflux pump [69].
This review identified a small number of K. pneumoniae isolates in waterbodies between 2015 and 2024, as summarized in Table 4. However, it is concerning that most of these isolates are MDR, carrying ARGs, including ESBL genes (blaSHV, blaCTX-M), as well as genes associated with aminoglycoside resistance (aadA) and sulfonamide resistance (sul1). Additionally, hypervirulent K. pneumoniae isolates resistant to multiple antibiotics were also identified in environmental settings, which is quite alarming [65]. Notably, K. pneumoniae isolated from the River Mur in Austria was found to be resistant to tigecycline, a last-resort antibiotic for treating MDR infections [69].

4.4. Acinetobacter baumannii

A. baumannii is a notable species within the genus Acinetobacter that has garnered significant research interest due to its role in hospital-acquired infections [129,130]. A. baumannii is often found in water, soil, and on surfaces in healthcare settings [74,131]. Its ability to survive in diverse environments, combined with its MDR nature, has made it a growing concern in hospital-associated infections [131,132].
Its introduction into river systems through various anthropogenic activities, including hospital effluents and agricultural runoff discharge, may contribute to the dissemination of the antibiotic-resistant strain [131,133]. Tsai et al. observed higher rates of A. baumannii in livestock wastewater channels (21.4%) and tributaries near livestock farms (15.4%) compared with areas adjacent to the Puzi River in Taiwan. Genotyping using ERIC-PCR identified two primary clusters of A. baumannii, suggesting that livestock wastewater contributes to the dissemination of the bacterium in aquatic ecosystems [80].
Recent research has raised concerns about the prevalence of extensively drug-resistant (XDR) A. baumannii in river environments, showing the potential transmission of resistance genes from clinical settings to natural waterbodies [75]. For instance, Sahoo et al. found high levels of XDR carbapenem-resistant A. baumannii in a river catchment near Cuttack City, Eastern India. This indicates the direct disposal of biomedical wastes into the river system [75]. Similarly, Havenga et al. (2022) [76] identified XDR A. baumannii isolates (AB14) in the Plankenbrug River, located near a local health clinic in South Africa, demonstrating antibiotic resistance to amikacin, ciprofloxacin, gentamicin, imipenem, levofloxacin, sulfamethoxazole/trimethoprim, and tobramycin. The isolate also exhibited biofilm formation and shared genetic relatedness with clinical isolates [76].
In a European study, Kettinger et al. identified the presence of classic intrinsic OXA carbapenemase (OXA-23 and OXA-51) in A. baumannii strains resistant to carbapenems (meropenem and imipenem), as well as strains carrying the genes encoding carbapenemase VIM-2 and broad-spectrum β-lactamases TEM-1 throughout the Danube River in Europe [82]. Studies in the United States and China documented the emergence of A. baumannii harboring msrE, and mphE genes both midstream (proximal to effluent pipe) and downstream (Mount Vernon WWTP) of the Kokosing River, a rural river in Ohio, and in the Qinhuai River. The studies observed a substantial increase in various ARGs because of the WWTP discharge [59,79]. Another study identified the MDR A. baumannii L13 strain harboring 314 resistance genes, including the blaOXA-69 gene, cephalosporin-hydrolyzing class C-β-lactamase gene (blaADC-2), glycopeptide resistance genes, and Na+-driven multidrug efflux pump genes (abeS, abeM, adeK, adeI, adeJ, adeH, adeR, adeG, adeF, adeN, adeA, and adeS), in the Tarim River in Xinjiang Uygur Autonomous Region of China, using draft genome sequencing to identify correlated MDR genes for further study of antimicrobial resistance mechanisms [81]. Adewoyin et al. discovered A. baumannii isolates in Great Fish, Keiskamma, and Tyhume Rivers in Eastern Cape Province, South Africa; these isolates carried a variety of resistance genes for β-lactamases, aminoglycosides, fluoroquinolones, and tetracyclines. They attributed the presence of MDR A. baumannii in these freshwater sources to likely wastewater discharge from nearby animal farms [78].
Wang et al. (2021) [77] discovered A. baumannii isolates carrying the blaOXA-2 ARG and mercury resistance operon downstream of the Xiangjiang River. These bacteria, identified as ampicillin-resistant opportunistic pathogens, were associated with areas impacted by metal mining activities. The researchers suggested that heavy metals might facilitate plasmid conjugative transfer, leading to the proliferation of resistant opportunistic pathogenic bacteria in the river [77]. Additionally, Turano et al. (2016) identified blaOXA-23-producing ST79 A. baumannii strains in Tietê and Pinheiros Rivers in São Paulo, Brazil, indicating the presence of clinically significant bacteria outside of hospital settings and showing the escalating public health risk [83]. In a similar study, Sotomayor et al. recently demonstrated that carbapenem-resistant A. baumannii were predominant in healthcare facilities and polluted river environments in Quito, Ecuador, with river-derived isolates only carrying the blaOXA-51 and possibly the blaOXA-259 genes [73].
In a study conducted in France, Hamidian et al. (2022) [74] identified ARGs in A. baumannii strain isolated from the Seine River, including genes encoding the tetracycline efflux protein (tetA), an ISAba1-activated chromosomal cephalosporinase (ampC), an oxacillinase (OXA-23), and an aminoglycoside 3′-phosphotransferase (strAB). The researchers suggested that this strain, which may have originated in nosocomial environments, have been released into the environment [74].
In this review, we found a limited number of reports specific to A. baumannii isolates from rivers between 2016 and 2024, as seen in Table 5, despite numerous studies on other Acinetobacter species in the same environments. Both the Kathajodi River in India and the Plankenbrug River in South Africa had a co-occurrence of MDR and XDR A. baumannii. Of the 42 isolates from the Kathajodi River, 41 were identified as MDR and XDR, while 4 of the seven isolates from the Plankenbrug River exhibited the same co-occurrence [75,76].
The presence of XDR A. baumannii in these rivers raises concerns about its potential impact on the local aquatic ecosystem. Additionally, other rivers, such as the Danube in Europe, also reported the presence of MDR A. baumannii carrying ESBL and/or carbapenemase, although at a lower prevalence [82]. The current trend shows increasing resistance in XDR and MDR A. baumannii strains, largely due to the dissemination of acquired resistance genes such as blaOXA-23, as demonstrated in this review. Only one study actively investigated the presence of the mcr variant (colistin resistance), a commonly sought acquired gene in environmental samples, but did not detect it in the A. baumannii strains isolated from the Plankenbrug River [76].

4.5. Pseudomonas aeruginosa

P. aeruginosa is a ubiquitous environmental Gram-negative bacterium inhabiting terrestrial and aquatic environments. Its wide-ranging metabolic adaptability helps it spread, proliferate, and survive despite unfavorable physical and chemical conditions [134,135]. P. aeruginosa’s resistance to multiple antibiotics is due to its low outer membrane permeability and a robust efflux pump system, which together enable it to survive in aquatic environments [136,137].
Multiple studies have shown that P. aeruginosa strains isolated from river environments often display high levels of resistance to antibiotics. The SPM-1 metallo- beta-lactamase is particularly concerning, as it confers resistance to a broad spectrum of β-lactam antibiotics that are crucial for treating severe infections [83]. For example, a study in southern Brazil identified the presence of blaSPM-1-producing P. aeruginosa strains in two locations in the metropolitan area of São Paulo (Tietê and Pinheiros Rivers). MLST analysis revealed that the isolated strains were closely related and belonged to sequence type ST277, which is environmentally persistent [83]. In a similar study, Fontes et al. identified MDR P. aeruginosa carrying blaSPM-1, blaOXA-56, rmtD1, aacA4, aadA7, sul1, and dhfr genes in the Tietê River in São Paulo state, Brazil. They suggested that strains carrying blaSPM-1 and rmtD1 genes are not limited to hospitals and can spread in communities through river environments [91].
Furthermore, the presence of MDR P. aeruginosa in rivers raises concerns about its potential to acquire and spread ARGs. Hosu et al. (2021) detected MDR P. aeruginosa harboring rare and important resistance genes such as ESBL (blaTEM, blaSHV, and blaCTX-M) and MBL (blaVIM) genes from the wastewater of the Umzikantu Red Meat Abattoir, Zimbane Mthatha, Mthatha River, and Mthatha Dam, Province of South Africa, with an MAR index > 0.2, indicating that the isolates originated from high-risk contamination sources [135]. Another study analyzed MDR strains of P. aeruginosa from seven distinct sites along the Buriganga River in Bangladesh, revealing resistance to common antibiotics such as cefotaxime, tetracycline, and ciprofloxacin, as well as to important antibiotics such as cefepime, imipenem, meropenem, and amikacin. They concluded that sources such as chemical waste, medical waste, and sewage disposal points may play an important role in the spread of MDR P. aeruginosa in the river [85]. Additionally, a previous study in Bangladesh observed similar MDR resistance patterns in strains from ponds, lakes, and rivers in Dhaka city, with resistance to common antibiotics such as ampicillin, tetracycline, and gentamicin [88].
Suzuki et al. (2013) [90] reported the distribution of P. aeruginosa, with counts ranging from 2 to 46 cfu/100 mL, and AMR to various antibiotics from both upstream and downstream locations of two rivers, the Kiyotake River and the Yae River, which flow through Miyazaki City, Japan. Between 0.2% and 2% of all P. aeruginosa isolates (516 isolates from the two rivers) exhibited resistance to piperacillin, cefotaxime, and imipenem [90]. Although the observed patterns of resistance to piperacillin, cefotaxime, and imipenem are relatively low, the presence of resistance to these antibiotics, especially imipenem, remains a significant threat [90]. Similarly, Xiao et al. (2024) [59] detected an abundance of P. aeruginosa in the Qinhuai River, Nanjing, China (the river receives effluent from many municipal WWTPs). The P. aeruginosa carried various ARGs, including blaOXA-101, mphF, blaTEM-1, LCR-1, and blaOXA-827, further emphasizing the microbial risks in urban rivers influenced by municipal wastewater. In Brazil, Magalhães et al. (2016) [89] detected the presence of MDR P. aeruginosa in the Mindu stream in Manaus, which drains into the Rio Negro.
Additionally, a recent study by Rojo-Bezares et al. in Spain recovered P. aeruginosa isolates from the Iregua River [84]. These isolates exhibited a low range of AMR patterns, with only one strain resistant to carbapenems (imipenem, meropenem, and doripenem) due to a mutation in the OprD porin gene. Notably, the isolates exhibited a high level of virulence factors, motility, as well as pigment production and elastase activity. A related study characterized a hemolytic and antibiotic-resistant strain of P. aeruginosa, designated S3, isolated from the Mahananda River in India. This strain exhibited significant hemolytic activity and multiple virulence factors, rendering it pathogenic to fish [86].
Relatively few studies have focused on analyzing the presence and AMR of P. aeruginosa in river water due to the primary focus on clinical settings. This review highlights the growing prevalence of antibiotic-resistant P. aeruginosa in river environments from 2011 to 2024, as shown in Table 6, indicating significant challenges to public health due to threats to animal, human, and environmental safety. Recent studies from diverse geographical locations, including Brazil, South Africa, and Bangladesh, have consistently highlighted the alarming presence of MDR strains and the dissemination of critical resistance genes [83,85,135]. The detection of blaSPM-1-producing strains and other resistance determinants such as blaOXA-56 and rmtD1 shows the potential for these bacteria to escape hospital confines and establish in community settings, particularly through aquatic ecosystems [91].

4.6. Enterobacter spp.

Enterobacter spp. are mobile Gram-negative rods and form part of the gut microbiota of animals and humans [138]. Enterobacter spp. are commonly found in the natural environment, including in soil and surface water [139,140]. Studies have shown that various Enterobacter spp., including E. cloacae, can carry multiple carbapenemase genes. In a 2018 study conducted near Netanya, Israel, Enterobacter spp. were identified in the Alexander River estuary, with two carbapenemase-producing Enterobacter isolates (E. asburiae and E. bugandensis) detected, indicating significant contamination in these aquatic environments. Genome sequencing revealed a high degree of genetic similarity between these isolates, suggesting a common source of contamination [95]. Furthermore, a study in the Philippines isolated carbapenemase-producing E. cloacae, E. kobei, E. tabaci, E. xiangfangensis, and E. hormaechei from different points along the Metro Manila River, identifying different carbapenemases, with the most prevalent gene being blaNDM [94]. Additionally, Adachi et al. reported the presence of imipenem and meropenem-resistant E. asburiae 17Nkhm-UP2 and Enterobacter spp. 18A13 in a river contaminated with discharge from a sewage treatment plant in Osaka, Japan. They found that E. asburiae 17Nkhm-UP2 harbored an FRI-4-like gene, while Enterobacter sp. 18A13 harbored FRI-8. The researchers concluded that FRI carbapenemase genes may have spread within the genus Enterobacter spp. in the river [93].
Environmental studies have drawn attention to the presence of ESBL and carbapenemase-producing Enterobacter spp. in aquatic environments, particularly in rivers [98]. In a study conducted in Germany, samples taken from the Danube River revealed the presence of antibiotic-resistant Enterobacteriaceae, including E. cloacae, E. cancerogenus, and E. asburiae [98]. The study highlighted the presence of multiple resistant strains, emphasizing the role of the river in the dissemination of these pathogens [98]. This corresponds with findings from a study in Switzerland, where researchers detected ESBL E. cloacae and E. amnigenus strains in the Landquart and Lorze rivers in the German-speaking part of Switzerland. The study concluded that the prevalence of ESBL producing Enterobacteriaceae in surface waters is highly concerning [99]. Additionally, in Spain, Piedra-Carrasco et al. (2017) identified one E. cloacae that was positive for blaKPC-2 and one that was positive for blaIMI-2 (the first IMI-2 determinant identified in environmental bacteria in Europe) and harbored new STs; they were collected from sediment and water samples at the Sant Joan Despí station of the Llobregat river, Catalunya, Spain [70]. Zarfel et al. also identified two blaVIM-1 and blaTEM-1-harboring E. cloacae in the Mur River in Austria [141]. Finally, a blaCTX-M-harboring E. cloacae isolate was also identified in water samples from the Choqueyapu River in La Paz, Bolivia. This river frequently receives untreated household, industrial, and hospital waste. WGS of the isolate confirmed the presence of conjugative plasmids, including IncH groups, which are commonly associated with ESBL and carbapenemase genes [97].
Bartholin et al. (2023) [92] reported the presence of MDR E. cloacae in the Cachapoal River and Villarrica Lake in Chile. They also identified the blaTEM gene, which encodes β-lactamase in E. cloacae [92]. MDR Enterobacter spp. were also detected in the Tsomo and Tyhume rivers in the Eastern Cape Province, South Africa. These bacteria harbored ESBLs (blaCTX-M, blaSHV) and the pAmpC gene (blaFOX), as well as non-β-lactam resistance genes (tetA, tetB, tetD, sul1, and catII) [96]. Xu et al. (2011) [100] reported the identification of fosA2 in E. cloacae. This fosA2 gene confers fosfomycin resistance in an MDR E. cloacae from the Salmon River in south-central British Columbia, Canada [100].
In this review, we found a limited number of studies on Enterobacter spp. isolates from rivers between 2011 and 2024, as shown in Table 7. The presence of MDR Enterobacter spp. harboring carbapenemase and ESBL genes, among other dangerous genes, in riverine environments is a growing concern worldwide. The detection of novel blaFRI-4 and blaFRI-8 carbapenemase genes in river water means that these ARGs are now present and mobile in the environment, increasing the risk of dissemination to human and animal pathogens through water, food, and ecological contact [93].
Finally, from the data in this review, we identified studies on individual ESKAPE pathogens in 109 major rivers, including springs, dams, beaches, and lakes across 32 different countries worldwide, with each pathogen exhibiting distinct resistance patterns. Some exhibited patterns similar to those observed in clinical settings. The resistance pattern in clinical settings is frequently characterized by XDR or MDR [142]. ESKAPE bacteria in these environments may increase the risk of human infections, especially in vulnerable populations. This literature review demonstrates the current trends in the prevalence and risks associated with ESKAPE bacteria in waterbodies, particularly rivers. Available data indicate that MDR Gram-positive ESKAPE pathogens, including E. faecium/faecalis and S. aureus, harbor critical resistance genes against vancomycin, aminoglycosides, and tetracyclines; similarly, data show that MDR Gram-negative ESKAPE pathogens carry resistance determinants targeting β-lactams and carbapenems. These resistance patterns closely mirror those observed in clinical settings, posing a serious threat given the essential role of these antibiotics in managing infections caused by these pathogens.
Limitations of this review.
  • Data collected for the analysis of the prevalence of individual ESKAPE pathogens in water systems in various regions are unevenly distributed across the globe.
  • Important data, such as VGs, ARGs, and MDR, were not included in some of the studies analyzed, limiting the available information on the patterns and mechanisms of resistance of the ESKAPE pathogens in the studied literature.

5. Conclusions

This review supports the fact that contaminated surface water such as rivers can be a source of pathogens associated with severe infections in the community. We reported the current trends in the identification of ESKAPE pathogens in aquatic environments. It is worth noting that the rate of recovery of this group of bacteria from aquatic environments is low. This could be due to the continuous flow of water, which often dislodges bacteria from surfaces; however, despite the lower rate of recovery, antimicrobial resistance among ESKAPE pathogens is on the increase, highlighting the possible transfer of resistant strains or genes into the aquatic environment, which could be due to anthropogenic activities or the influence of agricultural activities. This observation highlights the importance of adequate management of water before it is used in agriculture or as portable water to prevent the spread of resistant pathogens to the public.
The studies analyzed in this review used different methodologies, including cultural media, PCR, automated systems, and WGS, to identify the bacteria and their resistant genes, as well as the antimicrobial patterns in these pathogens. Although only a few members of the ESKAPE family were recovered from these rivers, and only a few of these were MDR, the presence of MDR ESKAPE pathogens could still pose a risk to the health of an immunocompromised individual who comes into contact with this waterbody. Carbapenemase and tet genes appear to be more prevalent in Gram-negative bacteria, while the van and tet genes are shared among two ESKAPE Gram-positive bacteria. A new carbapenemase gene, the blaFRI gene, a member of a group of carbapenemase genes found primarily in Enterobacter cloacae and other related bacteria, was isolated in one of the rivers reviewed in this study. Genomic technologies were well-represented in some of the studies; however, most did not conduct genomic analysis, resulting in less-documented genomic results. It is important that continuous surveillance and monitoring of waterbodies are conducted regularly to prevent the spread or acquisition of AMR ESKAPE pathogens. Studies determining the abundance, diversity, and survival of ESKAPE pathogens in different waterbodies will be helpful in this regard. Given these findings, it is crucial to implement robust monitoring and management strategies to mitigate the spread of antibiotic resistance in aquatic environments. Collaborative efforts by public health officials, environmental scientists, and healthcare providers are essential to address this pressing issue. Continued research is needed to better understand the resistance and virulence mechanisms of ESKAPE pathogens and to develop innovative approaches for controlling their spread in both environmental and clinical contexts.

Funding

Instituto Politécnico Nacional, grant numbers 20231514 and 20232270.

Data Availability Statement

Data are available upon request.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. WHO. Antimicrobial Resistance. 2023. Available online: https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance (accessed on 1 November 2024).
  2. CDC. Antibiotic Resistance Threats in the United States. 2019. Available online: https://www.cdc.gov/antimicrobial-resistance/data-research/threats/index.html (accessed on 1 November 2024).
  3. Maraki, S.; Mavromanolaki, V.E.; Kasimati, A.; Iliaki-Giannakoudaki, E.; Stafylaki, D. The evolving epidemiology of antimicrobial resistance of ESKAPE pathogens isolated in the intensive care unit of a Greek university hospital. Diagn. Microbiol. Infect. Dis. 2025, 112, 116804. [Google Scholar] [CrossRef]
  4. Dominey-Howes, D.; Bajorek, B.; Michael, C.A.; Betteridge, B.; Iredell, J.; Labbate, M. Applying the emergency risk management process to tackle the crisis of antibiotic resistance. Front. Microbiol. 2015, 6, 129597. [Google Scholar] [CrossRef]
  5. WHO. WHO Bacterial Priority Pathogens List; WHO: Geneva, Switzerland, 2024; Available online: https://iris.who.int/bitstream/handle/10665/376776/9789240093461-eng.pdf?sequence=1 (accessed on 1 September 2024).
  6. Pipitò, L.; Rubino, R.; D’Agati, G.; Bono, E.; Mazzola, C.V.; Urso, S.; Zinna, G.; Distefano, S.A.; Firenze, A.; Bonura, C.; et al. Antimicrobial Resistance in ESKAPE Pathogens: A Retrospective Epidemiological Study at the University Hospital of Palermo, Italy. Antibiotics 2025, 14, 186. [Google Scholar] [CrossRef]
  7. Safdar, N.; Saleem, S.; Salman, M.; Tareq, A.H.; Ishaq, S.; Ambreen, S.; Hameed, A.; Habib, M.B.; Ali, T.M. Economic burden of antimicrobial resistance on patients in Pakistan. Front. Public Health 2025, 13, 1481212. [Google Scholar] [CrossRef]
  8. Hampton, T. Report Reveals Scope of US Antibiotic Resistance Threat. JAMA 2013, 310, 1661–1663. [Google Scholar] [CrossRef]
  9. Shrestha, P.; Cooper, B.S.; Coast, J.; Oppong, R.; Do Thi Thuy, N.; Phodha, T.; Celhay, O.; Guerin, P.J.; Wertheim, H.; Lubell, Y. Enumerating the economic cost of antimicrobial resistance per antibiotic consumed to inform the evaluation of interventions affecting their use. Antimicrob. Resist. Infect. Control 2018, 7, 98. [Google Scholar] [CrossRef] [PubMed]
  10. Cassini, A.; Högberg, L.D.; Plachouras, D.; Quattrocchi, A.; Hoxha, A.; Simonsen, G.S.; Colomb-Cotinat, M.; Kretzschmar, M.E.; Devleesschauwer, B.; Cecchini, M.; et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015, a population-level modelling analysis. Lancet Infect. Dis. 2019, 19, 56–66. [Google Scholar] [CrossRef] [PubMed]
  11. Weist, K.; Högberg, L.D. ECDC publishes 2015 surveillance data on antimicrobial resistance and antimicrobial consumption in Europe. Eurosurveillance 2016, 21, 30401. [Google Scholar] [CrossRef] [PubMed]
  12. Gasser, M.; Zingg, W.; Cassini, A.; Kronenberg, A. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in Switzerland. Lancet Infect. Dis. 2019, 19, 17–18. [Google Scholar] [CrossRef]
  13. Kariuki, S.; Kering, K.; Wairimu, C.; Onsare, R.; Mbae, C. Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? Infect. Drug Resist. 2022, 15, 3589. [Google Scholar] [CrossRef]
  14. O’Neill, J. Review on Antimicrobial Resistance: Tackling Drug-Resistant Infections Globally. 2016. Available online: https://amr-review.org/sites/default/files/160525_Final paper_with cover.pdf (accessed on 23 August 2025).
  15. Magiorakos, A.P.; Srinivasan, A.; Carey, R.B.; Carmeli, Y.; Falagas, M.E.; Giske, C.G.; Harbarth, S.; Hindler, J.F.; Kahlmeter, G.; Olsson-Liljequist, B.; et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 2012, 18, 268–281. [Google Scholar] [CrossRef] [PubMed]
  16. Basak, S.; Singh, P.; Rajurkar, M. Multidrug Resistant and Extensively Drug Resistant Bacteria: A Study. J. Pathog. 2016, 2016, 4065603. [Google Scholar] [CrossRef] [PubMed]
  17. Santajit, S.; Indrawattana, N. Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens. Biomed. Res. Int. 2016, 2016, 2475067. [Google Scholar] [CrossRef] [PubMed]
  18. De Oliveira, D.M.P.; Forde, B.M.; Kidd, T.J.; Harris, P.N.A.; Schembri, M.A.; Beatson, S.A.; Paterson, D.L.; Walker, M.J. Antimicrobial resistance in ESKAPE pathogens. Clin. Microbiol. Rev. 2020, 33, e00181-19. [Google Scholar] [CrossRef]
  19. Partridge, S.R.; Kwong, S.M.; Firth, N.; Jensen, S.O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 2018, 31. [Google Scholar] [CrossRef]
  20. Scoffone, V.C.; Trespidi, G.; Barbieri, G.; Arshad, A.; Israyilova, A.; Buroni, S. The Evolution of Antimicrobial Resistance in Acinetobacter baumannii and New Strategies to Fight It. Antibiotics 2025, 14, 85. [Google Scholar] [CrossRef]
  21. Ravi, K.; Singh, B. ESKAPE: Navigating the Global Battlefield for Antimicrobial Resistance and Defense in Hospitals. Bacteria 2024, 3, 76–98. [Google Scholar] [CrossRef]
  22. European Commission. A European One Health Action Plan Against Antimicrobial Resistance (AMR). European Commission: Brussels, Belgium, 2017. Available online: https://health.ec.europa.eu/document/download/353f40d1-f114-4c41-9755-c7e3f1da5378_en?filename=amr_2017_action-plan.pdf (accessed on 1 September 2024).
  23. Savin, M.; Bierbaum, G.; Hammerl, J.A.; Heinemann, C.; Parcina, M.; Sib, E.; Voigt, A.; Kreyenschmidt, J. ESKAPe bacteria and extended-spectrum-β-lactamase-producing Escherichia coli isolated from wastewater and process water from German poultry slaughterhouses. Appl. Environ. Microbiol. 2020, 86, e02748-19. [Google Scholar] [CrossRef]
  24. Severino, N.; Reyes, C.; Fernandez, Y.; Azevedo, V.; De Francisco, L.E.; Ramos, R.T.; Maroto-Martín, L.O.; Franco, E.F. Bacterial Foodborne Diseases in Central America and the Caribbean: A Systematic Review. Microbiol. Res. 2025, 16, 78. [Google Scholar] [CrossRef]
  25. Mukwevho, F.N.; Mbanga, J.; Bester, L.A.; Ismail, A.; Essack, S.Y.; Abia, A.L.K. Potential environmental transmission of antibiotic-resistant Escherichia coli and Enterococcus faecium harbouring multiple antibiotic resistance genes and mobile genetic elements in surface waters close to informal settlements: A tale of two cities. Sci. Total Environ. 2025, 976, 179321. [Google Scholar] [CrossRef]
  26. Solís-Soto, L.; Castro-Delgado, Z.L.; García, S.; Heredia, N.; Avila-Sosa, R.; Dávila-Aviña, J.E. Pathogenic bacteria and their antibiotic resistance profile in irrigation water in farms from Mexico. J. Water Sanit. Hyg. Dev. 2024, 14, 565–571. [Google Scholar] [CrossRef]
  27. Nathan, L.S.; Pathak, R.K.; Paul, A. Incidence of Multi Drug Resistant Enterococcus spp. at Sangam Ghat at Prayagraj, India. Biochem. Cell. Arch. 2023, 23, 511–515. [Google Scholar] [CrossRef]
  28. Cinthi, M.; Coccitto, S.N.; Morroni, G.; D’achille, G.; Brenciani, A.; Giovanetti, E. Detection of an Enterococcus faecium Carrying a Double Copy of the PoxtA Gene from Freshwater River, Italy. Antibiotics 2022, 11, 1618. [Google Scholar] [CrossRef] [PubMed]
  29. dos Santos, L.D.R.; Furlan, J.P.R.; Gallo, I.F.L.; Ramos, M.S.; Savazzi, E.A.; Stehling, E.G. Occurrence of multidrug-resistant Enterococcus faecium isolated from environmental samples. Lett. Appl. Microbiol. 2021, 73, 237–246. [Google Scholar] [CrossRef] [PubMed]
  30. Biggel, M.; Nüesch-Inderbinen, M.; Raschle, S.; Stevens, M.J.A.; Stephan, R. Spread of vancomycin-resistant Enterococcus faecium ST133 in the aquatic environment in Switzerland. J. Glob. Antimicrob. Resist. 2021, 27, 31–36. [Google Scholar] [CrossRef] [PubMed]
  31. Cho, S.; Barrett, J.B.; Frye, J.G.; Jackson, C.R. Antimicrobial Resistance Gene Detection and Plasmid Typing Among Multidrug Resistant Enterococci Isolated from Freshwater Environment. Microorganism 2020, 8, 1338. [Google Scholar] [CrossRef]
  32. Pérez-Etayo, L.; González, D.; Leiva, J.; Vitas, A.I. Multidrug-Resistant Bacteria Isolated from Different Aquatic Environments in the North of Spain and South of France. Microorganism 2020, 8, 1425. [Google Scholar] [CrossRef]
  33. Ekwanzala, M.D.; Dewar, J.B.; Kamika, I.; Momba, M.N.B. Comparative genomics of vancomycin-resistant Enterococcus spp. revealed common resistome determinants from hospital wastewater to aquatic environments. Sci. Total Environ. 2020, 719, 137275. [Google Scholar] [CrossRef]
  34. Matlou, D.P.; Bissong, M.E.A.T.; Tchatchouang, C.D.K.; Adem, M.R.; Foka, F.E.T.; Kumar, A.; Ateba, C.N. Virulence profiles of vancomycin-resistant enterococci isolated from surface and ground water utilized by humans in the North West Province, South Africa: A public health perspective. Environ. Sci. Pollut. Res. 2019, 26, 15105–15114. [Google Scholar] [CrossRef]
  35. Giebułtowicz, J.; Tyski, S.; Wolinowska, R.; Grzybowska, W.; Zaręba, T.; Drobniewska, A.; Wroczyński, P.; Nałęcz-Jawecki, G. Occurrence of antimicrobial agents, drug-resistant bacteria, and genes in the sewage-impacted Vistula River (Poland). Environ. Sci. Pollut. Res. 2018, 25, 5788–5807. [Google Scholar] [CrossRef]
  36. Sacramento, A.G.; Cerdeira, L.T.; De Almeida, L.M.; Zanella, R.C.; Pires, C.; Sato, M.I.Z.; Costa, E.A.S.; Roberto, N.P.; Mamizuka, E.M.; Lincopan, N. Environmental dissemination of vanA-containing Enterococcus faecium strains belonging to hospital-associated clonal lineages. J. Antimicrob. Chemother. 2016, 71, 264–266. [Google Scholar] [CrossRef]
  37. Lata, P.; Ram, S.; Shanker, R. Multiplex PCR based genotypic characterization of pathogenic vancomycin resistant Enterococcus faecalis recovered from an Indian river along a city landscape. SpringerPlus 2016, 5, 1–11. [Google Scholar] [CrossRef] [PubMed]
  38. Nishiyama, M.; Iguchi, A.; Suzuki, Y. Identification of Enterococcus faecium and Enterococcus faecalis as vanC-type Vancomycin-Resistant Enterococci (VRE) from sewage and river water in the provincial city of Miyazaki, Japan. J. Environ. Sci. Health Part A 2015, 50, 16–25. [Google Scholar] [CrossRef] [PubMed]
  39. Bessa, L.J.; Barbosa-Vasconcelos, A.; Mendes, Â.; Vaz-Pires, P.; Da Costa, P.M. High prevalence of multidrug-resistant Escherichia coli and Enterococcus spp. in river water, upstream and downstream of a wastewater treatment plant. J. Water Health 2014, 12, 426–435. [Google Scholar] [CrossRef] [PubMed]
  40. Alipour, M.; Hajiesmaili, R.; Talebjannat, M.; Yahyapour, Y. Identification and Antimicrobial Resistance of Enterococcus. spp. Isolated from the River and Coastal Waters in Northern Iran. Sci. World J. 2014, 2014, 287458. [Google Scholar] [CrossRef]
  41. De Niederhäusern, S.; Bondi, M.; Anacarso, I.; Iseppi, R.; Sabia, C.; Bitonte, F.; Messi, P. Antibiotics and heavy metals resistance and other biological characters in enterococci isolated from surface water of Monte Cotugno Lake (Italy). J. Environ. Sci. Health Part A 2013, 48, 939–946. [Google Scholar] [CrossRef]
  42. Middleton, J.H.; Chamberlain, D. Antibiotic Resistance and Virulence Factor Expression of Enterococcus faecalis and Enterococcus faecium isolates from the Upper Passaic River, Morris County, NJ. New Jersey Acad. Sci. 2013, 58, 1–9. [Google Scholar]
  43. Rathnayake, I.U.; Hargreaves, M.; Huygens, F. Antibiotic resistance and virulence traits in clinical and environmental Enterococcus faecalis and Enterococcus faecium isolates. Syst. Appl. Microbiol. 2012, 35, 326–333. [Google Scholar] [CrossRef]
  44. Lanthier, M.; Scott, A.; Zhang, Y.; Cloutier, M.; Durie, D.; Henderson, V.C.; Wilkes, G.; Lapen, D.; Topp, E. Distribution of selected virulence genes and antibiotic resistance in Enterococcus species isolated from the South Nation River drainage basin, Ontario, Canada. J. Appl. Microbiol. 2011, 110, 407–421. [Google Scholar] [CrossRef]
  45. Mondragón, V.A.; Llamas-Pérez, D.F.; González-Guzmán, G.E.; Márquez-González, A.R.; Padilla-Noriega, R.; Durán-Avelar, M.D.J.; Franco, B. Identification of Enterococcus faecalis bacteria resistant to heavy metals and antibiotics in surface waters of the Mololoa River in Tepic, Nayarit, Mexico. Environ. Monit. Assess. 2011, 183, 329–340. [Google Scholar] [CrossRef]
  46. dos Santos, I.R.; da Silva, I.N.M.; de Oliveira Neto, J.R.; de Oliveira, N.R.L.; de Sousa, A.R.V.; de Melo, A.M.; De Paula, J.A.M.; Do Amaral, C.L.; Silveira-Lacerda, E.D.P.; Da Cunha, L.C.; et al. The presence of antibiotics and multidrug-resistant Staphylococcus aureus reservoir in a low-order stream spring in central Brazil. Braz. J. Microbiol. 2023, 54, 997–1007. [Google Scholar] [CrossRef]
  47. Gerken, T.J.; Roberts, M.C.; Dykema, P.; Melly, G.; Lucas, D.; De Los Santos, V.; Gonzalez, J.; Butaye, P.; Wiegner, T.N. Environmental Surveillance and Characterization of Antibiotic Resistant Staphylococcus aureus at Coastal Beaches and Rivers on the Island of Hawaiʻi. Antibiotics 2021, 10, 980. [Google Scholar] [CrossRef] [PubMed]
  48. Silva, V.; Vieira-Pinto, M.; Saraiva, C.; Manageiro, V.; Reis, L.; Ferreira, E.; Caniça, M.; Capelo, J.L.; Igrejas, G.; Poeta, P. Prevalence and Characteristics of Multidrug-Resistant Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) CC398 Isolated from Quails (Coturnix Coturnix Japonica) Slaughtered for Human Consumption. Animals 2021, 11, 2038. [Google Scholar] [CrossRef]
  49. Ramaite, K.; Deogratias Ekwanzala, M.; Dewar, J.B.; Ndombo, M.; Momba, B. Human-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 80 Isolated from Cattle and Aquatic Environments. Antibiotics 2021, 10, 1038. [Google Scholar] [CrossRef] [PubMed]
  50. Ramessar, K.; Olaniran, A.O. Antibiogram and molecular characterization of methicillin-resistant Staphylococcus aureus recovered from treated wastewater effluent and receiving surface water in Durban, South Africa. World J. Microbiol. Biotechnol. 2019, 35, 142. [Google Scholar] [CrossRef]
  51. Lepuschitz, S.; Mach, R.; Springer, B.; Allerberger, F.; Ruppitsch, W. Draft genome sequence of a community-acquired methicillin-resistant Staphylococcus aureus USA300 isolate from a river sample. Genome Announc. 2017, 5, e01166-17. [Google Scholar] [CrossRef]
  52. Akanbi, O.E.; Njom, H.A.; Fri, J.; Otigbu, A.C.; Clarke, A.M. Antimicrobial Susceptibility of Staphylococcus aureus Isolated from Recreational Waters and Beach Sand in Eastern Cape Province of South Africa. Int. J. Environ. Res. Public Health 2017, 14, 1001. [Google Scholar] [CrossRef]
  53. Skariyachan, S.; Mahajanakatti, A.B.; Grandhi, N.J.; Prasanna, A.; Sen, B.; Sharma, N.; Vasist, K.S.; Narayanappa, R. Environmental monitoring of bacterial contamination and antibiotic resistance patterns of the fecal coliforms isolated from Cauvery River, a major drinking water source in Karnataka, India. Environ. Monit. Assess. 2015, 187, 279. [Google Scholar] [CrossRef]
  54. Porrero, M.C.; Harrison, E.; Fernández-Garayzábal, J.F.; Paterson, G.K.; Díez-Guerrier, A.; Holmes, M.A.; Domínguez, L. Detection of mecC-Methicillin-resistant Staphylococcus aureus isolates in river water: A potential role for water in the environmental dissemination. Environ. Microbiol. Rep. 2014, 6, 705–708. [Google Scholar] [CrossRef]
  55. Sood, A.; Pandey, P.; Bisht, S.; Sharma, S. Anthropogenic activities as a source of high prevalence of antibiotic resistant Staphylococcus aureus in the River Ganga. Appl. Ecol. Environ. Res. 2014, 12, 33–48. [Google Scholar] [CrossRef]
  56. Levin-Edens, E.; Soge, O.O.; No, D.; Stiffarm, A.; Meschke, J.S.; Roberts, M.C. Methicillin-resistant Staphylococcus aureus from Northwest marine and freshwater recreational beaches. FEMS Microbiol. Ecol. 2012, 79, 412–420. [Google Scholar] [CrossRef]
  57. Soge, O.O.; Meschke, J.S.; No, D.B.; Roberts, M.C. Characterization of methicillin-resistant Staphylococcus aureus and methicillin-resistant coagulase-negative Staphylococcus spp. isolated from US West Coast public marine beaches. J. Antimicrob. Chemother. 2009, 64, 1148–1155. [Google Scholar] [CrossRef]
  58. Araújo, S.; Silva, V.; de Lurdes Enes Dapkevicius, M.; Pereira, J.E.; Martins, Â.; Igrejas, G.; Poeta, P. Comprehensive Profiling of Klebsiella in Surface Waters from Northern Portugal: Understanding Patterns in Prevalence, Antibiotic Resistance, and Biofilm Formation. Water 2024, 16, 1297. [Google Scholar] [CrossRef]
  59. Xiao, Z.; Qin, Y.; Han, L.; Liu, Y.; Wang, Z.; Huang, Y.; Ma, Y.; Zou, Y. Effects of wastewater treatment plant effluent on microbial risks of pathogens and their antibiotic resistance in the receiving river. Environ. Pollut. 2024, 345, 123461. [Google Scholar] [CrossRef]
  60. Sahoo, S.; Sahoo, R.K.; Dixit, S.; Behera, D.U.; Subudhi, E. NDM-5-carrying Klebsiella pneumoniae ST437 belonging to high-risk clonal complex (CC11) from an urban river in eastern India. 3 Biotech 2023, 13, 139. [Google Scholar] [CrossRef] [PubMed]
  61. Zou, H.; Zhou, Z.; Berglund, B.; Zheng, B.; Meng, M.; Zhao, L.; Zhang, H.; Wang, Z.; Wu, T.; Li, Q.; et al. Persistent transmission of carbapenem-resistant, hypervirulent Klebsiella pneumoniae between a hospital and urban aquatic environments. Water Res. 2023, 242, 120263. [Google Scholar] [CrossRef] [PubMed]
  62. Donato, D.; High, M.; Tapia-Arreola, A.K.; Ruiz-Garcia, D.A.; Rodulfo, H.; Sharma, A.; De Donato, M. High frequency of antibiotic resistance genes (ARGs) in the Lerma River Basin, Mexico. Int. J. Environ. Res. Public Health 2022, 19, 13988. [Google Scholar] [CrossRef]
  63. Lobato, A.; Souza, C.O.; Martins, W.M.B.S.; Barata, R.R.; Camargo, D.S.; Dutra, L.M.G.; Carneiro, I.C.; Costa, C.J.; Brasiliense, D.M. Genomic characterization of BKC-1–producing Klebsiella pneumoniae strain belonging to high-risk clone sequence type 11 isolated from a river in Brazil. Sci. Total Environ. 2022, 850, 157917. [Google Scholar] [CrossRef]
  64. Hassen, B.; Abbassi, M.S.; Benlabidi, S.; Ruiz-Ripa, L.; Mama, O.M.; Ibrahim, C.; Hassen, A.; Hammami, S.; Torres, C. Genetic characterization of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolated from wastewater and river water in Tunisia: Predominance of CTX-M-15 and high genetic diversity. Environ. Sci. Pollut. Res. 2020, 27, 44368–44377. [Google Scholar] [CrossRef]
  65. Furlan, J.P.R.; Savazzi, E.A.; Stehling, E.G. Genomic insights into multidrug-resistant and hypervirulent Klebsiella pneumoniae co-harboring metal resistance genes in aquatic environments. Ecotoxicol. Environ. Saf. 2020, 201, 110782. [Google Scholar] [CrossRef]
  66. Jelić, M.; Hrenović, J.; Dekić, S.; Goić-Barišić, I.; Tambić Andrašević, A. First evidence of KPC-producing ST258 Klebsiella pneumoniae in river water. J. Hosp. Infect. 2019, 103, 147–150. [Google Scholar] [CrossRef]
  67. Lepuschitz, S.; Schill, S.; Stoeger, A.; Pekard-Amenitsch, S.; Huhulescu, S.; Inreiter, N.; Hartl, R.; Kerschner, H.; Sorschag, S.; Springer, B.; et al. Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals. Sci. Total Environ. 2019, 662, 227–235. [Google Scholar] [CrossRef]
  68. Nascimento, T.; Cantamessa, R.; Melo, L.; Fernandes, M.R.; Fraga, E.; Dropa, M.; Sato, M.I.; Cerdeira, L.; Lincopan, N. International high-risk clones of Klebsiella pneumoniae KPC-2/CC258 and Escherichia coli CTX-M-15/CC10 in urban lake waters. Sci. Total Environ. 2017, 598, 910–915. [Google Scholar] [CrossRef]
  69. Hladicz, A.; Kittinger, C.; Zarfel, G. Tigecycline Resistant Klebsiella pneumoniae Isolated from Austrian River Water. Int. J. Environ. Res. Public Health 2017, 14, 1169. [Google Scholar] [CrossRef] [PubMed]
  70. Piedra-Carrasco, N.; Fàbrega, A.; Calero-Cáceres, W.; Cornejo-Sánchez, T.; Brown-Jaque, M.; Mir-Cros, A.; Muniesa, M.; González-López, J.J.; Chang, Y.-F. Carbapenemase-producing enterobacteriaceae recovered from a Spanish river ecosystem. PLoS ONE 2017, 12, e0175246. [Google Scholar] [CrossRef] [PubMed]
  71. Tafoukt, R.; Touati, A.; Leangapichart, T.; Bakour, S.; Rolain, J.M. Characterization of OXA-48-like-producing Enterobacteriaceae isolated from river water in Algeria. Water Res. 2017, 120, 185–189. [Google Scholar] [CrossRef] [PubMed]
  72. Al-Kareem, A.A.; Al-Arajy, K.; Jassim, K.A. Prevalence of CTX-M Gene in Klebsiella pneumonia isolated from Surface Water of Tigris River within Baghdad Province. Prevalence 2015, 30, 15–20. [Google Scholar]
  73. Sotomayor, N.; Villacis, J.E.; Burneo, N.; Reyes, J.; Zapata, S.; de los Ángeles Bayas-Rea, R. Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador. PeerJ 2024, 12, e17199. [Google Scholar] [CrossRef]
  74. Hamidian, M.; Maharjan, R.P.; Farrugia, D.N.; Delgado, N.N.; Dinh, H.; Short, F.L.; Kostoulias, X.; Peleg, A.Y.; Paulsen, I.T.; Cain, A.K. Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity. Microb. Genom. 2022, 8, 765. [Google Scholar] [CrossRef]
  75. Sahoo, S.; Sahoo, R.K.; Gaur, M.; Behera, D.U.; Sahu, A.; Das, A.; Dey, S.; Dixit, S.; Subudhi, E. Environmental carbapenem-resistant Acinetobacter baumannii in wastewater receiving urban river system of eastern India: A public health threat. Int. J. Environ. Sci. Technol. 2022, 20, 9901–9910. [Google Scholar] [CrossRef]
  76. Havenga, B.; Reyneke, B.; Ndlovu, T.; Khan, W. Genotypic and phenotypic comparison of clinical and environmental Acinetobacter baumannii strains. Microb. Pathog. 2022, 172, 105749. [Google Scholar] [CrossRef]
  77. Wang, Q.; Xu, Y.; Liu, L.; Li, L.-Y.; Lin, H.; Wu, X.-Y.; Bi, W.-J.; Wang, L.-T.; Mao, D.-Q.; Luo, Y. The prevalence of ampicillin-resistant opportunistic pathogenic bacteria undergoing selective stress of heavy metal pollutants in the Xiangjiang River, China. Environ. Pollut. 2021, 268, 115362. [Google Scholar] [CrossRef]
  78. Adewoyin, M.A.; Ebomah, K.E.; Okoh, A.I. Antibiogram profile of Acinetobacter baumannii recovered from selected freshwater resources in the Eastern Cape Province, South Africa. Pathogens 2021, 10, 1110. [Google Scholar] [CrossRef] [PubMed]
  79. Murphy, A.; Barich, D.; Fennessy, M.S.; Slonczewski, J.L. An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent. Microbiol. Spectr. 2021, 9, e0094121. [Google Scholar] [CrossRef] [PubMed]
  80. Tsai, H.-C.; Chou, M.-Y.; Shih, Y.-J.; Huang, T.-Y.; Yang, P.-Y.; Chiu, Y.-C.; Chen, J.-S.; Hsu, B.-M. Distribution and Genotyping of Aquatic Acinetobacter baumannii Strains Isolated from the Puzi River and Its Tributaries Near Areas of Livestock Farming. Water 2018, 10, 1374. [Google Scholar] [CrossRef]
  81. Liu, N.; Zhu, L.; Zhang, Z.; Huang, H.; Jiang, L. Draft genome sequence of a multidrug-resistant blaOXA-69-producing Acinetobacter baumannii L13 isolated from Tarim River sample in China. J. Glob. Antimicrob. Resist. 2019, 18, 145–147. [Google Scholar] [CrossRef]
  82. Kittinger, C.; Kirschner, A.; Lipp, M.; Baumert, R.; Mascher, F.; Farnleitner, A.H.; Zarfel, G.E. Antibiotic Resistance of Acinetobacter spp. Isolates from the River Danube: Susceptibility Stays High. Int. J. Environ. Res. Public Health 2018, 15, 52. [Google Scholar] [CrossRef]
  83. Turano, H.; Gomes, F.; Medeiros, M.; Oliveira, S.; Fontes, L.C.; Sato, M.I.Z.; Lincopan, N. Presence of high-risk clones of OXA-23-producing Acinetobacter baumannii (ST79) and SPM-1-producing Pseudomonas aeruginosa (ST277) in environmental water samples in Brazil. Diagn. Microbiol. Infect. Dis. 2016, 86, 80–82. [Google Scholar] [CrossRef]
  84. Rojo-Bezares, B.; Casado, C.; Ceniceros, T.; López, M.; Chichón, G.; Lozano, C.; Ruiz-Roldán, L.; Sáenz, Y. Pseudomonas aeruginosa from river water: Antimicrobial resistance, virulence and molecular typing. FEMS Microbiol. Ecol. 2024, 100, 28. [Google Scholar] [CrossRef]
  85. Sharif, D.I.; Amin, F.; Mehbub, H.; Ratul, R.I. Distribution and antibiotic resistance patterns of Pseudomonas aeruginosa across different point sources of pollution in the Buriganga River, Bangladesh. J. Water Health 2024, 22, 2358–2369. [Google Scholar] [CrossRef]
  86. Ghosh, D.; Mangar, P.; Choudhury, A.; Saha, A.K.A.; Basu, P.; Saha, D. Characterization of a hemolytic and antibiotic-resistant Pseudomonas aeruginosa strain S3 pathogenic to fish isolated from Mahananda River in India. PLoS ONE 2024, 19, e0300134. [Google Scholar] [CrossRef]
  87. Hosu, M.C.; Vasaikar, S.D.; Okuthe, G.E.; Apalata, T. Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa. Sci. Rep. 2021, 11, 7110. [Google Scholar] [CrossRef] [PubMed]
  88. Nasreen, M.; Sarker, A.; Malek, M.A.; Ansaruzzaman, M.; Rahman, M. Prevalence and Resistance Pattern of Pseudomonas aeruginosa Isolated from Surface Water. Adv. Microbiol. 2015, 5, 74–81. [Google Scholar] [CrossRef]
  89. Magalhães, M.J.T.L.; Pontes, G.; Serra, P.T.; Balieiro, A.; Castro, D.; Pieri, F.A.; Crainey, J.L.; Nogueira, P.A.; Orlandi, P.P. Multidrug resistant Pseudomonas aeruginosa survey in a stream receiving effluents from ineffective wastewater hospital plants. BMC Microbiol. 2016, 16, 193. [Google Scholar] [CrossRef] [PubMed]
  90. Suzuki, Y.; Kajii, S.; Nishiyama, M.; Iguchi, A. Susceptibility of Pseudomonas aeruginosa isolates collected from river water in Japan to antipseudomonal agents. Sci. Total Environ. 2013, 450–451, 148–154. [Google Scholar] [CrossRef]
  91. Fontes, L.C.; Neves, P.R.; Oliveira, S.; Silva, K.C.; Hachich, E.M.; Sato, M.I.Z.; Lincopan, N. Isolation of Pseudomonas aeruginosa Coproducing Metallo-β-Lactamase SPM-1 and 16S rRNA Methylase RmtD1 in an Urban River. Antimicrob. Agents Chemother. 2011, 55, 3063. [Google Scholar] [CrossRef]
  92. Jofré Bartholin, M.; Barrera Vega, B.; Berrocal Silva, L. Antibiotic-Resistant Bacteria in Environmental Water Sources from Southern Chile: A Potential Threat to Human Health. Microbiol. Res. 2023, 14, 1764–1773. [Google Scholar] [CrossRef]
  93. Adachi, F.; Sekizuka, T.; Yamato, M.; Fukuoka, K.; Yamaguchi, N.; Kuroda, M.; Kawahara, R. Characterization of FRI carbapenemase-producing Enterobacter spp. isolated from a hospital and the environment in Osaka, Japan. J. Antimicrob. Chemother. 2021, 76, 3061–3062. [Google Scholar] [CrossRef]
  94. Suzuki, Y.; Nazareno, P.J.; Nakano, R.; Mondoy, M.; Nakano, A.; Bugayong, M.P.; Bilar, J.; Perez, M.; Medina, E.J.; Saito-Obata, M.; et al. Environmental presence and genetic characteristics of carbapenemase-producing enterobacteriaceae from hospital sewage and river water in the philippines. Appl. Environ. Microbiol. 2020, 86, e01906-19. [Google Scholar] [CrossRef]
  95. Cohen, R.; Paikin, S.; Rokney, A.; Rubin-Blum, M.; Astrahan, P. Multidrug-resistant enterobacteriaceae in coastal water: An emerging threat. Antimicrob. Resist. Infect. Control 2020, 9, 169. [Google Scholar] [CrossRef]
  96. Fadare, F.T.; Adefisoye, M.A.; Okoh, A.I. Occurrence, identification, and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa. PLoS ONE 2020, 15, e0238084. [Google Scholar] [CrossRef]
  97. Guzman-Otazo, J.; Gonzales-Siles, L.; Poma, V.; Bengtsson-Palme, J.; Thorell, K.; Flach, C.F.; Iñiguez, V.; Sjöling, Å. Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia. PLoS ONE 2019, 14, e0210735. [Google Scholar] [CrossRef]
  98. Kittinger, C.; Lipp, M.; Folli, B.; Kirschner, A.; Baumert, R.; Galler, H.; Grisold, A.J.; Luxner, J.; Weissenbacher, M.; Farnleitner, A.H.; et al. Enterobacteriaceae isolated from the River danube: Antibiotic resistances, with a focus on the presence of ESBL and carbapenemases. PLoS ONE 2016, 11, e0165820. [Google Scholar] [CrossRef]
  99. Zurfluh, K.; Hächler, H.; Nüesch-Inderbinen, M.; Stephan, R. Characteristics of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae isolates from rivers and lakes in Switzerland. Appl. Environ. Microbiol. 2013, 79, 3021–3026. [Google Scholar] [CrossRef] [PubMed]
  100. Xu, H.; Miao, V.; Kwong, W.; Xia, R.; Davies, J. Identification of a novel fosfomycin resistance gene (fosA2) in Enterobacter cloacae from the Salmon River, Canada. Lett. Appl. Microbiol. 2011, 52, 427–429. [Google Scholar] [CrossRef]
  101. Vale de Macedo, G.H.R.; Costa, G.D.E.; Oliveira, E.R.; Damasceno, G.V.; Mendonça, J.S.P.; Silva, L.d.S.; Chagas, V.L.; Bazán, J.M.N.; Aliança, A.S.d.S.; Miranda, R.d.C.M.d.; et al. Interplay between ESKAPE Pathogens and Immunity in Skin Infections: An Overview of the Major Determinants of Virulence and Antibiotic Resistance. Pathogens 2021, 10, 148. [Google Scholar] [CrossRef]
  102. Gotkowska-Płachta, A. The Prevalence of Virulent and Multidrug-Resistant Enterococci in River Water and in Treated and Untreated Municipal and Hospital Wastewater. Int. J. Environ. Res. Public Health 2021, 18, 563. [Google Scholar] [CrossRef]
  103. Ibekwe, A.M.; Obayiuwana, A.C.; Murinda, S.E. Enterococcus Species and Their Antimicrobial Resistance in an Urban Watershed Affected by Different Anthropogenic Sources. Water 2024, 16, 116. [Google Scholar] [CrossRef]
  104. Maheux, A.F.; Bissonnette, L.; Boissinot, M.; Bernier, J.L.T.; Huppé, V.; Bérubé, È.; Boudreau, D.K.; Picard, F.J.; Huletsky, A.; Bergeron, M.G. Method for rapid and sensitive detection of Enterococcus sp. and Enterococcus faecalis/faecium cells in potable water samples. Water. Res. 2011, 45, 2342–2354. [Google Scholar] [CrossRef]
  105. Dubin, K.; Pamer, E.G. Enterococci and Their Interactions with the Intestinal Microbiome. Microbiol. Spectr. 2017, 5, 10.1128. [Google Scholar] [CrossRef]
  106. Suzuki, Y.; Kanda, N.; Furukawa, T. Abundance of Enterococcus species, Enterococcus faecalis and Enterococcus faecium, essential indicators of fecal pollution, in river water. J. Environ. Sci. Health—Part A Toxic/Hazard. Subst. Environ. Eng. 2012, 47, 1500–1505. [Google Scholar] [CrossRef]
  107. Thurlow, L.R.; Thomas, V.C.; Narayanan, S.; Olson, S.; Fleming, S.D.; Hancock, L.E. Gelatinase contributes to the pathogenesis of endocarditis caused by Enterococcus faecalis. Infect. Immun. 2010, 78, 4936–4943. [Google Scholar] [CrossRef] [PubMed]
  108. Ekwanzala, M.D.; Abia, A.L.K.; Ubomba-Jaswa, E.; Keshri, J.; Momba, N.B.M. Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa. AMB Express 2017, 7, 20. [Google Scholar] [CrossRef] [PubMed]
  109. Rosenberg Goldstein, R.E.; Micallef, S.A.; Gibbs, S.G.; Davis, J.A.; He, X.; George, A.; Kleinfelter, L.M.; Schreiber, N.A.; Mukherjee, S.; Joseph, S.W.; et al. Methicillin-resistant Staphylococcus aureus (MRSA) Detected at Four U.S. wastewater treatment plants. Environ. Health Perspect. 2012, 120, 1551–1558. [Google Scholar] [CrossRef] [PubMed]
  110. Tolba, O.; Loughrey, A.; Goldsmith, C.E.; Millar, B.C.; Rooney, P.J.; Moore, J.E. Survival of epidemic strains of healthcare (HA-MRSA) and community-associated (CA-MRSA) meticillin-resistant Staphylococcus aureus (MRSA) in river-, sea- and swimming pool water. Int. J. Hyg. Environ. Health 2008, 211, 398–402. [Google Scholar] [CrossRef]
  111. Carrel, M.; Perencevich, E.N.; David, M.Z. USA300 Methicillin-Resistant Staphylococcus aureus, United States, 2000–2013. Emerg. Infect. Dis. 2015, 21, 1973. [Google Scholar] [CrossRef]
  112. Azarian, T.; Daum, R.S.; Petty, L.A.; Steinbeck, J.L.; Yin, Z.; Nolan, D.; Boyle-Vavra, S.; Hanage, W.P.; Salemi, M.; David, M.Z. Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. J. Infect. Dis. 2016, 214, 895–905. [Google Scholar] [CrossRef]
  113. Lepuschitz, S.; Huhulescu, S.; Hyden, P.; Springer, B.; Rattei, T.; Allerberger, F.; Mach, R.L.; Ruppitsch, W. Characterization of a community-acquired-MRSA USA300 isolate from a river sample in Austria and whole genome sequence based comparison to a diverse collection of USA300 isolates. Sci. Rep. 2018, 8, 9467. [Google Scholar] [CrossRef]
  114. Fergestad, M.E.; Stamsås, G.A.; Morales Angeles, D.; Salehian, Z.; Wasteson, Y.; Kjos, M. Penicillin-binding protein PBP2a provides variable levels of protection toward different β-lactams in Staphylococcus aureus RN4220. Microbiologyopen 2020, 9, e1057. [Google Scholar] [CrossRef]
  115. Lade, H.; Kim, J.S. Molecular Determinants of β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus (MRSA): An Updated Review. Antibiotics 2023, 12, 1362. [Google Scholar] [CrossRef]
  116. Kilani, A.M.; Alabi, E.D.; Adeleke, O.E. Coexistence of the blaZ gene and selected virulence determinants in multidrug-resistant Staphylococcus aureus: Insights from three Nigerian tertiary hospitals. BMC Infect. Dis. 2024, 24, 1269. [Google Scholar] [CrossRef]
  117. Arêde, P.; Ministro, J.; Oliveira, D.C. Redefining the Role of the β-Lactamase Locus in Methicillin-Resistant Staphylococcus aureus: β-Lactamase Regulators Disrupt the MecI-Mediated Strong Repression on mecA and Optimize the Phenotypic Expression of Resistance in Strains with Constitutive mecA Expression. Antimicrob. Agents Chemother. 2013, 57, 3037. [Google Scholar] [CrossRef] [PubMed]
  118. Ballhausen, B.; Kriegeskorte, A.; Schleimer, N.; Peters, G.; Becker, K. The mecA homolog mecC confers resistance against β-lactams in Staphylococcus aureus irrespective of the genetic strain background. Antimicrob. Agents Chemother. 2014, 58, 3791–3798. [Google Scholar] [CrossRef] [PubMed]
  119. Silva, V.; Ferreira, E.; Manageiro, V.; Reis, L.; Tejedor-Junco, M.T.; Sampaio, A.; Capelo, J.L.; Caniça, M.; Igrejas, G.; Poeta, P. Distribution and Clonal Diversity of Staphylococcus aureus and Other Staphylococci in Surface Waters: Detection of ST425-t742 and ST130-t843 mecC-Positive MRSA Strains. Antibiotics 2021, 10, 1416. [Google Scholar] [CrossRef] [PubMed]
  120. Henriot, C.P.; Martak, D.; Cuenot, Q.; Loup, C.; Masclaux, H.; Gillet, F.; Bertrand, X.; Hocquet, D.; Bornette, G. Occurrence and ecological determinants of the contamination of floodplain wetlands with Klebsiella pneumoniae and pathogenic or antibiotic-resistant Escherichia coli. FEMS Microbiol. Ecol. 2019, 95, fiz097. [Google Scholar] [CrossRef] [PubMed]
  121. Podschun, R.; Pietsch, S.; Höller, C.; Ullmann, U. Incidence of Klebsiella Species in Surface Waters and Their Expression of Virulence Factors. Appl. Environ. Microbiol. 2001, 67, 3325. [Google Scholar] [CrossRef]
  122. Barati, A.; Ghaderpour, A.; Chew, L.L.; Bong, C.W.; Thong, K.L.; Chong, V.C.; Chai, L.C. Isolation and Characterization of Aquatic-Borne Klebsiella pneumoniae from Tropical Estuaries in Malaysia. Int. J. Environ. Res. Public Health 2016, 13, 426. [Google Scholar] [CrossRef]
  123. Liu, W.; Li, M.; Cao, S.; Ishaq, H.M.; Zhao, H.; Yang, F.; Liu, L. The Biological and Regulatory Role of Type VI Secretion System of Klebsiella pneumoniae. Infect. Drug Resist. 2023, 16, 6911–6922. [Google Scholar] [CrossRef]
  124. Arnold, R.S.; Thom, K.A.; Sharma, S.; Phillips, M.; Kristie Johnson, J.; Morgan, D.J. Emergence of Klebsiella pneumoniae Carbapenemase (KPC)-Producing Bacteria. South. Med. J. 2011, 104, 40. [Google Scholar] [CrossRef]
  125. Wang, G.; Zhao, G.; Chao, X.; Xie, L.; Wang, H. The Characteristic of Virulence, Biofilm and Antibiotic Resistance of Klebsiella pneumoniae. Int. J. Environ. Res. Public Health 2020, 17, 6278. [Google Scholar] [CrossRef]
  126. Kochan, T.J.; Nozick, S.H.; Medernach, R.L.; Cheung, B.H.; Gatesy, S.W.M.; Lebrun-Corbin, M.; Mitra, S.D.; Khalatyan, N.; Krapp, F.; Qi, C.; et al. Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates. BMC Infect. Dis. 2022, 22, 603. [Google Scholar] [CrossRef]
  127. Korczak, L.; Majewski, P.; Iwaniuk, D.; Sacha, P.; Matulewicz, M.; Wieczorek, P.; Majewska, P.; Wieczorek, A.; Radziwon, P.; Tryniszewska, E. Molecular mechanisms of tigecycline-resistance among Enterobacterales. Front. Cell. Infect. Microbiol. 2024, 14, 1289396. [Google Scholar] [CrossRef] [PubMed]
  128. Chirabhundhu, N.; Luk-In, S.; Phuadraksa, T.; Wichit, S.; Chatsuwan, T.; Wannigama, D.L.; Yainoy, S. Occurrence and mechanisms of tigecycline resistance in carbapenem- and colistin-resistant Klebsiella pneumoniae in Thailand. Sci. Rep. 2024, 14, 5215. [Google Scholar] [CrossRef] [PubMed]
  129. Lee, C.R.; Lee, J.H.; Park, M.; Park, K.S.; Bae, I.K.; Kim, Y.B.; Cha, C.-J.; Jeong, B.C.; Lee, S.H. Biology of Acinetobacter baumannii: Pathogenesis, antibiotic resistance mechanisms, and prospective treatment options. Front. Cell. Infect. Microbiol. 2017, 7, 249706. [Google Scholar] [CrossRef] [PubMed]
  130. Jacobs, A.C.; Zurawski, D.V. Laboratory Maintenance of Acinetobacter baumannii. Curr. Protoc. Microbiol. 2014, 35, 6G.1.1–6G.1.6. [Google Scholar] [CrossRef]
  131. Ahuatzin-Flores, O.E.; Torres, E.; Chávez-Bravo, E. Acinetobacter baumannii, a Multidrug-Resistant Opportunistic Pathogen in New Habitats: A Systematic Review. Microorganisms 2024, 12, 644. [Google Scholar] [CrossRef]
  132. Dijkshoorn, L.; Nemec, A.; Seifert, H. An increasing threat in hospitals: Multidrug-resistant Acinetobacter baumannii. Nat. Rev. Microbiol. 2007, 5, 939–951. [Google Scholar] [CrossRef]
  133. Ekundayo, T.C.; Adewoyin, M.A.; Ijabadeniyi, O.A.; Igbinosa, E.O.; Okoh, A.I. Machine learning-guided determination of Acinetobacter density in waterbodies receiving municipal and hospital wastewater effluents. Sci. Rep. 2023, 13, 7749. [Google Scholar] [CrossRef]
  134. Elshafiee, E.A.; Nader, S.M.; Dorgham, S.M.; Hamza, D.A. Carbapenem-resistant Pseudomonas aeruginosa originating from farm animals and people in Egypt. J. Vet. Res. 2019, 63, 333–337. [Google Scholar] [CrossRef]
  135. Hosu, M.C.; Vasaikar, S.; Okuthe, G.E.; Apalata, T. Molecular Detection of Antibiotic-Resistant Genes in Pseudomonas aeruginosa from Nonclinical Environment: Public Health Implications in Mthatha, Eastern Cape Province, South Africa. Int. J. Microbiol. 2021, 2021, 8861074. [Google Scholar] [CrossRef]
  136. Igbinosa, E.O.; Odjadjare, E.E.; Igbinosa, I.H.; Orhue, P.O.; Omoigberale, M.N.O.; Amhanre, N.I. Antibiotic Synergy Interaction against Multidrug-Resistant Pseudomonas aeruginosa Isolated from an Abattoir Effluent Environment. Sci. World J. 2012, 2012, 308034. [Google Scholar] [CrossRef]
  137. Aeschlimann, J.R. The Role of Multidrug Efflux Pumps in the Antibiotic Resistance of Pseudomonas aeruginosa and Other Gram-Negative Bacteria. Pharmacother. J. Hum. Pharmacol. Drug Ther. 2003, 23, 916–924. [Google Scholar] [CrossRef]
  138. Zagui, G.S.; Moreira, N.C.; Santos, D.V.; Paschoalato, C.F.P.R.; Sierra, J.; Nadal, M.; Domingo, J.L.; Darini, A.L.C.; Andrade, L.N.; Segura-Muñoz, S.I. Multidrug-resistant Enterobacter spp. in wastewater and surface water: Molecular characterization of β-lactam resistance and metal tolerance genes. Environ. Res. 2023, 233, 116443. [Google Scholar] [CrossRef] [PubMed]
  139. Patel, C.B.; Shanker, R.; Gupta, V.K.; Upadhyay, R.S. Q-PCR based culture-independent enumeration and detection of enterobacter: An emerging environmental human pathogen in riverine systems and potable water. Front. Microbiol. 2016, 7, 173935. [Google Scholar] [CrossRef] [PubMed]
  140. Davin-Regli, A.; Lavigne, J.P.; Pagès, J.M. Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin. Microbiol. Rev. 2019, 32, e00002-19. [Google Scholar] [CrossRef]
  141. Zarfel, G.; Lipp, M.; Gürtl, E.; Folli, B.; Baumert, R.; Kittinger, C. Troubled water under the bridge: Screening of River Mur water reveals dominance of CTX-M harboring Escherichia coli and for the first time an environmental VIM-1 producer in Austria. Sci. Total Environ. 2017, 593–594, 399–405. [Google Scholar] [CrossRef] [PubMed]
  142. Pandey, R.; Mishra, S.K.; Shrestha, A. Characterisation of ESKAPE Pathogens with Special Reference to Multidrug Resistance and Biofilm Production in a Nepalese Hospital. Infect. Drug. Resist. 2021, 14, 2201. [Google Scholar] [CrossRef]
Figure 1. Research publications on individual ESKAPE pathogens in surface water between 2000 and 2025.
Figure 1. Research publications on individual ESKAPE pathogens in surface water between 2000 and 2025.
Microbiolres 16 00201 g001
Table 1. Geographical distribution of ESKAPE pathogens in waterbodies in different continents.
Table 1. Geographical distribution of ESKAPE pathogens in waterbodies in different continents.
ESKAPE PathogenContinent
AfricaAmericasAsiaEuropeOceaniaTotal no. of Each ESKAPE Pathogen per Continent
Enterococcus faecium/faecalis3746121
Staphylococcus aureus3423-12
Klebsiella pneumoniae2544-15
Acinetobacter baumannii2243-11
Pseudomonas aeruginosa1241-8
Enterobacter spp.2322-9
Total number of used articles13232019176
Five studies were duplicated.
Table 2. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of E. faecium/faecalis in waterbodies worldwide.
Table 2. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of E. faecium/faecalis in waterbodies worldwide.
Year/CountryAquatic
System
Number of
Isolates
ARGVGMDR E.
faecium
/faecalis
ST/CCGenomic AnalysisReference
2025
South Africa
Palmiet River streamE. faecium (11)aac(6′)-Ii
ant(6)-Ia
dfrG
ermB
msrC
tetL
tetM
n. d.4ST94
ST361
ST2013
ST2042
ST2431
WGS[25]
2024
Mexico
River in VeracruzE. faecalis (2)n. d.eda1
ccf
0n. d.No[26]
2023
India
Ganga, Yamuna, and Sangam riversE. faecium (19)
E. faecalis (7)
n. d.n. d.n. d.n. d.No[27]
2022
Italy
Salinello
Estuary River
E. faecium (2)aph(3′)-III
aac(6′)-Ii
ant(6)-Ia
aac(6′)-aph(2″)
ermB
fexB
msrC
tetM
tetL
poxtA
n. d.1n. d.WGS[28]
2021
Brazil
Rivers and beaches in the southeastern regionE. faecium (16)ermBgelE
esp
ace
6n. d.No[29]
2021
Switzerland
Aare, Rhein, and Rhone rivers
Streams
E. faecium (6)aac(6′)-Ii
catA
efrA
msrC
tetM
vanA
n. d.n. d.ST133WGS[30]
2020
USA
Oconee RiverE. faecium (33)
E. faecalis (169)
n. d.n. d.7/8n. d.No[31]
2020
Spain
Alhama RiverE. faecium (1)vanBn. d.1n. d.No[32]
2020
South Africa
Apies RiverE. faecium (13)
E. faecalis (5)
aac(6′)-Ii
vanA/C/N/L/G
isaA
tetM
Acm
esp
hylE
n. d.ST80, ST203,WGS,
comparative genomic analysis
[33]
2019
South Africa
Rivers and dam in the Northwest ProvinceE. faecium (11)
E. faecalis (9)
vanA
vanB
asa1
esp
gel
hyla
11/9n. d.No[34]
2018
Poland
Vistula RiverE. faecium (75)
E. faecalis (39)
ermC
tetA
tetO
tetW
43/6n. d.No[35]
2016
Brazil
Tiete ˆand Pinheiros riversE. faecium (5)
E. faecalis (1)
vanAn. d.5/1ST17, ST18, ST78, ST117, ST192, ST280, ST412 and ST478Comparative genomic analysis[36]
2016
India
River GomtiE. faecalis (33)vanBgelE
ace
efaA
esp
33n. d.No[37]
2015
Japan
Yae RiverE. faecium (38)
E. faecalis (20)
vanC1
vanC2/3
n. d.2/3n. d.No[38]
2014
Portugal
Ave RiverE. faecium (18)
E. faecalis (15)
vanAn. d.16/10n. d.No[39]
2014
Iran
Babolrud RiverE. faecium (7)
E. faecalis (20)
n. d.n. d.n. d.n. d.No[40]
2013
Italy
Monte Cotugno LakeE. faecium (132)
E. faecalis (21)
n. d.Agg
efaA
gelE
n. d.n. d.No[41]
2013
USA
Passaic RiverE. faecium (103)
E. faecalis (396)
n. d.gelE
β hemolysis cylA/B/M
bacteriocin
33/10n. d.No[42]
2012
Australia
Coomera RiverE. faecium (47)
E. faecalis (55)
vanA
vanB
gelE0/0n. d.No[43]
2011
Canada
South Nation RiverE. faecium (145)
E. faecalis (567)
n. d.ccf
cpd
esp
enlA
gelE
n. d.n. d.No[44]
2011
Mexico
Mololoa RiverE. faecalis (38)n. d.n. d.n. d.n. d.No[45]
ARG = Antimicrobial-resistant gene; VG = Virulence gene; STC/CC = Sequence Type; n. d.= not determined; WGS = Whole-Genome Sequencing.
Table 3. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of S. aureus in waterbodies worldwide.
Table 3. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of S. aureus in waterbodies worldwide.
CountryAquatic
System
Number of IsolatesARGVGMDRMolecular
Typing
Genomic AnalysisReference
spa-TypeST/CC
2023
Brazil
Extrema River SpringMRSA (20)n.d.n. d.14n. d.n. d.No[46]
2021
USA
Lehia, Richardson’s, Honoliʻi, Pohoiki, Kealoha, Onekahakaha beach parks, Wailuku River EstuarymecA-MRSA (9)aph(3′)-III
blaZ
ermC
mecA,
mphC
msrA
hlgA
hlgB
hlgC
lukD
lukE
lukF-PV
lukS-PV
sek
seq
9n. d.ST8 (CC8).WGS assembly and analysis[47]
MSSA (27)blaZ
ermT
aph(3′)-III
ant(6)-Ia
mphC
tetK
hlgA/B/C
hemolysin genes
lukE
seg
4n. d.ST5
ST398
ST72
ST15 (CC15)
ST508 (CC45)
ST97 (CC97)
ST518
ST6
ST1155
ST3269
ST1181
2021
Portugal
Rivers from the Douro River BasinmecC-MRSA (3)blaZ-SCCmecIXHld0t742ST425No[48]
MSSA (9)blaZ
ermT
vgaA
hla
hlb
hld
0t008 t571 t742 t208 t098 t4735 t8083ST398
ST8 (CC8) ST49 (CC49)
ST3223
ST49 (CC49) ST6835
ST133
ST6836
2021
South Africa
Rivers from Bon Accord DammecA-MRSA
(6)
blaZ
ermA
sec and seq.0n. d.ST80 (CC80) ST728No[49]
2019
South Africa
Durban area RiversmecA-MRSA (80)aac(6′)
aph(2)
blaZ
ermC
msrA
tetK
hlgA
hlgD lukS/FPV
sea
80n. d.n. d.No[50]
2017
Austria
River MurmecA-MRSA (1)n. d.hlgA/B/C
agr type
arcA/B/C
aur
cap5H
1t008ST8 (CC8)WGS[51]
2017
South Africa
Beaches in Eastern Cape ProvincemecA-MRSA (5)
MSSA (25)
blaZ
mecA
rpoB
ermB
tetM
n. d.30n. d.n. d.No[52]
2015
India
River CauveryMRSA (42)n. d.n. d.42n. d.n. d.No[53]
2014
Spain
Game estate RiversmecC-MRSA (3)blaZLGA251n. d.n. d.t11212ST425WGS[54]
2014
India
Ganga RiverMRSA (16)n. d.n. d.n. d.n. d.n. d.No[55]
MSSA (72)n. d.n. d.n. d.n. d.n. d.
2012
USA
Beaches in the Marine, Freshwater, and Lake WashingtonmecA-MRSA (31),tetK
ermC
msrA
aadD
n. d.26n. d.ST8, ST30, ST45, ST88, ST15, ST88, ST97
ST1875 ST133
ST1956
ST2049
No[56]
MSSA (14)n. d.n. d.n. d.n. d.n. d.
2009
USA
Washington State beachesMRSA (6)ccrB
ermA
tetK
tetM
n. d.5n. d.ST145
ST45
ST59
ST30
No[57]
MSSA (4)Nonen. d.0n. d.ST15
ST59
ST30
ARG = Antimicrobial-resistant gene; VG = Virulence gene; STC/CC = Sequence Type Cluster/Clonal Complex; n. d. = not determined; WGS = Whole-Genome Sequencing.
Table 4. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of K. pneumoniae waterbodies worldwide.
Table 4. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of K. pneumoniae waterbodies worldwide.
CountryAquatic
System
Number of IsolatesARGVGMDRST/CCGenomic
Analysis
Reference
2024
Portugal
Rivers and dam along the Douro River Basin9aadA1
blaAmpC
blaCTX-U
blaCTX-M9
blaSHV
strA
sul2
bfp
papC,
4n. d.No[58]
2024 ChinaQinhuai River5AcrB
aph(3′)-Ib
aph(6)-Id
bacA
mdtB
oqxB
rsmA
blaSHV-1
ugd
n. d.n. d.n. d.No[59]
2023
India
Kathajodi River1blaCTX-M
blaNDM-5
blaSHV
blaTEM
FimH
entB
irp-1
mrkD
ybtS
1ST437No[60]
2023 ChinaDongluo, Quanfu, and Shunhe rivers4aadA
blaCTX-M
blaKPC-2
blaNDM-1
blaTEM
fosA
rmtB
entA/B/C/D/E/F
entD
fepA/B/C/D/G
iutA
4ST17
ST11
ST730
WGS[61]
2022
Mexico
Rivers and dam along the Lerma River basin7aac(3)-IIa
aac(6′)Ib-cr
blaCTX-M-15
blaOXA-1
blaOXA-232
blaSHV-11
blaTEM-1B
catB4
dfrA14
fosA
oqxA/B
QnrS1
QnrB66
strA/B
sul2
tetA
Dam, fimH ppdD6n. d.WGS[62]
2022
Brazil
Guajará Bay River1blaBKC-1
blaCTX-M-15
blaSHV-11
aph(3′)-VIa
aac(6′)-Ib-cr
aac(3)-Iia
qnrE1
qnrB19
rsmA
emrR
crp
fosA6
catB3
rsmA
iutA
acrA/B
mrkA/C/D/F/H/I
fimA/B/C/D/E/F/G/H/I/K
1ST11
CC258
WGS[63]
2020
Tunisia
Rouriche River2aadA2
blaCTX-M-15
dfrA12
blaSHV
qacE1
sul1
sul2
tetA
2ST1540 ST661.No[64]
2020
Brazil
Sertãozinho Stream, Euclides Moreli Lake, and Monjolinho River3blaSHV-26
blaSHV-27
blaSHV-81
fosA
sul1
tetA
iutA
entB
ybtPQ
irp1
fimA/B/C/D/E/F/G/H/I/K, mrkA/B/C/D/F
ecpA/B/C/D/E7R, pulB/C/D/E/F/G/H/I/J/K/L/M/
fepCG
iroCN
mceG
kfuBC,
3ST661
(CC661)
ST4415
(CC515)
ST4416 (CC2654)
WGS, genomic islands, phage-related sequences[65]
2019
Croatia
Krapina River4blaKPC-2
blaSHV-1
aac (3′)-II
aac(6′)-Ib
aph(3′)-Ia
n. d.4ST258.No[66]
2019
Austria
Inn, Drau, Glan, Traun, and Danube Rivers5aac(3)-Iic
aac(6′)-Ib
aph(3′)-Ia
aadA
baeR
blaCTX-M-15
blaOXA-1
blaSHV-1
blaVIM-1
ermB/R
fosA6
QnrB1
mphA
iutA
mrkA/mrkB/C/D/F/H/I/J
ybtS/tX
5ST11
ST985
ST405
ST3400
ST323
WGS[67]
2017
Brazil
Ibirapuera Lake2blaKPC-2
blaSHV-11
oqxA/B
dfrA30
tetA
fosA
n. d.2ST11/CC258WGS[68]
2017
Austria
River Mur2RamRn. d.0ST2392 ST2394No[69]
2017
Spain
Llobregat River1blaKPC-2fimH
mrkD
wabG
uge
magA
rmpA
ureA
allS
kfuBC
1ST634No[70]
2017
Algeria
Soummam River3blaOXA 48
blaSHV
n. d.3ST133
ST2192
ST2055
No[71]
2015
Iraq
Tigris River40blaCTX-Mn. d.n. d.n. d.No[72]
ARG = Antimicrobial-resistant gene; VG = Virulence gene; STC/CC = Sequence Type Cluster/Clonal Complex; n. d. = not determined; WGS = Whole-Genome Sequencing.
Table 5. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of A. baumannii in waterbodies worldwide.
Table 5. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of A. baumannii in waterbodies worldwide.
CountryAquatic SystemNumber of IsolatesARGVGMDR/
XDR
ST/CCGenomic
Analysis
Reference
2024
Ecuador
Machángara and
Monjas rivers
10blaOXA-51n. d.3n. d.No[73]
2024
China
Qinhuai River2msrE
mphE
n. d.n. d.n. d.No[59]
2022
France
Seine River1blaAmpC
blaOXA-23
parC
strAB
tetA
blc
ompA
smpA
csuA,
csuC
pgaA
bmfR/S
gigA
gacA/S
1ST2WGS[74]
2022
India
Kathajodi River42blaNDM
blaOXA-48
blaTEM
Type 1 fimbriae
Biofilm,
Hemolytic activity,
Gelatinase
23/19n. d.No[75]
2022
South Africa
Plankenbrug River70n. d.3/1ST945, ST2520.No[76]
2021
China
Xiangjiang River1blaOXA-2n. d.0n. d.No[77]
2021
South Africa
Great Fish,
Keiskamma, and
Tyhume rivers
410apHA1
apHA2
blaCTX-M
blaCTX-M1/2
blaCTX-M-9
blaVEB
blaGES
blaIMP
blaKPC
blaPER,
blaOXA-48-like
blaOXA-51
blaSHV
blaTEM
blaVIM
qnrB
qnrD
tetA
tetB
tetL
tetC
tetM
n. d.n. d.n. d.No[78]
2021
USA
Kokosing River5aadA4
cfxA6
msrE
mphE
tet (39)
n. d.5n. d.Shotgun sequencing[79]
2018
Taiwan
Puzi River11n. d.n. d.0n. d.No[80]
2019
China
Tarim River1blaOXA-69
blaADC-2
n. d.1n. d.WGS[81]
2017
Germany to Romania
Danube River135blaOXA-23
blaOXA-24
blaOXA-51
blaTEM-1
blaVIM-2
n. d.16n. d.No[82]
2016
Brazil
Tietê
Pinheiros Rivers
3blaOXA-23
blaOXA-51
n. d.3ST79/CC79No[83]
ARG = Antimicrobial-resistant gene; VG = Virulence gene; STC/CC = Sequence Type Cluster/Clonal Complex; n. d. = not determined; WGS = Whole-Genome Sequencing.
Table 6. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of P. aeruginosa in waterbodies worldwide.
Table 6. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of P. aeruginosa in waterbodies worldwide.
CountryAquatic
System
Number of IsolatesARGVGMDRST/CCGenomic
Analysis
Reference
2024
China
Qinhuai River4blaLCR-1
mphF
blaOXA-101
blaOXA-827
blaTEM-1
n. d.n. d.n. d.Metagenomic
sequencing
[59]
2024
Spain
Iregua River52n. d.exoU/S/Y/T/A lasI/R
aprA
rhlAB/I/R
exlA
0ST136
ST274
ST679
ST782 ST2540
No[84]
2024
Bangladesh
Buriganga River70n. d.n. d.3n. d.No[85]
2024
India
Mahananda River1aph (3′)-IIb
catB/B7
fosA
emrE
gyrA
mexA/B/C/D/E/F/L/G/H
oprD/M/N
opmD/E/H
blaOXA-50
pmrA
algW
exoT/Y
flhB
hfq
modA
mucA
nuoD
PA0082
pilD
phzS
purD/H
pyrF
relA
1n. d.NGS,
Comparative genomic analysis
[86]
2021
South Africa
Mthatha Dam
Mthatha River
36blaSHV
blaCTX-M
blaTEM
blaVIM
n. d.20n. d.No[87]
2016
Brazil
Tietê and
Pinheiros
Rivers
3blaSPM-1n. d.3ST277No[83]
2015
Bangladesh.
Lake and River in Dhaka City28n. d.n. d.28n. d.No[88]
2016
Brazil
Mindu stream8n. d.n. d.0n. d.No[89]
2013
Japan
Kiyotake River
Yae River
516n. d.n. d.n. d.n. d.No[90]
2011
Brazil
Tietê River1blaSPM-1
blaOXA-56
rmtD1
aacA4
aadA7
sul1
dhfr
n. d.1n. d.No[91]
ARG = Antimicrobial-resistant gene; VG = Virulence gene; STC/CC = Sequence Type Cluster/Clonal Complex; n. d. = not determined; WGS = Whole-Genome Sequencing.
Table 7. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of Enterobacter spp. in waterbodies worldwide.
Table 7. Studies describing the prevalence, ARGs, VGs, MDR, and ST/CC of Enterobacter spp. in waterbodies worldwide.
CountryAquatic
System
Number of IsolatesARGVGMDRST/CCGenomic
Analysis
Reference
2024
China
Qinhuai RiverE. cloacae (2)
E. hormaechei (1)
DHA-7
mexB
ugd
n. d.n. d.n. d.Metagenomic sequencing[59]
2023
Chile
Cachapoal River and Villarrica LakeE. cloacae (2)blaTEM
blaCTX-M
n. d2n. d.No.[92]
2021
Japan
River in OsakaE. asburiae (1),
E. spp. (1)
blaFRI-4
blaFRI-8
n. d.2n. d.WGS[93]
2020
Philippines
Metro Manila
River
E. cloacae (1)
E. hormaechei (1)
E. kobei (1)
E. tabaci (1)
E. xiangfangensis (1)
blaGES-20
blaIMI18
n. d.n. d.n. d.WGS[94]
2020
Israel
Alexander
River estuary
E. asburiae (1)
E. bugandensis (1)
blaIMI,
NmcR
fosA4
marA
ramA
n. d.2n. d.Metagenomic sequencing[95]
2020
South Africa
Tsomo and
Tyhume rivers
E. aerogenes (7)
E. amnigenus (1)
E. asburiae (2)
E. cloacae (4)
blaCTX-M
blaSHV
blaFOX,
catII
sul1
tetA
tetB
tetD
n. d.14n. d.No[96]
2019
Bolivia
Choqueyapu RiverE. cloacae (1)AAC(3)-Iic AAC(6′)-Ib-cr
aadA
APH(3′)-Ib
APH(6)-Id
blaCTX-M-3
blaOXA-1
Sul2
blaTEM-1
Tet(A)
n. d.n. d.n. d.WGS[97]
2017
Spain
Llobregat RiverE. cloacae (2)blaIMI-2
blaKPC-2 blaOXA-1
qnrB6
n. d.2ST822
ST823
No[70]
2016
Germany
Denube RiverE. cloacae (3)
E. cancerogenus (1)
E. asburiae (1)
blaSHV-2
blaSHV-12
blaTEM-3
blaCTX-M-1
n. d.5ST145
ST159 ST505
No[98]
2013
Switzerland
Landquart and Lorze riversE. cloacae (1)
E. amnigenus (1)
blaTEM
blaCTXM-15
n. d.2n. d.No[99]
2011
Canada
Salmon RiverE. cloacae (1)fosA2n. d-1n. d.No[100]
ARG = Antimicrobial-resistant gene; VG = Virulence gene; STC/CC= Sequence Type Cluster/-Clonal Complex; n. d.= not determined; WGS = Whole-Genome Sequencing.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Olaniyan, T.O.; Martínez-Vázquez, A.V.; Escobedo-Bonilla, C.M.; López-Rodríguez, C.; Huerta-Luévano, P.; Castrejón-Sánchez, O.; de la Cruz-Flores, W.L.; Cedeño-Castillo, M.J.; de Luna-Santillana, E.d.J.; Cruz-Hernández, M.A.; et al. The Prevalence of ESKAPE Pathogens and Their Drug Resistance Profiles in Aquatic Environments Around the World. Microbiol. Res. 2025, 16, 201. https://doi.org/10.3390/microbiolres16090201

AMA Style

Olaniyan TO, Martínez-Vázquez AV, Escobedo-Bonilla CM, López-Rodríguez C, Huerta-Luévano P, Castrejón-Sánchez O, de la Cruz-Flores WL, Cedeño-Castillo MJ, de Luna-Santillana EdJ, Cruz-Hernández MA, et al. The Prevalence of ESKAPE Pathogens and Their Drug Resistance Profiles in Aquatic Environments Around the World. Microbiology Research. 2025; 16(9):201. https://doi.org/10.3390/microbiolres16090201

Chicago/Turabian Style

Olaniyan, Tunde Olarinde, Ana Verónica Martínez-Vázquez, Cesar Marcial Escobedo-Bonilla, Cristina López-Rodríguez, Patricia Huerta-Luévano, Oziel Castrejón-Sánchez, Wendy Lizeth de la Cruz-Flores, Manuel J. Cedeño-Castillo, Erick de Jesús de Luna-Santillana, Maria Antonia Cruz-Hernández, and et al. 2025. "The Prevalence of ESKAPE Pathogens and Their Drug Resistance Profiles in Aquatic Environments Around the World" Microbiology Research 16, no. 9: 201. https://doi.org/10.3390/microbiolres16090201

APA Style

Olaniyan, T. O., Martínez-Vázquez, A. V., Escobedo-Bonilla, C. M., López-Rodríguez, C., Huerta-Luévano, P., Castrejón-Sánchez, O., de la Cruz-Flores, W. L., Cedeño-Castillo, M. J., de Luna-Santillana, E. d. J., Cruz-Hernández, M. A., Rivera, G., & Bocanegra-García, V. (2025). The Prevalence of ESKAPE Pathogens and Their Drug Resistance Profiles in Aquatic Environments Around the World. Microbiology Research, 16(9), 201. https://doi.org/10.3390/microbiolres16090201

Article Metrics

Back to TopTop