Antibiotics and Antibiotic Resistance in Aquatic Environments

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics Use and Antimicrobial Stewardship".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 35552

Special Issue Editors


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Guest Editor
Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy
Interests: antibiotics as environmental pollutant; antibiotic resistance in wild biota; antibiotic bioaccumulation in plants; ecotoxicology; analysis of microbial communities in the wild

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Guest Editor
Department of Biology, University of “Tor Vergata”, Rome, Italy
Interests: antibiotic resistance mechanisms; genetic bases for the diffusion of antibiotic resistance genes; microbial bioinformatics; new antimicrobial drugs; bacteriophages; bacteriophages as tools for phage therapy
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Special Issue Information

Dear Colleagues,

Water is the most important element at the basis of life of all organisms; Both fresh- and sea-water constitute invaluable resources, providing fundamental services ranging from food production to recreational activities. Although at different rates and for diverse threats, waters are continuously subjected to a number of pollutants, including antibiotics.

Antibiotics as a pollutant of aquatic environments may play multiple roles: They may elicit toxic effects due to their intrinsic affinity for biological matrices, or they may change the structure and composition of natural microbial communities, by killing the most sensitive members of the communities, or they may also positively select opportunistic and pathogenic resistant bacteria, with the well-known effects on human and animal populations, including the effects on animal husbandry.

The aim of this Special Issue is to collect original research investigating the presence and effects of antibiotics and antibiotic-resistant bacteria (ARB) in water systems. We expect that this Special Issue will collect contributions investigating the presence of antibiotics and ARB in all kinds of waters (from fresh to drinkable water, from brackish to seawaters, etc.), their effects on natural and/or anthropic systems, but also new methods and procedures to identify antibiotics and ARB in waters.

Dr. Luciana Migliore
Dr. Marco Maria D'Andrea
Guest Editors

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Keywords

  • antibiotic resistance in freshwater
  • antibiotic resistance in seawater
  • incidence of antibiotic resistance
  • prevalence of antibiotic resistance
  • antibiotic resistance determinants

Published Papers (11 papers)

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Research

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16 pages, 1526 KiB  
Article
Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa
by Hlengiwe N. Mtetwa, Isaac D. Amoah, Sheena Kumari, Faizal Bux and Poovendhree Reddy
Antibiotics 2021, 10(11), 1362; https://doi.org/10.3390/antibiotics10111362 - 8 Nov 2021
Cited by 12 | Viewed by 4029
Abstract
Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to [...] Read more.
Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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15 pages, 1430 KiB  
Article
Human-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 80 Isolated from Cattle and Aquatic Environments
by Khuliso Ramaite, Mutshiene Deogratias Ekwanzala, John Barr Dewar and Maggy Ndombo Benteke Momba
Antibiotics 2021, 10(9), 1038; https://doi.org/10.3390/antibiotics10091038 - 25 Aug 2021
Cited by 4 | Viewed by 2108
Abstract
Background: Human-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) has mainly been reported in South African pig and chicken farms. The prevalence of antibiotic-resistant genes (ARGs), virulence factors (VFs), and multilocus sequence types (MLSTs) associated with HA-MRSA in cattle farms has not been reported. Consequently, this [...] Read more.
Background: Human-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) has mainly been reported in South African pig and chicken farms. The prevalence of antibiotic-resistant genes (ARGs), virulence factors (VFs), and multilocus sequence types (MLSTs) associated with HA-MRSA in cattle farms has not been reported. Consequently, this study characterised LA-MRSA and its spread from cattle farms into the environment. Method: Husbandry soil (HS), nearby river water (NRW), animal manure (AM) and animal drinking water (ADW) were collected on and around a cattle farm. Presumptive MRSA isolates were identified from these samples using CHROMagar media and genotyped as MRSA sequence types (STs), selected ARGs, and VFs, using polymerase chain reaction. An MLST-based dendrogram was generated to link the farm MRSA strains with those in a nearby river. Results: The prevalence of MRSA was 30.61% for HS, 28.57% for ADW, 22.44% for NRW, and 10.20% for AM. Isolates from HS harboured the highest number of resistant genes, with 100% for mecA, 91.66% for ermA, and 58.33% for blaZ. However, no ermC or tetM genes were detected. MRSA isolates from AM harboured the lowest number of resistant genes. Only sec and seq enterotoxins were found in all the assessed MRSA isolates. MRSA from the farm revealed six STs (ST80, ST728, ST1931, ST2030, ST3247, and ST5440); all of STs belonged to clonal complex 80 (CC80). An MLST-based dendrogram based on the concatenated sequences of MLST genes under the maximum likelihood criterion revealed four clades of amalgamated MRSA isolates from various livestock environmental matrices, including the NRW. Conclusion: The results suggest that livestock environmental matrices might be reservoirs of MRSA that could subsequently disseminate through runoff to pollute water resources. Therefore, continued surveillance of HA-MRSA in livestock environments is warranted. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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11 pages, 1281 KiB  
Article
Evidence of Another Anthropic Impact on Iguana delicatissima from the Lesser Antilles: The Presence of Antibiotic Resistant Enterobacteria
by Gustavo Di Lallo, Marco Maria D’Andrea, Samanta Sennati, Maria Cristina Thaller, Luciana Migliore and Gabriele Gentile
Antibiotics 2021, 10(8), 885; https://doi.org/10.3390/antibiotics10080885 - 21 Jul 2021
Cited by 3 | Viewed by 2900
Abstract
The improper use of antibiotics by humans may promote the dissemination of resistance in wildlife. The persistence and spread of acquired antibiotic resistance and human-associated bacteria in the environment, while representing a threat to wildlife, can also be exploited as a tool to [...] Read more.
The improper use of antibiotics by humans may promote the dissemination of resistance in wildlife. The persistence and spread of acquired antibiotic resistance and human-associated bacteria in the environment, while representing a threat to wildlife, can also be exploited as a tool to monitor the extent of human impact, particularly on endangered animal species. Hence, we investigated both the associated enterobacterial species and the presence of acquired resistance traits in the cloacal microbiota of the critically endangered lesser Antillean iguana (Iguana delicatissima), by comparing two separate populations living in similar climatic conditions but exposed to different anthropic pressures. A combination of techniques, including direct plating, DNA sequencing and antimicrobial susceptibility testing allowed us to characterize the dominant enterobacterial populations, the antibiotic resistant strains and their profiles. A higher frequency of Escherichia coli was found in the samples from the more anthropized site, where multi-drug resistant strains were also isolated. These results confirm how human-associated bacteria as well as their antibiotic-resistance determinants may be transferred to wildlife, which, in turn, may act as a reservoir of antibiotic resistance. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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13 pages, 1202 KiB  
Article
Prevalence, Genetic Diversity, Antimicrobial Resistance, and Toxigenic Profile of Vibrio vulnificus Isolated from Aquatic Environments in Taiwan
by I-Ching Lin, Bashir Hussain, Bing-Mu Hsu, Jung-Sheng Chen, Yu-Ling Hsu, Yi-Chou Chiu, Shih-Wei Huang and Jiun-Ling Wang
Antibiotics 2021, 10(5), 505; https://doi.org/10.3390/antibiotics10050505 - 29 Apr 2021
Cited by 7 | Viewed by 2728
Abstract
Vibrio vulnificus is a gram-negative, opportunistic human pathogen associated with life-threatening wound infections and is commonly found in warm coastal marine water environments, globally. In this study, two fishing harbors and three tributaries of the river basin were analyzed for the prevalence of [...] Read more.
Vibrio vulnificus is a gram-negative, opportunistic human pathogen associated with life-threatening wound infections and is commonly found in warm coastal marine water environments, globally. In this study, two fishing harbors and three tributaries of the river basin were analyzed for the prevalence of V. vulnificus in the water bodies and shellfish that are under the pressure of external pollutions. The average detection rate of V. vulnificus in the river basins and fishing harbors was 8.3% and 4.2%, respectively, in all seasons. A total of nine strains of V. vulnificus were isolated in pure cultures from 160 samples belonging to river basins and fishing harbors to analyze the antibiotic susceptibility, virulence gene profiles, and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) fingerprinting. All isolates were susceptible to 10 tested antibiotics. The genotypic characterization revealed that 11.1% (n = 1/9) strain was nonvirulent, whereas 88.9% (n = 8/9) isolates were virulent strains, which possessed the four most prevalent toxin genes such as vcgC (88.9%), 16S B (88.9%), vvhA (88.9%), and manIIA (88.9%), followed by nanA (77.8%), CPS1 (66.7), and PRXII (44.4%). Additionally, ERIC-PCR fingerprinting grouped these nine isolates into two main clusters, among which the river basin isolates showed genetically diverse profiles, suggesting multiple sources of V. vulnificus. Ultimately, this study highlighted the virulent strains of V. vulnificus in the coastal aquatic environments of Taiwan, harboring a potential risk of infection to human health through water-borne transmission. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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15 pages, 1423 KiB  
Article
Wastewaters, with or without Hospital Contribution, Harbour MDR, Carbapenemase-Producing, but Not Hypervirulent Klebsiella pneumoniae
by Adela Teban-Man, Anca Farkas, Andreea Baricz, Adriana Hegedus, Edina Szekeres, Marcel Pârvu and Cristian Coman
Antibiotics 2021, 10(4), 361; https://doi.org/10.3390/antibiotics10040361 - 29 Mar 2021
Cited by 12 | Viewed by 2884
Abstract
Carbapenemase-producing Klebsiella pneumoniae (CPKP) isolated from influent (I) and effluent (E) of two wastewater treatment plants, with (S1) or without (S2) hospital contribution, were investigated. The strains belonged to the Kp1 phylogroup, their highest frequency being observed in S1, followed by S2. The [...] Read more.
Carbapenemase-producing Klebsiella pneumoniae (CPKP) isolated from influent (I) and effluent (E) of two wastewater treatment plants, with (S1) or without (S2) hospital contribution, were investigated. The strains belonged to the Kp1 phylogroup, their highest frequency being observed in S1, followed by S2. The phenotypic and genotypic hypervirulence tests were negative for all the strains tested. At least one carbapenemase gene (CRG), belonging to the blaKPC, blaOXA-48, blaNDM and blaVIM families, was observed in 63% of CPKP, and more than half co-harboured two to four CRGs, in different combinations. Only five CRG variants were observed, regardless of wastewater type: blaKPC-2, blaNDM-1, blaNDM-6, blaVIM-2, and blaOXA-48. Sequence types ST258, ST101 and ST744 were common for both S1 and S2, while ST147, ST525 and ST2502 were found only in S1 and ST418 only in S2. The strains tested were multi-drug resistant (MDR), all being resistant to beta-lactams, cephalosporins, carbapenems, monobactams and fluoroquinolones, followed by various resistance profiles to aminoglycosides, trimethoprim-sulphamethoxazole, tigecycline, chloramphenicol and tetracycline. After principal component analysis, the isolates in S1 and S2 groups did not cluster independently, confirming that the antibiotic susceptibility patterns and gene-type profiles were both similar in the K. pneumoniae investigated, regardless of hospital contribution to the wastewater type. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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19 pages, 1590 KiB  
Article
Characterization of Environmental and Cultivable Antibiotic-Resistant Microbial Communities Associated with Wastewater Treatment
by Alicia Sorgen, James Johnson, Kevin Lambirth, Sandra M. Clinton, Molly Redmond, Anthony Fodor and Cynthia Gibas
Antibiotics 2021, 10(4), 352; https://doi.org/10.3390/antibiotics10040352 - 26 Mar 2021
Cited by 6 | Viewed by 2747
Abstract
Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used [...] Read more.
Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify phenotypically resistant cultivable portions of these bacterial communities and characterized the composition of the culturable subset of these populations. Resistant taxa were more abundant in raw sewage and wastewater before the biological aeration treatment stage. While some antibiotic-resistant bacteria (ARB) were detectable downstream of treated wastewater release, these organisms are not enriched relative to effluent-free upstream water, indicating efficient removal during treatment. Combined culture-dependent and -independent analyses revealed a stark difference in community composition between culturable fractions and the environmental source material, irrespective of culturing conditions. Higher proportions of the environmental populations were recovered than predicted by the widely accepted 1% culturability paradigm. These results represent baseline abundance and compositional data for ARB communities for reference in future studies addressing the dissemination of antibiotic resistance associated with urban wastewater treatment ecosystems. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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12 pages, 1163 KiB  
Article
Occurrence and Antimicrobial Resistance of Arcobacter spp. Recovered from Aquatic Environments
by Sonia Sciortino, Pietro Arculeo, Vincenzina Alio, Cinzia Cardamone, Luisa Nicastro, Marco Arculeo, Rosa Alduina and Antonella Costa
Antibiotics 2021, 10(3), 288; https://doi.org/10.3390/antibiotics10030288 - 10 Mar 2021
Cited by 26 | Viewed by 3135
Abstract
Arcobacter spp. are emerging waterborne and foodborne zoonotic pathogens responsible for gastroenteritis in humans. In this work, we evaluated the occurrence and the antimicrobial resistance profile of Arcobacter isolates recovered from different aquatic sources. Besides, we searched for Arcobacter spp. in seaweeds and [...] Read more.
Arcobacter spp. are emerging waterborne and foodborne zoonotic pathogens responsible for gastroenteritis in humans. In this work, we evaluated the occurrence and the antimicrobial resistance profile of Arcobacter isolates recovered from different aquatic sources. Besides, we searched for Arcobacter spp. in seaweeds and the corresponding seawater samples. Bacteriological and molecular methods applied to 100 samples led to the isolation of 28 Arcobacter isolates from 27 samples. The highest prevalence was detected in rivers followed by artificial ponds, streams, well waters, and spring waters. Seaweeds contained a higher percentage of Arcobacter than the corresponding seawater samples. The isolates were identified as Arcobacter butzleri (96.4%) and Arcobacter cryaerophilus (3.6%). All the isolates showed a multi-drug resistance profile, being resistant to at least three different classes of antibiotics. Molecular analysis of genetic determinants responsible for tetracycline resistance in nine randomly chosen isolates revealed the presence of tetO and/or tetW. This work confirms the occurrence and the continuous emergence of antibiotic-resistant Arcobacter strains in environmental samples; also, the presence of quinolone-resistant Arcobacter spp. in aquatic sources used for water supply and irrigation represents a potential risk for human health. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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13 pages, 4652 KiB  
Article
Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis
by Keunje Yoo and Gihan Lee
Antibiotics 2021, 10(2), 188; https://doi.org/10.3390/antibiotics10020188 - 15 Feb 2021
Cited by 13 | Viewed by 2755
Abstract
Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is [...] Read more.
Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide–lincosamide–streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5–2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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17 pages, 279 KiB  
Article
Occurrence of Antibiotic-Resistant Bacteria and Genes in Two Drinking Water Treatment and Distribution Systems in the North-West Province of South Africa
by Collins Njie Ateba, Naledi Mahalia Tabi, Justine Fri, Marie Ebob Agbortabot Bissong and Cornelius Carlos Bezuidenhout
Antibiotics 2020, 9(11), 745; https://doi.org/10.3390/antibiotics9110745 - 28 Oct 2020
Cited by 21 | Viewed by 2872
Abstract
With the increasing spread of antimicrobial resistance, there is growing attention to the contribution made by drinking water systems. The potential health impact of two drinking water treatment and distribution systems (A and B) in the North-West Province of South Africa was determined [...] Read more.
With the increasing spread of antimicrobial resistance, there is growing attention to the contribution made by drinking water systems. The potential health impact of two drinking water treatment and distribution systems (A and B) in the North-West Province of South Africa was determined by investigating the water quality and occurrence of antimicrobial-resistant heterotrophic bacteria and genes in the raw and treated water over four seasons. Most of the physicochemical parameters except for electrical conductivity were within permissible limits. Coliform bacteria reduced from raw to potable water except for counts higher than the threshold recorded in Summer and Winter. A total of 203 heterotrophic bacterial isolates were recovered on chromogenic R2A medium and subjected to susceptibility testing to twelve antibiotics. Most of the isolates were resistant to β-lactam antibiotics and Trimethoprim, whereas they were susceptible to Ciprofloxacin, Erythromycin, and Neomycin. The proportions of Cephalothin and Kanamycin-resistant isolates were significantly higher (p < 0.05) after treatment for site A, compared to significantly lower β-lactam, Oxytetracycline, and Trimethoprim-resistant isolates for B. Over 50% of isolates were of high risk, indicating their origin from high antibiotic-use sources. Seventy-one (35%) isolates were multidrug-resistant, out of which the majority (53.5%, n = 38) possessed the strA gene, followed by strB 21 (29.6%), dfrB 13 (18.3%), aadA 11 (15.5%), blaCTX-M 5 (7.0%), and tetA 3 (4.2%). The 16S rRNA gene sequences of the isolates revealed strains belonging to eight bacterial families, some of which are clinically important. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)

Review

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13 pages, 989 KiB  
Review
Antibiotics, Multidrug-Resistant Bacteria, and Antibiotic Resistance Genes: Indicators of Contamination in Mangroves?
by Oskar A. Palacios, Jaime Raúl Adame-Gallegos, Blanca Estela Rivera-Chavira and Guadalupe Virginia Nevarez-Moorillon
Antibiotics 2021, 10(9), 1103; https://doi.org/10.3390/antibiotics10091103 - 13 Sep 2021
Cited by 7 | Viewed by 3436
Abstract
Multidrug-resistant bacteria and antibiotic resistance genes can be monitored as indicators of contamination in several environments. Mangroves are among the most productive ecosystems, and although they can be resilient to the action of climate phenomena, their equilibrium can be affected by anthropogenic activities. [...] Read more.
Multidrug-resistant bacteria and antibiotic resistance genes can be monitored as indicators of contamination in several environments. Mangroves are among the most productive ecosystems, and although they can be resilient to the action of climate phenomena, their equilibrium can be affected by anthropogenic activities. Regarding the presence and persistence of multidrug-resistant bacteria in mangroves, it is common to think that this ecosystem can function as a reservoir, which can disperse the antibiotic resistance capacity to human pathogens, or serve as a filter to eliminate drug-resistant genes. The possible impact of anthropogenic activities carried out near mangroves is reviewed, including wastewater treatment, food production systems, leisure, and tourism. Adverse effects of antibiotic resistance genes or multidrug-resistant bacteria, considered as emerging contaminants, have not been reported yet in mangroves. On the contrary, mangrove ecosystems can be a natural way to eliminate antibiotics, antibiotic-resistant bacteria, and even antibiotic-resistant genes from the environment. Although mangroves’ role in decreasing antibiotics and antibiotic resistance genes from the environment is being proposed, the mechanisms by which these plants reduce these emerging contaminants have not been elucidated and need further studies. Additionally, further evaluation is needed on the effects of antibiotics and antibiotic-resistant bacteria in mangroves to generate an analysis of the human contribution to the degradation of this specific ecosystem as well as to define if these contaminants can be used as indicators of contamination in mangrove ecosystems. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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18 pages, 542 KiB  
Review
Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures
by Teresa Nogueira and Ana Botelho
Antibiotics 2021, 10(7), 787; https://doi.org/10.3390/antibiotics10070787 - 28 Jun 2021
Cited by 8 | Viewed by 4466
Abstract
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of [...] Read more.
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union’s 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance in Aquatic Environments)
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