Search Results (932)

Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems. Full article

The perianal skin is a unique “skin–gut” boundary that serves as a critical hotspot for the exchange and evolution of antibiotic resistance genes (ARGs). However, its role in the dissemination of antimicrobial resistance (AMR) has often been underestimated. To characterize the resistance patterns in the perianal skin environment of patients with perianal diseases and to investigate the drivers of AMR in this niche, a total of 51 bacterial isolates were selected from a historical strain bank containing isolates originally collected from patients with perianal diseases. All the isolates originated from the skin site and were subjected to antimicrobial susceptibility testing, whole-genome sequencing, and co-occurrence network analysis. The analysis revealed a highly structured resistance pattern, dominated by two distinct modules: one representing a classic Staphylococcal resistance platform centered around mecA and the bla operon, and a broad-spectrum multidrug resistance module in Gram-negative bacteria centered around tet(A) and predominantly carried by IncFIB and other IncF family plasmids. Further analysis pinpointed IncFIB-type plasmids as potent vehicles driving the efficient dissemination of the latter resistance module. Moreover, numerous unexplained resistance phenotypes were observed in a subset of isolates, indicating the potential presence of emerging and uncharacterized AMR threats. These findings establish the perianal skin as a complex reservoir of multidrug resistance genes and a hub for mobile genetic element exchange, highlighting the necessity of enhanced surveillance and targeted interventions in this clinically important ecological niche. Full article

Ceftazidime–avibactam (CAZ-AVI) is a second-generation intravenous β-lactam/β-lactamase inhibitor combination. In recent years, substantial evidence has emerged regarding the efficacy and safety of CAZ-AVI. However, data on its use in critically ill patients remain limited. Background/Objectives: This multicenter, retrospective, observational cohort study was conducted across four Intensive Care Units (ICUs) in three hospitals in the Marche region of Italy. The primary objective was to evaluate the 30-day clinical outcomes and identify risk factors associated with 30-day clinical failure—defined as death, microbiological recurrence, or persistence within 30 days after discontinuation of therapy—in critically ill patients treated with CAZ-AVI. Methods: The study included all adult critically ill patients admitted to the participating ICUs between January 2020 and September 2023 who received CAZ-AVI for at least 72 h for the treatment of a confirmed or suspected Gram-negative bacterial (GNB) infection. Results: Among the 161 patients included in the study, CAZ-AVI treatment resulted in a positive clinical outcome (i.e., clinical improvement and 30-day survival) in 58% of cases (n = 93/161), while the overall mortality rate was 24% (n = 38/161). Relapse or persistent infection occurred in a substantial proportion of patients (25%, n = 41/161). Notably, acquired resistance to CAZ-AVI was observed in 26% of these cases, likely due to suboptimal use of the drug in relation to its pharmacokinetic/pharmacodynamic (PK/PD) properties in critically ill patients. Furthermore, treatment failure was more frequent among immunosuppressed individuals, particularly liver transplant recipients. Conclusions: This study demonstrates that the mortality rate among ICU patients treated with this novel antimicrobial combination is consistent with findings from other studies involving heterogeneous populations. However, the rapid emergence of resistance underscores the need for vigilant surveillance and the implementation of robust antimicrobial stewardship strategies. Full article

Background: The COVID-19 pandemic has profoundly altered the clinical and microbiological landscape of respiratory tract infections (RTIs), potentially reshaping pathogen distribution and antimicrobial resistance (AMR) profiles across care settings. Objectives: The objective of this study was to assess temporal trends in respiratory bacterial pathogens, antimicrobial resistance, and polymicrobial infections across three pandemic phases—pre-COVID (2018–2019), COVID (2020–2022), and post-COVID (2022–2024)—in hospitalized and ambulatory patients. Methods: We retrospectively analyzed 1827 respiratory bacterial isolates (hospitalized patients, n = 1032; ambulatory patients, n = 795) collected at a tertiary care center in Northern Italy. Data were stratified by care setting, anatomical site, and pandemic phase. Species identification and susceptibility testing followed EUCAST guidelines. Statistical analysis included chi-square and Fisher’s exact tests. Results: In hospitalized patients, a significant increase in Pseudomonas aeruginosa (from 45.5% pre-COVID to 58.6% post-COVID, p < 0.0001) and Acinetobacter baumannii (from 1.2% to 11.1% during COVID, p < 0.0001) was observed, with 100% extensively drug-resistant (XDR) rates for A. baumannii during the pandemic. Conversely, Staphylococcus aureus significantly declined from 23.6% pre-COVID to 13.7% post-COVID (p = 0.0012). In ambulatory patients, polymicrobial infections peaked at 41.2% during COVID, frequently involving co-isolation of Candida spp. Notably, resistance to benzylpenicillin in Streptococcus pneumoniae reached 80% (4/5 isolates) in hospitalized patients during COVID, and carbapenem-resistant P. aeruginosa (CRPA) significantly increased post-pandemic in ambulatory patients (0% pre-COVID vs. 23.5% post-COVID, p = 0.0014). Conclusions: The pandemic markedly shifted respiratory pathogen dynamics and resistance profiles, with distinct trends observed in hospital and community settings. Persistent resistance phenotypes and frequent polymicrobial infections, particularly involving Candida spp. in outpatients, underscore the need for targeted surveillance and antimicrobial stewardship strategies. Full article

Measuring antimicrobial use (AMU) in animal production can provide useful data for monitoring AMU over time, which will promote antimicrobial resistance (AMR) reduction. This study involved the daily collation and validation of active primary drug sales and prescription data from veterinary outlets and clinics of the Kaduna metropolis. In total, 83.7% of the identified antimicrobials were in the form of oral medication, and most were registered antibiotics (52.8%). Parenteral and topical forms were also identified, with 94% also being antibiotics. The estimated AMU was 282 mg/kg population correction unit (PCU). Poultry represented the most significant population, constituting 99% (31,502,004) of the study population. The class-specific AMU was antibiotics, with 274 mg/kg PCU. The antiprotozoal AMU was 418 mg/kg PCU. The anthelminthic AMU was the highest at 576 mg/kg PCU. This study has provided useful and practical information on the trends in antimicrobial use in animals, with poultry being the most important animal population involved in AMU and oxytetracycline being the most abused antibiotic in animal production. Antimicrobial stewardship (AMS) should be targeted at poultry populations, with an emphasis on reducing antibiotic use/consumption. Full article

Background/Objectives: Enterococci, particularly Enterococcus faecalis and Enterococcus faecium, are Gram-positive cocci that can cause severe infections in hospitalized patients. The rise of vancomycin-resistant enterococci (VRE) and vancomycin-variable enterococci (VVE) poses significant challenges in healthcare settings due to their resistance to multiple antibiotics. Methods: We conducted a point prevalence survey (PPS) to assess the prevalence of VRE and VVE colonization in hospitalized patients. Rectal swabs were collected from 160 patients and analyzed using molecular assays (MAs) and culture. Whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST) were performed to identify the genetic diversity. Results: Of the 160 rectal swabs collected, 54 (33.7%) tested positive for the vanA and/or vanB genes. Culture-based methods identified 47 positive samples (29.3%); of these, 44 isolates were identified as E. faecium and 3 as E. faecalis. Based on the resistance profiles, 35 isolates (74.5%) were classified as VRE, while 12 (25.5%) were classified as VVE. WGS and cgMLST analyses identified seven clusters of E. faecium, with sequence type (ST) 80 being the most prevalent. Various resistance genes and virulence factors were identified, and this study also highlighted intra- and inter-ward transmission of VRE strains. Conclusions: Our findings underscore the potential for virulence and resistance of both the VRE and VVE strains, and they highlight the importance of effective infection control measures to prevent their spread. VVE in particular should be carefully monitored as they often escape detection. Integrating molecular data with clinical information will hopefully enhance our ability to predict and prevent future VRE infections. Full article

Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China’s nationally protected captive giant and red pandas. This study isolated Proteus mirabilis from panda feces to assess AMR and virulence traits, and used whole-genome sequencing (WGS) to evaluate the spread of resistance genes (ARGs) and virulence genes (VAGs). In this study, 37 isolates were obtained, 20 from red pandas and 17 from giant pandas. Multidrug-resistant (MDR) strains were present in both hosts. Giant panda isolates showed the highest resistance to ampicillin and cefazolin (58.8%), while red panda isolates were most resistant to trimethoprim/sulfamethoxazole (65%) and imipenem (55%). Giant panda-derived strains also exhibited stronger biofilm formation and swarming motility. WGS identified 31 ARGs and 73 VAGs, many linked to mobile genetic elements (MGEs) such as plasmids, integrons, and ICEs. In addition, we found frequent co-localization of drug resistance genes/VAGs with MGEs, indicating a high possibility of horizontal gene transfer (HGT). This study provides crucial insights into AMR and virulence risks in P. mirabilis from captive pandas, supporting targeted surveillance and control strategies. Full article

Background/Objectives: Helicobacter pylori (H. pylori) is a common gastric pathogen linked to gastritis, gastroduodenal ulcers, and gastric cancer. Rising antimicrobial resistance (AMR) poses challenges for effective treatment and has prompted the WHO to classify H. pylori as a high-priority pathogen. This study aimed to detect the prevalence of AMR genes in H. pylori-positive gastric samples from patients in Algarve, Portugal, where regional data is scarce. Methods: Eighteen H. pylori-positive gastric biopsy samples from patients undergoing upper gastrointestinal endoscopy were analyzed. PCR and sequencing were used to identify genes associated with resistance to amoxicillin (Pbp1A), metronidazole (rdxA, frxA), tetracycline (16S rRNA mutation) and clarithromycin (23S rRNA). Sequence identity and homologies were verified using tBLASTx and the Comprehensive Antibiotic Resistance Database (CARD). Results: Out of the 18 H. pylori-positive samples, 16 (88.9%) contained at least one AMR gene. The most frequent genes were rdxA (83.3%) and frxA (66.7%) for metronidazole resistance, and the 16S rRNA mutation (66.7%) for tetracycline. Resistance to amoxicillin and clarithromycin was detected in 27.8% and 16.7% of cases, respectively. Most samples (72.2%) had multiple resistance genes. A significantly strong association was found between female sex and the presence of the rdxA gene (p = 0.043). Conclusions: The study reveals a high prevalence of H. pylori resistance genes in Algarve, particularly against metronidazole and tetracycline. These findings highlight the need for local surveillance and tailored treatment strategies. Further research with larger populations is warranted to assess regional resistance patterns and improve eradication efforts. Full article

Contaminated poultry is one of the major sources of food-borne non-typhoidal Salmonella (NTS). The aim of this study was to evaluate the presence of Salmonella along the slaughter process in low- and high-throughput poultry abattoirs in South Africa and to determine their characteristics. Samples were collected from 500 chicken carcass rinsates at various processing stages in three abattoirs. Salmonella detection and identification was conducted in accordance with the ISO 6579 methodology. NTS serotyping was performed with serotype-specific PCRs. The Kirby–Bauer disk diffusion method was used to determine antimicrobial resistance in Salmonella. PCR was used to analyze thirteen antimicrobial genes and four virulence genes. Salmonella spp. was detected in 11.8% (59/500; CI: 9.5–15) of the samples tested. The predominant serovars were Salmonella Enteritidis (n = 21/59; 35.59%) and Salmonella Typhimurium (n = 35; 59.32%). Almost all Salmonella isolates were susceptible to all tested antimicrobials except three. Despite the low resistance to tetracyclines at the phenotypic level, approximately half of the strains carried tetA genes, which may be due to “silent” antimicrobial resistance genes. Diverse virulence genes were detected among the confirmed NTS serotypes. We found a predominance of S. Enteritidis and S. Typhimurium from chicken carcasses with diverse virulence and resistance genes. As we detected differences between the slaughterhouses, an in-depth study should be performed on the risk of Salmonella in low- and high-throughput abattoirs. The integrated monitoring and surveillance of NTS in poultry is warranted in South Africa to aid in the design of mitigation strategies. Full article

The illegal sale of mussels is a persistent problem for food safety and public health in the Campania region, where bivalve molluscs are often sold without traceability, evading regulatory controls. In this study, ten batches of mussels seized from unauthorized vendors were analyzed to evaluate their microbiological safety and trace their geographical origin. High loads of Escherichia coli, exceeding European regulatory limits (Regulation (EC) No 2073/2005), were detected in all samples. In addition, Salmonella Infantis strains resistant to trimethoprim-sulfamethoxazole and azithromycin were isolated, raising further concerns about antimicrobial resistance. Of the 93 Vibrio isolates, identified as V. alginolyticus and V. parahaemolyticus, 37.63% showed multidrug resistance. Approximately 68.57% of the isolates were resistant to tetracyclines and cephalosporins. The presence of resistance to last-resort antibiotics such as carbapenems (11.43%) is particularly alarming. Near-infrared spectroscopy, combined with chemometric models, was used to obtain traceability information, attributing a presumed origin to the seized mussel samples. Of the ten samples, seven were attributed to the Phlegraean area. These findings have provided valuable insights, reinforcing the need for continuous and rigorous surveillance and the integration of innovative tools to ensure seafood safety and support One Health approaches. Full article

Background: The spread of ESBL-producing Enterobacteriaceae (ESBL-PE) strains in food poses a potential risk to human health. The aim of the study was to determine the occurrence of ESBL-PE and to investigate their distribution on foods. Methods: A total of 1000 food samples, including both raw and ready-to-eat products, was analyzed for the presence of ESBL-producing Enterobacteriaceae using chromogenic selective agar. Antibiotic resistance in the isolated strains was assessed using conventional methods, while whole-genome sequencing was employed to predict antimicrobial resistance and virulence genes. Results: The overall occurrence of ESBL-PE strains was 2.8%, with the highest contamination in raw meat samples (10%). A total of 31 multidrug-resistant (MDR) strains was isolated, mainly Escherichia coli, followed by Klebsiella pneumoniae, Salmonella enterica, and Enterobacter hormaechei. All strains exhibited high levels of resistance to at least four different β-lactam antibiotics, as well as to other antimicrobial classes including sulfonamides, tetracyclines, aminoglycosides, and quinolones. Whole-genome sequencing identified 63 antimicrobial resistance genes, with bla_CTX-M being the most prevalent ESBL gene. Twenty-eight (90%) isolates carried Inc plasmids, known vectors of multiple antimicrobial resistance genes, including those associated with ESBLs. Furthermore, several virulence genes were identified. Conclusions: The contamination of food with ESBL-PE represents a potential public health risk, underscoring the importance of the implementation of genomic surveillance to monitor and control the spread of antimicrobial resistance. Full article

Antimicrobial resistance (AMR) has emerged as a planetary health emergency, driven not only by the clinical misuse of antibiotics but also by diverse environmental dissemination pathways. This review critically examines the role of environmental compartments—water, soil, and air—as dynamic reservoirs and transmission routes for antibiotic-resistant bacteria (ARB) and resistance genes (ARGs). Recent metagenomic, epidemiological, and mechanistic evidence demonstrates that anthropogenic pressures—including pharmaceutical effluents, agricultural runoff, untreated sewage, and airborne emissions—amplify resistance evolution and interspecies gene transfer via horizontal gene transfer mechanisms, biofilms, and mobile genetic elements. Importantly, it is not only highly polluted rivers such as the Ganges that contribute to the spread of AMR; even low concentrations of antibiotics and their metabolites, formed during or after treatment, can significantly promote the selection and dissemination of resistance. Environmental hotspots such as European agricultural soils and airborne particulate zones near wastewater treatment plants further illustrate the complexity and global scope of pollution-driven AMR. The synergistic roles of co-selective agents, including heavy metals, disinfectants, and microplastics, are highlighted for their impact in exacerbating resistance gene propagation across ecological and geographical boundaries. The efficacy and limitations of current mitigation strategies, including advanced wastewater treatments, thermophilic composting, biosensor-based surveillance, and emerging regulatory frameworks, are evaluated. By integrating a One Health perspective, this review underscores the imperative of including environmental considerations in global AMR containment policies and proposes a multidisciplinary roadmap to mitigate resistance spread across interconnected human, animal, and environmental domains. Full article

Purpose: The adenoid microbiota plays a key role in adenoid hypertrophy (AH). This study explored the molecular epidemiology and antimicrobial resistance of Haemophilus. Influenzae (H. influenzae) strains in pediatric AH patients. Methods: Retrospective analysis of pediatric AH patients undergoing endoscopic adenoidectomy. Adenoid tissue samples were cultured to screen for pathogens. H. influenzae strains were identified by 16S rRNA sequencing and serotyped via q-PCR. Multilocus sequence typing (MLST) and ftsI gene analysis were conducted using PubMLST. β-lactamase genes (bla_TEM-1, bla_ROB-1) were detected by PCR, and antibiotic susceptibility testing (AST) was performed using the Etest method. For imipenem-resistant strains, the acrRAB efflux pump gene cluster and ompP2 porin gene were sequenced and compared with those of the wild-type strain Rd KW20. Results: Over 8 months, 56 non-duplicate H. influenzae strains were isolated from 386 patients. The detection rate was highest in children under 5 years (30.5%) compared to those aged 5–10 years (13.4%) and 10–15 years (8.7%). Of 49 sub-cultured strains, all were non-typeable H. influenzae (NTHi). MLST identified 22 sequence types (STs) and 13 clonal complexes (CCs), with CC11 (26.5%), CC3 (14.3%), and CC107 (14.3%) being predominant. Common STs included ST103 (22.4%), ST57 (10.2%), and ST107 (10.2%). Most strains belonged to the ftsI group III-like+ (57.1%). β-lactamase positivity was 98.0% (48/49), with bla_TEM-1 (95.9%) and bla_ROB-1 (18.4%) detected. AST showed low susceptibility to ampicillin (10.2%), amoxicillin–clavulanate (34.7%), azithromycin (12.2%), and trimethoprim–sulfamethoxazole (14.3%). Among the β-lactamase-positive strains, 44/48 were β-lactamase-positive ampicillin-resistant (BLPAR); none were β-lactamase-negative ampicillin-resistant (BLNAR). Imipenem susceptibility was 91.8% (45/49). No carbapenemases were found in the imipenem-resistant strains, but mutations in acrRAB (88.12–94.94% identity) and ompP2 (77.10–82.94% identity) were observed. Conclusions: BLPAR NTHi strains of CC11 are major epidemic strains in pediatric AH. Imipenem resistance in H. influenzae likely results from porin mutations rather than carbapenemase activity. Enhanced surveillance of H. influenzae’s role in AH and its resistance patterns is warranted. Full article

Global antibiotic use saturates ecosystems with selective pressure, driving mobile genetic element (MGE)-mediated antibiotic resistance gene (ARG) dissemination that destabilizes ecological integrity and breaches public health defenses. This review synthesizes the sources, environmental distribution, and ecological risks of antibiotics and ARGs, emphasizing the mechanisms of horizontal gene transfer (HGT) driven by MGEs such as plasmids, transposons, and integrons. We further conduct a comparative critical analysis of the effectiveness and limitations of antibiotics and ARGs remediation strategies for adsorption (biochar, activated carbon, carbon nanotubes), chemical degradation (advanced oxidation processes, Fenton-based systems), and biological treatment (microbial degradation, constructed wetlands). To effectively curb the spread of antimicrobial resistance and safeguard the sustainability of ecosystems, we propose an integrated “One Health” framework encompassing enhanced global surveillance (antibiotic residues and ARGs dissemination) as well as public education. Full article

Background/Objectives: Campylobacteriosis in human populations is an ongoing issue in both developed and developing countries. Poultry production is recognized as a reservoir for antimicrobial resistance and main source of human Campylobacter infection. Methods: In this study, sixty-five Campylobacter isolates were cultured from fecal samples collected from 17 flocks of broiler chickens in Alberta, Canada over two years (2015–2016). Susceptibility assays and PCR assays were performed to characterize resistance phenotypes and resistance genes. Conjugation assays were used to examine the mobility of AMR phenotypes. Results: Campylobacter jejuni was the predominant species recovered during both years of sampling. There were no Campylobacter coli isolates found in 2015; however, approximately 33% (8/24) of isolates collected in 2016 were Campylobacter coli. The two most frequent antimicrobial resistance patterns in C. jejuni collected in 2015 were tetracycline (39%) and azithromycin/clindamycin/erythromycin/telithromycin resistance (29%). One isolate collected in 2015 has resistance pattern ciprofloxacin/nalidixic acid/tetracycline. The tetO gene was detected in all tetracycline resistant isolates from 2015. The cmeB gene was detected in all species isolates with resistance to azithromycin/clindamycin/erythromycin/telithromycin, and from two isolates with tetracycline resistance. Alignment of the nucleotide sequences of the cmeB gene from C. jejuni isolates with different resistance patterns revealed several single nucleotide polymorphisms. A variety of multi-drug resistance patterns were observed through conjugation experiments. Conclusions: These data suggest that poultry production may serve as a potential reservoir for and source of transmission of multi-drug resistant Campylobacter jejuni and supports the need for continued surveillance. Full article