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306900.9867The hospital sink drain biofilm resistome is independent of the corresponding microbiota, the environment and disinfection measures. In hospitals, the transmission of antibiotic-resistant bacteria (ARB) may occur via biofilms present in sink drains, which can lead to infections. Despite the potential role of sink drains in the transmission of ARB in nosocomial infections, routine surveillance of these drains is lacking in most hospitals. As a result, there is currently no comprehensive understanding of the transmission of ARB and the dissemination of antimicrobial resistance genes (ARGs) and associated mobile genetic elements (MGEs) via sink drains. This study employed a multifaceted approach to monitor the total aerobic bacteria as well as the presence of carbapenemase-producing Enterobacterales (CPEs), the microbiota and the resistome of sink drain biofilms (SDBs) and hospital wastewater (WW) of two separate intensive care units (ICUs) in the same healthcare facility in France. Samples of SDB and WW were collected on a monthly basis, from January to April 2023, in the neonatal (NICU) and the adult (AICU) ICUs of Grenoble Alpes University Hospital. In the NICU, sink drain disinfection with surfactants was performed routinely. In the AICU, routine disinfection is not carried out. Culturable aerobic bacteria were quantified on non-selective media, and CPEs were screened using two selective agars. Isolates were identified by MALDI-TOF MS, and antibiotic susceptibility testing (AST) was performed on Enterobacterales and P. aeruginosa. The resistome was analyzed by high-throughput qPCR targeting >80 ARGs and MGEs. The overall bacterial microbiota was assessed via full-length 16S rRNA sequencing. No CPEs were isolated from SDBs in either ICU by bacterial culture. Culture-independent approaches revealed an overall distinct microbiota composition of the SDBs in the two ICUs. The AICU SDBs were dominated by pathogens containing Gram-negative bacterial genera including Pseudomonas, Stenotrophomona, Klebsiella, and Gram-positive Staphylococcus, while the NICU SDBs were dominated by the Gram-negative genera Achromobacter, Serratia, and Acidovorax, as well as the Gram-positive genera Weisella and Lactiplantibacillus. In contrast, the resistome of the SDBs exhibited no significant differences between the two ICUs, indicating that the abundance of ARGs and MGEs is independent of microbiota composition and disinfection practices. The AICU WW exhibited more distinct aerobic bacteria than the NICU WW. In addition, the AICU WW yielded 15 CPEs, whereas the NICU WW yielded a single CPE. All the CPEs were characterized at the species level. The microbiota of the NICU and AICU WW samples differed from their respective SDBs and exhibited distinct variations over the four-month period:the AICU WW contained a greater number of genes conferring resistance to quinolones and integron integrase genes, whereas the NICU WW exhibited a higher abundance of streptogramin resistance genes. Our study demonstrated that the resistome of the hospital SDBs in the two ICUs of the investigated healthcare institute is independent of the microbiota, the environment, and the local disinfection measures. However, the prevalence of CPEs in the WW pipes collecting the waste from the investigated drains differed. These findings offer valuable insights into the resilience of resistance genes in SDBs in ICUs, underscoring the necessity for innovative strategies to combat antimicrobial resistance in clinical environments.202540483807
180210.9865Exploring water, sediment, and avifauna from an urban recreational lagoon: focus on WHO priority pathogens. AIMS: Environmental dissemination of antimicrobial-resistant (AMR) pathogens is a growing global concern under the One Health framework, yet remains underexplored in biodiverse and human-impacted ecosystems such as Brazil's coastal lagoons. This study assessed the occurrence and distribution of AMR bacteria, including WHO-designated critical-priority pathogens, in water, sediment, and avifauna from Lagoa da Conceição, a coastal lagoon in southern Brazil. METHODS AND RESULTS: From December 2022 to November 2023, 96 environmental and 251 avian samples were collected and analyzed using selective culture, antimicrobial susceptibility testing, and molecular screening for resistance genes. A total of 625 bacterial isolates were recovered from water and sediment, of which 35.5% were multidrug-resistant and 26.7% met WHO critical-priority criteria. Key resistance genes identified included blaTEM, blaCTX-M, blaNDM, blaOXA-143, and mcr-1, with high spatial heterogeneity across sampling sites. WHO critical-priority pathogens were also isolated from 9.6% of sampled birds, suggesting the role of avifauna as environmental sentinels and reservoirs. Generalized linear models revealed that population density and precipitation were positively associated with the abundance of critical-priority isolates. CONCLUSIONS: These findings highlight anthropogenic and climatic drivers of AMR dissemination in coastal environments and underscore the urgent need for integrated monitoring and mitigation strategies to protect ecosystems and public health.202541100178
181120.9864Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut. The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface. IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.202539945541
562030.9861Genomic analysis of multidrug-resistant Escherichia coli isolated from dairy cows in Shihezi city, Xinjiang, China. INTRODUCTION: Dairy farming plays a vital role in agriculture and nutrition; however, the emergence of antimicrobial resistance (AMR) among bacterial pathogens poses significant risks to public health and animal welfare. Multidrug-resistant (MDR) Escherichia coli strains are of particular concern due to their potential for zoonotic transmission and resistance to multiple antibiotics. In this study, we investigated the prevalence of AMR and analyzed the genomes of two MDR E. coli isolated from dairy cows in Shihezi City. METHODS: Fecal samples were collected from dairy cows, and E. coli strains were isolated. Antibiotic susceptibility testing was conducted using the Kirby-Bauer disk diffusion method against 14 antibiotics. Two MDR isolates (E.coli_30 and E.coli_45) were selected for whole-genome sequencing and comparative genomic analysis. The Comprehensive Antibiotic Resistance Database (CARD) was used to identify AMR genes, and virulence factors were analyzed. Phylogenetic analysis was performed to determine the evolutionary relationships of the isolates, and a pangenome analysis of 50 E. coli strains was conducted to assess genetic diversity. The presence of mobile genetic elements (MGEs), including insertion sequences (IS) and transposons, was also examined. RESULTS: Among the E. coli isolates, 22.9% exhibited MDR, with high resistance to imipenem and ciprofloxacin, while gentamicin and tetracycline remained the most effective antibiotics. Genomic analysis revealed key AMR genes, including mphA, qnrS1, and bla (CTX-M-55) (the latter found only in E.coli_45), conferring resistance to macrolides, quinolones, and beta-lactams, respectively. Virulence genes encoding type III secretion systems (TTSS) and adhesion factors were identified, indicating pathogenic potential. Phylogenetic analysis showed that E.coli_30 and E.coli_45 originated from distinct ancestral lineages. The presence of two extended-spectrum β-lactamase (ESBL) genes in E.coli_45 was noticeable, so we studied their global and national distribution using evolutionary analysis. We found that they are endemic in E. coli, Salmonella enterica, and Klebsiella pneumoniae. Pangenome analysis revealed significant genetic diversity among E. coli strains, with unique genes related to metabolism and stress response. This indicates the bacteria's adaptation to various environments. MGEs were identified as key contributors to genetic variability and adaptation. DISCUSSION: This study highlights the growing threat of MDR E. coli in dairy farms, emphasizing the critical role of MGEs in the spread of resistance genes. The genetic diversity observed suggests strong adaptive capabilities, justifying the need for continuous AMR surveillance in livestock. Effective monitoring and mitigation strategies are essential to prevent the dissemination of MDR bacteria, thereby protecting both animal and public health.202540135051
560740.9861Phenotypic and genotypic characterization of antimicrobial resistance and virulence profiles of Salmonella enterica serotypes isolated from necropsied horses in Kentucky. Salmonella is a foodborne pathogen that poses a significant threat to global public health. It affects several animal species, including horses. Salmonella infections in horses can be either asymptomatic or cause severe clinical illness. Infections caused by Salmonella are presently controlled with antibiotics. Due to the formation of biofilms and the emergence of antimicrobial resistance, the treatment has become more complicated. Our study focused on investigating the prevalence of Salmonella enterica in necropsied horses, assessing the capability for biofilm formation, and motility, determining the phenotypic and genotypic profiles of antibiotic resistance, and detecting virulence genes. A total of 2,182 necropsied horses were tested for the presence of Salmonella. Intestinal samples were enriched in selenite broth and cultured on hektoen and eosin methylene blue agar plates, whereas other samples were directly cultured on aforementioned plates. Confirmation of the serotypes was performed according to the Kauffmann-White-Le Minor Scheme followed by biofilm formation screening using crystal violet assay. The resistance profile of the isolates was determined by broth microdilution assay using the Sensititre️ Vet (Equine EQUIN2F). The genotypic antimicrobial resistance (AMR) and virulence profiles were detected using polymerase chain reaction (PCR). The overall prevalence of Salmonella was 1.19% (26/2182), with 11 different serotypes identified. Salmonella Typhimurium was the most prevalent serotype with 19.2% prevalence. All of the isolates were identified as biofilm producers and motile. Virulence genes related to invasion (invA, hilA, mgtC, and spiA), biofilm formation (csgA and csgB), and motility (filA, motA, flgG, figG, flgH, fimC, fimD, and fimH) of Salmonella were detected among 100% of the isolates. An overall 11.4% of the isolates were identified as multidrug-resistant (MDR), with resistance to gentamicin, amikacin, ampicillin, ceftazidime, ceftiofur, chloramphenicol, and trimethoprim/sulfamethoxazole. We found that beta-lactamase-producing genes bla(TEM), bla(CTXM), and bla(SHV2) were identified in 11.5% of the isolates, while only 3.8% carried the bla(OXA-9) gene. The presence of MDR pathogenic Salmonella in horses is alarming for human and animal health, especially when they have a high affinity for forming biofilm. Our study found horses as potential sources of pathogenic Salmonella transmission to humans. Thus, it is important to perform continuous monitoring and surveillance studies to track the source of infection and develop preventive measures. IMPORTANCE: This study focuses on understanding how Salmonella, specifically isolated from horses, can resist antibiotics and cause disease. Salmonella is a well-known foodborne pathogen that can pose risks not only to animals but also to humans. By studying the bacteria from necropsied horses, the research aims to uncover how certain Salmonella strains develop resistance to antibiotics and which genetic factors make them more dangerous. In addition to antibiotic resistance, the research explores the biofilm-forming ability of these strains, which enhances their survival in harsh environments. The study also investigates their motility, a factor that contributes to the spread of infection. The findings can improve treatment strategies for horses and help prevent the transmission of resistant bacteria to other animals as well as humans. Ultimately, the research could contribute to better management of antibiotic resistance in both veterinary and public health contexts, helping to safeguard animal welfare and public health.202539846771
252350.9860Antibiotic resistance and virulence of bacteria in spices: a systematic review. BACKGROUND: Spices, widely valued for their flavor, color, and antioxidant properties, are increasingly used in culinary and food industries. Despite their benefits, spices may act as carriers for antibiotic-resistant and potentially pathogenic bacteria, posing a threat to food safety and public health. METHODS: This systematic review followed the PRISMA 2020 guidelines. A comprehensive search of six databases (Web of Science, PubMed, Scopus, Cochrane Library, Google Scholar, and Embase) was conducted for English-language articles from inception to 2023, focusing on bacterial contamination, antibiotic resistance, and virulence in spices. Inclusion was limited to peer-reviewed articles, and methodological quality was assessed using the JBI checklist. RESULTS: Of the 3,458 initially identified articles, 16 met the inclusion criteria. Most studies originated from Asia (n = 5) and the Americas (n = 4). Bacteria commonly isolated from spices included Bacillus cereus, Escherichia coli, Salmonella spp., and Staphylococcus aureus. High resistance levels were observed against ampicillin (83.3%) and penicillin (82.1%), while most isolates were susceptible to polymyxin B and cephalothin. Resistance genes such as bla, tetK, and ermB were frequently detected, along with virulence genes like nheA, hblC, cytK, and tpeL. CONCLUSION: Spices may serve as reservoirs for multidrug-resistant and virulent bacteria. Improved handling, processing, and decontamination practices are essential to mitigate foodborne risks and curb the spread of antimicrobial resistance. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42522-025-00172-6.202541088443
121160.9860Molecular characterization of multidrug-resistant Escherichia coli of the phylogroups A and C in dairy calves with meningitis and septicemia. Escherichia coli is an important cause of septicemia (SEPEC) and neonatal meningitis (NMEC) in dairy calves. However, the diversity of virulence profiles, phylogroups, antimicrobial resistance patterns, carriage of integron structures, and fluoroquinolone (FQ) resistance mechanisms have not been fully investigated. Also, there is a paucity of knowledge about the virulence profiles and frequency of potential SEPEC in feces from calves with or without diarrhea. This study aimed to characterize the virulence potential, phylogroups, antimicrobial susceptibility, integron content, and FQ-resistance mechanisms in Escherichia coli isolated from calves with meningitis and septicemia. Additionally, the virulence genes (VGs) and profiles of E. coli isolated from diarrheic and non-diarrheic calves were compared between them and together with NMEC and SEPEC in order to identify shared profiles. Tissue and fluid samples from eight dairy calves with septicemia, four of which had concurrent meningitis, were processed for bacteriology and histopathology. Typing of VGs was assessed in 166 isolates from diverse samples of each calf. Selected isolates were evaluated for antimicrobial susceptibility by the disk diffusion test. Phylogroups, integron gene cassettes cartography, and FQ-resistance determinants were analyzed by PCR, sequencing, and bioinformatic tools. Furthermore, 109 fecal samples and 700 fecal isolates from dairy calves with or without diarrhea were evaluated to detect 19 VGs by uniplex PCR. Highly diverse VG profiles were characterized among NMEC and SEPEC isolates, but iucD was the predominant virulence marker. Histologic lesions in all calves supported their pathogenicity. Selected isolates mainly belonged to phylogroups A and C and showed multidrug resistance. Classic (dfrA17 and arr3-dfrA27) and complex (dfrA17-aadA5::ISCR1::bla(CTX-M-2)) class 1 integrons were identified. Target-site mutations in GyrA (S83L and D87N) and ParC (S80I) encoding genes were associated with FQ resistance. The VGs detected more frequently in fecal samples included f17G (50%), papC (30%), iucD (20%), clpG (19%), eae (16%), and afaE-8 (13%). Fecal isolates displaying the profiles of f17 or potential SEPEC were found in 25% of calves with and without diarrhea. The frequency of E. coli VGs and profiles did not differ between both groups (p > 0.05) and were identical or similar to those found in NMEC and SEPEC. Overall, multidrug-resistant E. coli isolates with diverse VG profiles and belonging to phylogroups A and C can be implicated in natural cases of meningitis and septicemia. Their resistance phenotypes can be partially explained by class 1 integron gene cassettes and target-site mutations in gyrA and parC. These results highlight the value of antimicrobial resistance surveillance in pathogenic bacteria isolated from food-producing animals. Besides, calves frequently shed potential SEPEC in their feces as commensals ("Trojan horse"). Thus, these bacteria may be disseminated in the farm environment, causing septicemia and meningitis under predisposing factors.202234982979
560970.9860Antimicrobial Resistance in Commensal Bacteria from Large-Scale Chicken Flocks in the Dél-Alföld Region of Hungary. Background: Antimicrobial resistance (AMR) is increasingly acknowledged as a critical global challenge, posing serious risks to human and animal health and potentially disrupting poultry production systems. Commensal bacteria such as Staphylococcus spp., Enterococcus spp., and Escherichia coli may serve as important reservoirs and vectors of resistance genes. Objectives: This study aimed to assess the AMR profiles of bacterial strains isolated from industrial chicken farms in the Dél-Alföld region of Hungary, providing region-specific insights into resistance dynamics. Methods: A total of 145 isolates, including Staphylococcus spp., Enterococcus spp., and E. coli isolates, were subjected to minimum inhibitory concentration (MIC) testing against 15 antimicrobial agents, following Clinical and Laboratory Standards Institute (CLSI) guidelines. Advanced multivariate statistics, machine learning algorithms, and network-based approaches were employed to analyze resistance patterns and co-resistance associations. Results Multidrug resistance (MDR) was identified in 43.9% of Staphylococcus spp. isolates, 28.8% of Enterococcus spp. isolates, and 75.6% of E. coli isolates. High levels of resistance to florfenicol, enrofloxacin, and potentiated sulfonamides were observed, whereas susceptibility to critical antimicrobials such as imipenem and vancomycin remained largely preserved. Discussion: Our findings underscore the necessity of implementing region-specific AMR monitoring programs and strengthening multidisciplinary collaboration within the "One Health" framework with proper animal hygiene and biosecurity measures to limit the spread of antimicrobial resistance and protect both animal and human health.202540872642
307280.9859Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use. Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (bla(TEM), bla(KPC) and bla(NDM)), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, bla(TEM), and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (bla(KPC)) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.202133872913
252590.9859Review of antimicrobial resistance surveillance programmes in livestock and meat in EU with focus on humans. OBJECTIVES: In this review, we describe surveillance programmes reporting antimicrobial resistance (AMR) and resistance genes in bacterial isolates from livestock and meat and compare them with those relevant for human health. METHODS: Publications on AMR in European countries were assessed. PubMed was reviewed and AMR monitoring programmes were identified from reports retrieved by Internet searches and by contacting national authorities in EU/European Economic Area (EEA) member states. RESULTS: Three types of systems were identified: EU programmes, industry-funded supranational programmes and national surveillance systems. The mandatory EU-financed programme has led to some harmonization in national monitoring and provides relevant information on AMR and extended-spectrum β-lactamase/AmpC- and carbapenemase-producing bacteria. At the national level, AMR surveillance systems in livestock apply heterogeneous sampling, testing and reporting modalities, resulting in results that cannot be compared. Most reports are not publicly available or are written in a local language. The industry-funded monitoring systems undertaken by the Centre Européen d'Etudes pour la Santé Animale (CEESA) examines AMR in bacteria in food-producing animals. CONCLUSIONS: Characterization of AMR genes in livestock is applied heterogeneously among countries. Most antibiotics of human interest are included in animal surveillance, although results are difficult to compare as a result of lack of representativeness of animal samples. We suggest that EU/EEA countries provide better uniform AMR monitoring and reporting in livestock and link them better to surveillance systems in humans. Reducing the delay between data collection and publication is also important to allow prompt identification of new resistance patterns.201828970159
3112100.9859Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique. Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e., scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiomes and resistome diversity between chicken breeds and along the supply chain. Fecal samples (n = 26) were collected from commercial and local chickens at production sites and markets and carcass (n = 49) and rinse bucket samples (n = 26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on potential human pathogens and "high-risk" ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray-Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal potential pathogens and resistomes at production and market sites. Many potentially pathogenic bacteria and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of exposure to potentially pathogenic bacteria and high-risk ARGs. IMPORTANCE: While chicken eggs and meat are a critical protein source in low-income settings, antibiotics are routinely fed to chickens with consequences for selection of antimicrobial resistance. Evaluating how poultry gut bacterial communities, including potential human pathogens and high-risk antimicrobial resistance genes, differ from farm to market could help identify where to target interventions to minimize transmission risks to human populations. In this study in Maputo City, Mozambique, we found compositional differences between commercial and local chicken breeds at production and market sites. We also found that while all potentially pathogenic bacteria and many high-risk antimicrobial resistance genes persisted from production and market through processing, some resistance genes were detected on carcass samples only after processing, suggesting human or environmental contamination is occurring within markets. Overall, our findings indicate that open-air markets may represent a critical juncture for human exposures to pathogens and antimicrobial resistance genes from poultry and poultry products.202539699181
3068110.9858Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes. Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.202540833454
2585120.9858A scoping review of the prevalence of antimicrobial-resistant pathogens and signatures in ready-to-eat street foods in Africa: implications for public health. BACKGROUND AND OBJECTIVE: Despite its critical role in individual and societal health, food hygiene remains underexplored. Antibiotic-resistant pathogenic bacteria in ready-to-eat (RTE) food threaten public health. This scoping review collected data on the epidemiological prevalence of RTE food-contaminated pathogens resistant to antimicrobial drugs and resistance genes in Africa. METHOD: Using electronic databases, such as PubMed, Scopus, and Web of Science (WoS), handpicked from references, pre-reviewed published articles were retrieved and analyzed according to the PRISMA-ScR guidelines. RESULTS: The findings indicate 40 previewed published articles qualified for meta-synthesis in the scoping review with a population/case ratio of 11,653/5,338 (45.80%). The most frequently reported RTE foods were meat or beef/beef-soup, chicken or poultry products, salads, vegetable salads, and sandwiches, which harboured pathogens such as E. coli, Salmonella, and Staphylococcus. Antibiotic susceptibility tests revealed the use of 48 antibiotics to manage infections, following CLSI (Clinical and Laboratory Standards Institute) protocols. Moreover, 10 authors reported 54 resistance genes associated with pathogenic resistant bacteria. In addition, only 15 studies received funding or financial support. CONCLUSION: These findings from several researchers indicate that RTE street foods in African and resource-limited nations harbour enteric pathogens and are a significant concern to the public health system and reservoir of the spread of antibiotic resistance. This underscores the necessity of implementing effective control strategies to address challenges and limit the spread of resistant bacteria in RTE foods. The antimicrobial resistance surveillance system in the region is a significant concern. Notably, Africa needs to strengthen the national and international regulatory bodies and a health surveillance system on antimicrobial resistance, particularly among developing nations.202540270817
5612130.9858Epidemiological factors associated with the prevalence of mobile genetic elements, and antimicrobial resistance patterns in Klebsiella pneumoniae of farm environments in Bangladesh. Farm environments serve as reservoirs for antibiotic-resistant bacteria and mobile genetic elements (MGEs), spreading resistance genes. Klebsiella pneumoniae, a nosocomial opportunistic pathogen, often acquires resistance through MGEs. This study examined the prevalence, resistance patterns, and factors associated with MGEs in K. pneumoniae isolates, focusing on environmental and management practices. 48 pooled samples were collected from environmental niches in three major districts of Bangladesh including Dhaka, Barisal, and Sylhet and analyzed using standard microbiological techniques and PCR. Antibiotic susceptibility was assessed per CLSI (2020) guidelines, and multidrug-resistant (MDR) strains were identified. Genotypic resistance patterns and mobile genetic elements (MGEs), including class 1 integrons and plasmids, were detected via PCR. Fisher's exact test evaluated factors associated with MGEs. Overall, 66.66% tested positive for K. pneumoniae. Regarding resistance patterns, the highest resistance was observed to ertapenem (90.6%) and ampicillin (84%), while complete sensitivity was noted to several antibiotics, including amikacin and tigecycline. Among the tested isolates, 53.12% were identified as MDR. Genotypic analysis revealed that bla(CTX-M), bla(NDM-5,)bla(Oxa-1) and bla(Oxa-48) were the most prevalent. Additionally, the presence of MGEs including class 1 integron and IncQ type plasmid were significantly associated with factors such as poor sanitation, antibiotic misuse, and high cattle density, highlighting critical areas for intervention. This study revealed that MDR K. pneumoniae circulates in food animals' farm environments in Bangladesh, with environmental factors strongly linked to the presence of MGEs. Farm niches, particularly soil, act as key reservoirs of MGEs and resistance genes. Importantly, these also carry serious implications for human health, as resistance genes may transfer to clinical settings, exacerbating the burden of AMR. Strengthening environmental and agricultural policies through a One Health approach is essential to mitigate the public health threat posed by antimicrobial resistance.202540619416
2720140.9858Phenotypic and genotypic characterization of antimicrobial resistance in Enterococcus spp. Isolated from the skin microbiota of channel catfish (Ictalurus punctatus) in Southeastern United States. BACKGROUND: Aquaculture systems may contribute to the emergence and persistence of antimicrobial-resistant (AMR) bacteria, posing risks to animal, environmental, and human health. This study characterized the phenotypic and genotypic antimicrobial resistance profiles of Enterococcus spp. isolated from the skin microbiota of 125 channel catfish (Ictalurus punctatus) harvested from two earthen ponds in Alabama, USA. METHODS: Skin swabs from the body of channel catfish were enriched in Enterococcosel broth and cultured on Enterococcosel agar at 28 °C for 24 h. Isolates were confirmed using Biolog Gen III and VITEK(®)2, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Thirty-five randomly sampled isolates underwent whole-genome sequencing for genotypic characterization. RESULTS: 36% of isolates exhibited multidrug resistance (resistance to ≥ 3 antimicrobial classes), with the highest resistance rates observed for ampicillin (44.8%), rifampicin (42.4%), and tetracycline (38.4%). The most prevalent resistance genes were aac(6')-Iid (65.7%), aac(6')-Ii (22.9%), efmA, and msr(C) (20.0% each). Plasmid replicons rep1 and repUS15 frequently co-occurred with resistance genes. Biofilm-associated genes, including efaA, fsrA, fsrB, sprE, ebpABC, ace, and scm, were commonly detected. Multivariate analyses (PERMANOVA, PCA) revealed no significant species-level differences in resistance burden or biofilm gene carriage, indicating similar resistance and virulence gene carriage across species in this dataset. CONCLUSIONS: The skin microbiota of pond-raised catfish harbors antimicrobial-resistant Enterococcus spp. with mobile resistance elements and biofilm-associated virulence factors, suggesting a potential role in AMR persistence within aquaculture settings. These findings support the need for targeted AMR surveillance in fish-associated microbiota as part of integrated One Health strategies.202540760424
3113150.9857Resistome in the indoor dust samples from workplaces and households: a pilot study. The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored. This pilot study aimed to analyze resistome in indoor dust samples from participants' workplaces (a pediatric hospital, a maternity hospital, and a research center) and households and compare two different approaches to the ARGs analysis; high-throughput quantitative PCR (HT-qPCR) and whole metagenome shotgun sequencing (WMGS). In total, 143 ARGs were detected using HT-qPCR, with ARGs associated with the macrolides, lincosamides, and streptogramin B (MLSB) phenotype being the most abundant, followed by MDR (multi-drug resistance) genes, and genes conferring resistance to aminoglycosides. A higher overall relative quantity of ARGs was observed in indoor dust samples from workplaces than from households, with the pediatric hospital being associated with the highest relative quantity of ARGs. WMGS analysis revealed 36 ARGs, of which five were detected by both HT-qPCR and WMGS techniques. Accordingly, the efficacy of the WMGS approach to detect ARGs was lower than that of HT-qPCR. In summary, our pilot data revealed that indoor dust in buildings where people spend most of their time (workplaces, households) can be a significant source of antimicrobial-resistant microorganisms, which may potentially pose a health risk to both humans and animals.202439691696
5237160.9857Phenotypic and genomic analysis of Enterococcus avium MC09 pathogenicity isolated from Scylla spp. (mud crab) in a Thai market. Enterococcus avium is a Gram-positive pathogenic bacterium classified under the Enterococcaceae family. E. avium has been isolated from diverse environmental sources, raising concerns about its potential role in the spread of antibiotic resistance. E. avium MC09, isolated from a mud crab in a Thai market, was analyzed for its antibiotic resistance and pathogenic potential in this study. The isolation of E. avium from mud crab is significant as it highlights the potential role of seafood as a reservoir for antibiotic-resistant bacteria, which may pose risks to public health throughout the food chain. Antibiotic susceptibility testing using the Kirby-Bauer disk diffusion method revealed that E. avium MC09 is resistant to clindamycin, erythromycin, streptomycin, and tetracycline, and exhibits alpha hemolysis on blood agar, indicating its potential virulence. Genomic DNA was extracted and sequenced using the Oxford Nanopore Technologies (ONT) platform, revealing the presence of resistance genes for macrolides (ermB) and tetracyclines (tetL and tetM). Furthermore, several virulence-associated genes were detected, such as srtC, ecbA, efaA, dltA, cpsA/uppS, cpsB/cdsA, cylR2, icps4I, cpsY, epsE, vctC, mgtB, ndk, lisR, and lgt suggesting a pathogenic potential. Additionally, the study identified several insertion sequences (ISs), including (IS1216, IS1216E, IS1216V, IS6770, ISEfa7, ISEfa8, and ISS1W which are commonly found in pathogenic Enterococcus strains. The presence of these IS elements further emphasizes the strain's potential for virulence and genetic adaptability. This study provides comprehensive insights into both the phenotypic and genotypic characteristics of E. avium MC09, highlighting its antimicrobial resistance and pathogenic mechanisms, and underlines the importance of monitoring antibiotic resistance in seafood-associated bacteria.202540015576
2582170.9857The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering. Households provide a habitat for bacteria originating from humans, animals, foods, contaminated clothes, or other sources. Thus, bacteria carrying antibiotic resistance genes (ARGs) may be introduced via household members, animals, or the water supply from external habitats into private households and vice versa. Since data on antibiotic resistance (ABR) in the domestic environment are limited, this study aimed to determine the abundance of β-lactamase, mobile colistin resistance, and class 1 integron genes and the correlation of their presence and to characterize phenotypically resistant strains in 54 private households in Germany. Additionally, the persistence of antibiotic-resistant bacteria during automated dishwashing compared to that during laundering was assessed. Shower drains, washing machines, and dishwashers were sampled and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using a Vitek 2 system. The results showed a significantly higher relative ARG abundance of 0.2367 ARG copies/16S rRNA gene copies in shower drains than in dishwashers (0.1329 ARG copies/16S rRNA gene copies) and washing machines (0.0006 ARG copies/16S rRNA gene copies). bla(CMY-2), bla(ACT/MIR), and bla(OXA-48) were the most prevalent ARG, and intI1 occurred in 96.3% of the households, while no mcr genes were detected. Several β-lactamase genes co-occurred, and the resistance of bacterial isolates correlated positively with genotypic resistance, with carbapenemase genes dominating across isolates. Antibiotic-resistant bacteria were significantly reduced during automated dishwashing as well as laundering tests and did not differ from susceptible strains. Overall, the domestic environment may represent a potential reservoir of β-lactamase genes and β-lactam-resistant bacteria, with shower drains being the dominant source of ABR.IMPORTANCE The abundance of antibiotic-resistant bacteria and ARGs is steadily increasing and has been comprehensively analyzed in natural environments, animals, foods, and wastewater treatment plants. In this respect, β-lactams and colistin are of particular interest due to the emergence of multidrug-resistant Gram-negative bacteria. Despite the connection of private households to these environments, only a few studies have focused on the domestic environment so far. Therefore, the present study further investigated the occurrence of ARGs and antibiotic-resistant bacteria in shower drains, washing machines, and dishwashers. The analysis of the domestic environment as a potential reservoir of resistant bacteria is crucial to determine whether households contribute to the spread of ABR or may be a habitat where resistant bacteria from the natural environment, humans, food, or water are selected due to the use of detergents, antimicrobial products, and antibiotics. Furthermore, ABR could limit the options for the treatment of infections arising in the domestic environment.202032978137
2581180.9857Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region. INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state. METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed. RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases. DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.202439896720
2588190.9857Exposure factors associated with antimicrobial resistance and identification of management practices for preharvest mitigation along broiler production systems: A systematic review. OBJECTIVE: This systematic review aimed to (i) determine the risk of antimicrobial resistance (AMR) development associated with antimicrobial use (AMU) and other exposure factors in broilers, and (ii) identify best management practices to mitigate preharvest AMR development of enteric bacteria alongside broiler production. METHODS: Study selection criteria comprised the population, exposure or intervention, comparator, and outcome framework and included broiler (population), AMU or other management practices (exposure or intervention), organic or antibiotic-free production (comparator), and the presence of AMR-enteric bacteria/genes (outcome). Peer-reviewed primary research studies were searched in PubMed on 19 December 2022, and AGRICOLA, Embase, Scopus, and Web of Science on 10 February 2023. The risk of bias in studies was assessed using the modified ROBIS-E risk of bias assessment tool. The results were synthesised and presented narratively according to PRISMA 2020 guidelines. RESULTS: In total, 205/2699 studies were subjected to full-text review, with 15 included in the final synthesis. Enteric bacteria Escherichia coli, Salmonella(,) and Campylobacter exhibited AMR and multidrug resistance against several critically important antimicrobials (aminoglycoside, cephalosporin, chloramphenicol, macrolide, penicillin, quinolone, tetracycline, and sulfonamide) for human health. The risk of AMR development in bacteria was shown to be potentially higher with AMU in broiler production. Substandard farm management practices, poor biosecurity measures, and conventional production systems have also been associated with the dissemination of AMR in bacteria. CONCLUSIONS: Our findings indicate that AMU exposure is associated with considerably higher risk of AMR development in enteric bacteria. Antimicrobial stewardship, organic/antibiotic-free broiler production, good farm management practices, and high-level biosecurity measures are able to substantially mitigate preharvest AMR development in enteric bacteria. However, most of studies were cross-sectional, and therefore causal inference cannot be established.202439490979