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660500.9957Antimicrobial Resistance in African Great Apes. BACKGROUND/OBJECTIVES: Antibiotic-resistant bacteria pose a significant global public health threat that demands serious attention. The proliferation of antimicrobial resistance (AMR) is primarily attributed to the overuse of antibiotics in humans, livestock, and the agro-industry. However, it is worth noting that antibiotic-resistant genes (ARGs) can be found in all ecosystems, even in environments where antibiotics have never been utilized. African great apes (AGAs) are our closest living relatives and are known to be susceptible to many of the same pathogens (and other microorganisms) as humans. AGAs could therefore serve as sentinels for human-induced AMR spread into the environment. They can potentially also serve as reservoirs for AMR. AGAs inhabit a range of environments from remote areas with little anthropogenic impact, over habitats that are co-used by AGAs and humans, to captive settings with close human-animal contacts like zoos and sanctuaries. This provides opportunities to study AMR in relation to human interaction. This review examines the literature on AMR in AGAs, identifying knowledge gaps. RESULTS: Of the 16 articles reviewed, 13 focused on wild AGAs in habitats with different degrees of human presence, 2 compared wild and captive apes, and 1 study tested captive apes alone. Ten studies included humans working with or living close to AGA habitats. Despite different methodologies, all studies detected AMR in AGAs. Resistance to beta-lactams was the most common (36%), followed by resistance to aminoglycosides (22%), tetracyclines (15%), fluoroquinolones (10%), sulphonamides (5%), trimethoprim (5%), macrolide (3%), phenicoles (2%) and fosfomycin (1%). CONCLUSIONS: While several studies suggest a correlation between increased human contact and higher AMR in AGAs, resistance was also found in relatively pristine habitats. While AGAs clearly encounter bacteria resistant to diverse antibiotics, significant gaps remain in understanding the underlying processes. Comparative studies using standardized methods across different sites would enhance our understanding of the origin and distribution of AMR in AGAs.202439766531
354810.9957From flagellar assembly to DNA replication: CJSe's role in mitigating microbial antibiotic resistance genes. The emergence of Antibiotic Resistance Genes (ARGs) in Campylobacter jejuni (CJ) poses a severe threat to food safety and human health. However, the specific impact of CJ and its variants on ARGs and other related factors remains to be further elucidated. Herein, integrated metagenomic sequencing and co-occurrence network analysis approach were employed to investigate the impact of CJ and CJ incorporated with biogenic selenium (CJSe) on ARGs, flagellar assembly pathways, microbial communities, and DNA replication pathways in chicken manure. Compared to the Control (CON) and CJ groups, the CJSe group exhibited 2.4-fold increase selenium levels (P < 0.01) in chicken manure. Notable differences were also observed between the CJ and CJSe groups, with sequence results showing a CJ > CJSe > CON trend in total ARG copy numbers. Furthermore, the CJSe group showed 31.6 % fewer flagellar assembly genes compared to the CJ group. Additionally, compared to the CJ group, CJSe inhibited pathways such as basal body/hook (e.g., FliH, FliO, FliQ reduced by 25-52 %) and stator (MotB downregulated by 42.3 %), suppressing flagellar assembly. We also found that both CJ and CJSe influenced bacterial DNA replication pathways, with the former increasing ARG-carrying bacteria and the latter, under selenium-induced selective pressure, reducing ARG-carrying bacteria. Moreover, compared to the CJ group, the CJSe group showed a significantly lower 9.72 % copy number of total archaeal DNA replication genes. Furthermore, through intricate co-occurrence network analysis, we discovered the complex interplay between changes in ARGs and bacterial and archaeal DNA replication dynamics within the microbial community. These findings indicate that CJSe mitigates the threat posed by CJ and reduces ARG prevalence, while its dual functionality enables applications in biofortified crop production and soil remediation in selenium-deficient regions, thereby advancing circular economy systems. While the current study demonstrates CJSe's dual functionality under controlled conditions, future work will implement a dedicated ecological risk assessment framework encompassing Se speciation/leaching tests and non-target organism assays to confirm environmental safety under field-relevant scenarios. This approach aligns with sustainable strategies for food security and public health safeguarding.202541108960
659820.9956Shallow shotgun sequencing of healthcare waste reveals plastic-eating bacteria with broad-spectrum antibiotic resistance genes. The burgeoning crises of antimicrobial resistance and plastic pollution are converging in healthcare settings, presenting a complex challenge to global health. This study investigates the microbial populations in healthcare waste to understand the extent of antimicrobial resistance and the potential for plastic degradation by bacteria. Our metagenomic analysis, using both amplicon and shallow shotgun sequencing, provided a comprehensive view of the taxonomic diversity and functional capacity of the microbial consortia. The viable bacteria in healthcare waste samples were analyzed employing full-length 16S rRNA sequencing, revealing a diverse bacterial community dominated by Firmicutes and Proteobacteria phyla. Notably, Proteus mirabilis VFC3/3 and Pseudomonas sp. VFA2/3 were detected, while Stenotrophomonas maltophilia VFV3/2 surfaced as the predominant species, holding implications for the spread of hospital-acquired infections and antimicrobial resistance. Antibiotic susceptibility testing identified multidrug-resistant strains conferring antimicrobial genes, including the broad-spectrum antibiotic carbapenem, underscoring the critical need for improved waste management and infection control measures. Remarkably, we found genes linked to the breakdown of plastic that encoded for enzymes of the esterase, depolymerase, and oxidoreductase classes. This suggests that specific bacteria found in medical waste may be able to reduce the amount of plastic pollution that comes from biological and medical waste. The information is helpful in formulating strategies to counter the combined problems of environmental pollution and antibiotic resistance. This study emphasises the importance of monitoring microbial communities in hospital waste in order to influence waste management procedures and public health policy. The findings highlight the need for a multidisciplinary approach to mitigate the risks associated with antimicrobial resistance and plastic waste, especially in hospital settings where they intersect most acutely.202539551377
660130.9955Use of Wastewater to Monitor Antimicrobial Resistance Trends in Communities and Implications for Wastewater-Based Epidemiology: A Review of the Recent Literature. Antimicrobial resistance (AMR) presents a global health challenge, necessitating comprehensive surveillance and intervention strategies. Wastewater-based epidemiology (WBE) is a promising tool that can be utilized for AMR monitoring by offering population-level insights into microbial dynamics and resistance gene dissemination in communities. This review (n = 29 papers) examines the current landscape of utilizing WBE for AMR surveillance with a focus on methodologies, findings, and gaps in understanding. Reported methods from the reviewed literature included culture-based, PCR-based, whole genome sequencing, mass spectrometry, bioinformatics/metagenomics, and antimicrobial susceptibility testing to identify and measure antibiotic-resistant bacteria and antimicrobial resistance genes (ARGs) in wastewater, as well as liquid chromatography-tandem mass spectrometry to measure antibiotic residues. Results indicate Escherichia coli, Enterococcus spp., and Pseudomonas spp. are the most prevalent antibiotic-resistant bacterial species with hospital effluent demonstrating higher abundances of clinically relevant resistance genes including bla, bcr, qnrS, mcr, sul1, erm, and tet genes compared to measurements from local treatment plants. The most reported antibiotics in influent wastewater across studies analyzed include azithromycin, ciprofloxacin, clindamycin, and clarithromycin. The influence of seasonal variation on the ARG profiles of communities differed amongst studies indicating additional factors hold significance when examining the conference of AMR within communities. Despite these findings, knowledge gaps remain, including longitudinal studies in multiple and diverse geographical regions and understanding co-resistance mechanisms in relation to the complexities of population contributors to AMR. This review underscores the urgent need for collaborative and interdisciplinary efforts to safeguard public health and preserve antimicrobial efficacy. Further investigation on the use of WBE to understand these unique population-level drivers of AMR is advised in a proposed framework to inform best practice approaches moving forward.202541011405
322340.9955A cross-sectional comparison of gut metagenomes between dairy workers and community controls. BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.202439033279
771150.9954Beyond the desert sands: decoding the relationship between camels, gut microbiota, and antibiotic resistance through metagenomics. BACKGROUND: Camels, known as the enduring "ships of the desert," host a complex gut microbiota that plays a crucial role in their survival in extreme environments. However, amidst the fascinating discoveries about the camel gut microbiota, concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations. Indeed, the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria, which has worsened through gene transfer. METHODS: This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel (Camelus ferus) gut microbiota and antibiotic resistance. RESULTS: Samples from wild camels yielded varying amounts of raw and clean data, generating scaftigs and open reading frames. The camel fecal microbiome was dominated by bacteria (mainly Bacillota and Bacteriodota), followed by viruses, archaea, and eukaryota. The most abundant genera were the Bacteroides, Ruminococcus, and Clostridium. Functional annotation revealed enriched pathways in metabolism, genetic information processing, and cellular processes, with key pathways involving carbohydrate transport and metabolism, replication, and amino acid transport. CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases. Antibiotic resistance gene (ARG) analysis identified Bacillota and Bacteroidota as the main reservoirs, with vancomycin resistance genes being the most prevalent. This study identified three major resistance mechanisms: antibiotic target alteration, antibiotic target protection, and antibiotic efflux. CONCLUSION: These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.202439763640
668660.9954The Impact of Wastewater on Antimicrobial Resistance: A Scoping Review of Transmission Pathways and Contributing Factors. BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a global issue driven by the overuse of antibiotics in healthcare, agriculture, and veterinary settings. Wastewater and treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The One Health approach emphasizes the interconnectedness of human, animal, and environmental health in addressing AMR. This scoping review analyzes wastewater's role in the AMR spread, identifies influencing factors, and highlights research gaps to guide interventions. METHODS: This scoping review followed the PRISMA-ScR guidelines. A comprehensive literature search was conducted across the PubMed and Web of Science databases for articles published up to June 2024, supplemented by manual reference checks. The review focused on wastewater as a source of AMR, including hospital effluents, industrial and urban sewage, and agricultural runoff. Screening and selection were independently performed by two reviewers, with conflicts resolved by a third. RESULTS: Of 3367 studies identified, 70 met the inclusion criteria. The findings indicated that antibiotic residues, heavy metals, and microbial interactions in wastewater are key drivers of AMR development. Although WWTPs aim to reduce contaminants, they often create conditions conducive to horizontal gene transfer, amplifying resistance. Promising interventions, such as advanced treatment methods and regulatory measures, exist but require further research and implementation. CONCLUSIONS: Wastewater plays a pivotal role in AMR dissemination. Targeted interventions in wastewater management are essential to mitigate AMR risks. Future studies should prioritize understanding AMR dynamics in wastewater ecosystems and evaluating scalable mitigation strategies to support global health efforts.202540001375
322270.9954Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study. BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes. CONCLUSIONS: This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.202337215025
326880.9954Resistomic features and novel genetic element identified in hospital wastewater with short- and long-read metagenomics. The global spread of antimicrobial resistance (AMR) poses a serious threat to public health, with hospital wastewater treatment plants (WWTPs) recognized as a key hotspot for resistant pathogens and antibiotic resistance genes (ARGs). This study employed advanced hybrid sequencing platforms to provide a comprehensive resistomic analysis of a Qingdao WWTP in China, revealing previously uncovered AMR transmission risks. We identified 175 ARG subtypes conferring resistance to 38 antimicrobials, including the last-resort antibiotics, highlighting the extensive and concerning resistance reservoir within this environment. Multidrug resistance genes predominated, followed by ARGs targeting aminoglycoside, β-lactam, tetracycline, glycopeptide, and macrolide classes, reflecting clinically relevant resistance patterns. Co-occurrence analysis revealed ARGs were strongly associated with mobile genetic elements, especially for ARGs targeting sulfonamide, glycopeptide, macrolide, tetracycline, aminoglycoside, and β-lactam classes, providing concrete evidence of their high dissemination potential. A striking 85 % of 131 metagenome-assembled genomes (MAGs) carried ARGs, demonstrating prevalent resistance in the wastewater microbiome. Furthermore, the identification of several rarely studied genomic islands (GIs), including those conferring resistance to antibiotics and heavy metals, and notably, the novel variant GIAS409 carrying transposases and heavy metal resistance operons, reveals a significant and previously neglected mechanism for co-selection and dissemination. This study significantly advances our understanding of AMR dynamics in hospital WWTPs, demonstrating that current treatment approaches (42 % ARG removal) have limited efficacy and that WWTP may serve as potential hotspots for multidrug resistance development. Collectively, these findings emphasize the urgent need for improved wastewater management to safeguard public health.202540915207
326390.9954Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms. Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and bla(CTX-M)). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.202235259381
3224100.9954Assessing phenotypic and genotypic antibiotic resistance in bacillus-related bacteria isolated from biogas digestates. Antibiotic resistance poses a significant public health challenge, with biogas digestate, a byproduct of anaerobic digestion (AD), presenting potential risks when applied as a biofertilizer. Understanding the actual resistance levels in digestate is crucial for its safe application. While many studies have investigated antibiotic resistance in AD processes using culture-independent molecular methods, these approaches are limited by their reliance on reference databases and inability to account for gene expression, leading to potential inaccuracies in resistance assessment. This study addresses these limitations by combining culture-independent whole-genome sequencing (WGS) with culture-dependent phenotypic testing to provide a more accurate understanding of antibiotic resistance in digestate. We investigated the phenotypic and genotypic resistance profiles of 18 antibiotic-resistant bacteria (ARB) isolated from digestates produced from food waste and animal manure. Resistance was assessed using WGS and Estrip testing across 12 antibiotics from multiple classes. This is the first study to directly compare phenotypic and genotypic resistance in bacteria isolated from digestate, revealing significant discrepancies between the two methods. Approximately 30 % of resistance levels were misinterpreted when relying solely on culture-independent methods, with both over- and underestimation observed. These findings highlight the necessity of integrating both methods for reliable resistance assessments. Additionally, our WGS analysis indicated low potential for transferability of detected ARGs among the isolated ARB, suggesting a limited risk of environmental dissemination. This study provides new insights into antibiotic resistance in digestate and underscores the importance of integrating methodological approaches to achieve accurate evaluations of resistance risks.202539947064
6593110.9953Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics. Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.202540204742
3078120.9953Microbiome of Dipteran vectors associated with integron and antibiotic resistance genes in South Korea. The spread of antibiotic resistance genes (ARGs) across the environment and the role that organisms that interact with humans play as reservoirs of resistant bacteria pose important threats to public health. Flies are two-winged insects composing the order Diptera, which includes synanthropic species with significant ecological roles as pollinators, vectors, and decomposers. Here, we used iSeq100 metabarcoding to characterize the microbiome of six dipteran species in South Korea: Lucilia sericata, Lucilia illustris, Culex pipiens, Aedes vexans, Psychoda alternata and Clogmia albipunctata. We profiled a panel of common ARGs and performed correlation network analysis of the microbiome and resistome to identify co-occurrence patterns of bacterial amplicon sequence variants (ASVs) and resistance genes. We detected blaTEM, ermB, tetB, tetC, aac(6')-Ib-cr, cat2, sul1, qepA, int1 and int2, but no blaSHV, mecA, tetA or cat1. Notably, co-occurrence analysis showed highly mobile genes such as qepA, ermB and sul1 were associated with integron of class 1 integrase presence. These, along with aac(6')-Ib-cr were detected at higher rates across multiple species. Microbiome composition was distinct across species. Amplicon sequence variants (ASVs) of Pseudomonas, Corynebacterium, Clostridium, Ignatzschineria, Bacteroides, Streptococcus, Treponema and Dietzia showed strong co-occurrence with multiple ARGs. This study contributes to the understanding of the role of dipterans as reservoirs of antibiotic resistance.202541046045
6861130.9953Investigating the antibiotic resistance genes and mobile genetic elements in water systems impacted with anthropogenic pollutants. A wide range of pollutants, including heavy metals, endocrine-disrupting chemicals (EDCs), residual pesticides, and pharmaceuticals, are present in various water systems, many of which strongly drive the proliferation and dissemination of antimicrobial resistance genes (ARGs), heightening the antimicrobial resistance (AMR) crisis and creating a critical challenge for environmental and health management worldwide. This study addresses the impact of anthropogenic pollutants on AMR through an extensive analysis of ARGs and mobile genetic elements (MGEs) in urban wastewater, source water, and drinking water supplies in India. Results indicated that bla(TEM) and bla(CTXM-32) were the dominant ARGs across all water systems, underscoring the prevalence and dominance of resistance against β-lactam antibiotics. Moreover, transposase genes such as tnpA-02, tnp-04, and tnpA-05 were detected across all water systems, indicating potential mechanisms for genetic transfer. The ubiquitous presence of intI-1 and clin-intI-1 genes underscores the widespread dissemination of MGEs, posing challenges for water quality management. Besides, human pathogenic bacteria such as Clostridium, Acinetobacter, and Legionella were also detected, highlighting potential health risks associated with contaminated water. The identified pathogenic bacterial genera belong to the phyla Pseudomonadota and Firmicutes. Leveraging linear regression to analyze correlations between EDCs and ARG-MGEs provides deeper insights into their interconnected dynamics. DMP showed a significant influence on tnpA-02 (p = 0.005), tnpA-07 (p = 0.015), sul-1 (p = 0.008), intI-1 (p = 0.03), and clin-intI1 (p = 0.012), while DiNOP demonstrated a very high impact on tnpA-05 (p = 0). Redundancy analysis revealed significant correlations between resistance genes and EDCs. Additionally, environmental parameters such as pH were highly correlated with the majority of MGEs and bla(CTXM-32). Furthermore, we found that F(-), NO(-3), and SO(4)(-2) were significantly correlated with sul-1, with F(-) exhibiting the highest impact, emphasizing the intricate interplay of pollutants in driving AMR. Understanding these interconnected factors is crucial for developing effective strategies and sustainable solutions to combat antibiotic resistance in environmental settings.202539824274
3249140.9952Department-specific patterns of bacterial communities and antibiotic resistance in hospital indoor environments. The hospital indoor environment has a crucial impact on the microbial exposures that humans encounter. Resistance to antibiotics is a mechanism used by bacteria to develop resilience in indoor environments, and the widespread use of antibiotics has led to changes in the ecological function of resistance genes and their acquisition by pathogens. By integrating the 16S rRNA Illumina sequencing and high-throughput-quantitative PCR approaches with water and air dust samples across seven departments in Peking University Shenzhen Hospital, China, this study yields intriguing findings regarding the department-specific variations, correlations and source tracing of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) within the hospital indoor environment. A notable observation was the pivotal role played by seasonal variations in shaping the bacterial composition across the entire hospital indoor environment. Another department-specific finding was the correlation between ARGs and MGEs abundance, which was evident in the overall hospital indoor environment, but not found in the blood test room, ophthalmology, and gynecology departments. Notably, as an important source of bacteria and ARGs/MGEs for the blood test room, the gynecology department also presented a close link between bacterial communities and the presence of ARGs/MGEs. Additionally, the results reiterate the importance of surveillance and monitoring of antibiotic resistance, specifically in Legionella spp. in man-made water systems, and highlight the significance of understanding genetic elements like Tp614 involved in gene transfer and recombination, and their impact on antimicrobial treatment efficacy. KEY POINTS: • The department-specific variations, correlations and source tracing of bacteria, ARGs, and MGEs were uncovered in the hospital's indoor environment. • Although each department exhibited consistent seasonal impacts on bacterial compositions, the co-occurrence between the presence of ARGs and MGEs was exclusively evident in the emergency, surgery, pneumology and otolaryngology departments. • The gynecology department emerged as a crucial source of bacteria, ARGs and MGEs within the hospital. Additionally, it was found to exhibit a significant correlation between bacterial communities and the presence of ARGs and MGEs.202439412549
3275150.9952The hidden threat: Comprehensive assessment of antibiotic and disinfectant resistance in commercial pig slaughterhouses. The presence of antibiotic resistance genes (ARGs), disinfectant resistance genes (DRGs), and pathogens in animal food processing environments (FAPE) poses a significant risk to human health. However, knowledge of the contamination and risk profiles of a typical commercial pig slaughterhouse with periodic disinfectant applications is limited. By creating the overall metagenomics-based behavior and risk profiles of ARGs, DRGs, and microbiomes in a nine-section pig slaughterhouse, an important FAPE in China. A total of 454 ARGs and 84 DRGs were detected in the slaughterhouse with resistance genes for aminoglycosides and quaternary ammonium compounds, respectively. The entire slaughtering chain is a hotspot for pathogens, including 83 human pathogenic bacteria (HPB), with 47 core HPB. In addition, 68 high-risk ARGs were significantly correlated with 55 HPB, 30 of which were recognized as potential bacteria co-resistant to antibiotics and disinfectants, confirm a three-fold risk of ARGs, DRGs, and pathogens prevailing throughout the chain. Pre-slaughter pig house (PSPH) was the major risk source for ARGs, DRGs, and HPB. Moreover, 75 Escherichia coli and 47 Proteus mirabilis isolates showed sensitivity to potassium monopersulfate and sodium hypochlorite, suggesting that slaughterhouses should use such related disinfectants. By using whole genome multi-locus sequence typing and single nucleotide polymorphism analyses, genetically closely related bacteria were identified across distinct slaughter sections, suggesting bacterial transmission across the slaughter chain. Overall, this study underscores the critical role of the PSPH section as a major source of HPB, ARGs, and DRGs contamination in commercial pig slaughterhouses. Moreover, it highlights the importance of addressing clonal transmission and cross-contamination of antibiotic- and disinfectant-resistant bacteria within and between slaughter sections. These issues are primarily attributed to the microbial load carried by animals before slaughter, carcass handling, and content exposure during visceral treatment. Our findings provide valuable insights for One Health-oriented slaughterhouse management practices.202438945230
7726160.9952Distribution and comparison of bacterial communities in HVAC systems of two university buildings: Implications for indoor air quality and public health. The installation of HVAC systems in building is meant to enhance indoor air quality as well as increase comfort to occupants. However, HVAC systems have also become a vehicle of contamination of indoor air with potentially pathogenic microorganisms. DNA was extracted from ten HVAC filter dust samples collected from two buildings and subjected to high throughput sequencing analysis to determine the bacterial community structure. Further, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software was used to predict the potential functional capabilities of the bacterial communities. Sequencing analysis led to the identification of five major bacterial phyla, including Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes and Bacteroidetes. At genus level, Mycobacterium, Bacillus, Cupriavidus, Hyphomicrobium and Mesorhizobium were the most dominant. With the exception of the later two bacterial genera, the first three are potential pathogens whose presence in HVAC systems poses a significant public health risk, especially among immunocompromised individuals. Nine pathways associated with antibiotics resistance and bacterial pathogenicity were identified, including polymyxin resistance and peptidoglycan biosynthesis pathways. Further, investigation of the relationship between the detected bacterial meta-communities and predicted potential virulence factors (antibiotic resistance and pathogenic genes) led to the detection of 350 positive associations among 43 core bacteria, 2 pathogenic genes (sitA and uidA) and 14 resistance genes. Overall, the heterogeneous nature of microorganisms found in HVAC systems observed in this study shows that HVAC systems are the origin of airborne infections in indoor environments, and must be periodically cleaned and disinfected to avoid the build-up of pathogens, and the subsequent exposure of human occupants of these pathogens.202133415530
6719170.9952Impacts of Antibiotic Residues in the Environment on Bacterial Resistance and Human Health in Eastern China: An Interdisciplinary Mixed-Methods Study Protocol. Antibiotic resistance is a global health challenge that threatens human and animal lives, especially among low-income and vulnerable populations in less-developed countries. Its multi-factorial nature requires integrated studies on antibiotics and resistant bacteria in humans, animals, and the environment. To achieve a comprehensive understanding of the situation and management of antibiotic use and environmental transmission, this paper describes a study protocol to document human exposure to antibiotics from major direct and indirect sources, and its potential health outcomes. Our mixed-methods approach addresses both microbiological and pathogen genomics, and epidemiological, geospatial, anthropological, and sociological aspects. Implemented in two rural residential areas in two provinces in Eastern China, linked sub-studies assess antibiotic exposure in population cohorts through household surveys, medicine diaries, and biological sampling; identify the types and frequencies of antibiotic resistance genes in humans and food-stock animals; quantify the presence of antibiotic residues and antibiotic resistance genes in the aquatic environment, including wastewater; investigate the drivers and behaviours associated with human and livestock antibiotic use; and analyse the national and local policy context, to propose strategies and systematic measurements for optimising and monitoring antibiotic use. As a multidisciplinary collaboration between institutions in the UK and China, this study will provide an in-depth understanding of the influencing factors and allow comprehensive awareness of the complexity of AMR and antibiotic use in rural Eastern China.202235805804
3267180.9952Characterization of antibiotic resistance across Earth's microbial genomes. Widespread antibiotic resistance across Earth's habitats has become a critical health concern. However, large-scale investigation on the distribution of antibiotic resistance genes (ARGs) in the microbiomes from most types of ecosystem is still lacking. In this study, we provide a comprehensive characterization of ARGs for 52,515 microbial genomes covering various Earth's ecosystems, and conduct the risk assessment for ARG-carrying species based on further identification of mobile genetic elements (MGEs) and virulence factor genes (VFGs). We identify a total of 6159 ARG-carrying metagenome-assembled genomes (ACMs), and most of them are recovered from human gut and city subway. Our results show that efflux pump is the most common mechanism for bacteria to acquire multidrug resistance genes in Earth's microbiomes. Enterobacteriaceae species are the largest hosts of ARGs, accounting for 14% of total ACMs with 64% of the total ARG hits. Most of ARG-carrying species are unique in the different ecosystem categories, while 33 potential background ARGs are commonly shared by all ecosystem categories. We then detect 36 high-risk ARGs that likely threat public health in all ACMs. Based on ranking the importance of ARG-carrying species in the different ecosystem categories, several bacterial taxa such as Escherichia coli, Enterococcus faecalis, and Pseudomonas_A stutzeri are recognized as priority species for surveillance and control. Overall, our study gives a broad view of ARG-host associations in the environments.202234774941
6879190.9952Airborne antibiotic and metal resistance genes - A neglected potential risk at e-waste recycling facilities. Heavy metal-rich environments can promote the selection of metal-resistance genes (MRGs) in bacteria, often leading to the simultaneous selection of antibiotic-resistance genes (ARGs) through a process known as co-selection. To comprehensively evaluate the biological pollutants at electronic-waste (e-waste) recycling facilities, air, soil, and river samples were collected at four distinct Swiss e-waste recycling facilities and analyzed for ARGs, MRGs, mobile genetic elements (MGEs), endotoxins, and bacterial species, with correlations drawn to heavy metal occurrence. To our knowledge, the present work marks the first attempt to quantify these bio-pollutants in the air of e-waste recycling facilities, that might pose a significant health risk to workers. Although ARG and MRG's profiles varied among the different sample types, intl1 consistently exhibited high relative abundance rates, identifying it as the predominant MGE across all sample types and facilities. These findings underscore its pivol role in driving diverse bacterial adaptations to extreme heavy metal exposure by selection and dissemination of ARGs and MRGs. All air samples exhibited consistent profiles of ARGs and MRGs, with blaTEM emerging as the predominant ARG, alongside pbrT and nccA as the most prevalent MRGs. However, one facility, engaged in batteries recycling and characterized by exceptionally high concentrations of heavy metals, showcased a more diverse resistance gene profile, suggesting that bacteria in this environment required more complex resistance mechanisms to cope with extreme metal exposure. Furthermore, this study unveiled a strong association between gram-negative bacteria and ARGs and less with MRGs. Overall, this research emphasizes the critical importance of studying biological pollutants in the air of e-waste recycling facilities to inform robust safety measures and mitigate the risk of resistance gene dissemination among workers. These findings establish a solid foundation for further investigations into the complex interplay among heavy metal exposure, bacterial adaptation, and resistance patterns in such distinctive ecosystems.202438365028