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518700.9362Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics. We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes.202337695121
518610.9362Occurrence of Antimicrobial Resistance Genes in the Oral Cavity of Cats with Chronic Gingivostomatitis. Feline chronic gingivostomatitis (FCGS) is a severe immune-mediated inflammatory disease with concurrent oral dysbiosis (bacterial and fungal). Broad-spectrum antibiotics are used empirically in FCGS. Still, neither the occurrence of antimicrobial-resistant (AMR) bacteria nor potential patterns of co-occurrence between AMR genes and fungi have been documented in FCGS. This study explored the differential occurrence of AMR genes and the co-occurrence of AMR genes with oral fungal species. Briefly, 14 clinically healthy (CH) cats and 14 cats with FCGS were included. Using a sterile swab, oral tissue surfaces were sampled and submitted for 16S rRNA and ITS-2 next-generation DNA sequencing. Microbial DNA was analyzed using a proprietary curated database targeting AMR genes found in bacterial pathogens. The co-occurrence of AMR genes and fungi was tested using point biserial correlation. A total of 21 and 23 different AMR genes were detected in CH and FCGS cats, respectively. A comparison of AMR-gene frequencies between groups revealed statistically significant differences in the occurrence of genes conferring resistance to aminoglycosides (ant4Ib), beta-lactam (mecA), and macrolides (mphD and mphC). Two AMR genes (mecA and mphD) showed statistically significant co-occurrence with Malassezia restricta. In conclusion, resistance to clinically relevant antibiotics, such as beta-lactams and macrolides, is a significant cause for concern in the context of both feline and human medicine.202134944364
519320.9361Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia. BACKGROUND: Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. METHODS: These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. RESULTS: Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. CONCLUSION: Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.202438128408
311330.9360Resistome 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
259440.9352Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing. INTRODUCTION: Nasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort. METHODS: As a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. RESULTS: AMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period. CONCLUSION: This study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche.202032320455
198950.9351Prevalence and characterization of IncQ1α-mediated multi-drug resistance in Proteus mirabilis Isolated from pigs in Kunming, Yunnan, China. BACKGROUND: Proteus mirabilis is a conditionally pathogenic bacterium that is inherently resistant to polymyxin and tigecycline, largely due to antibiotic resistance genes (ARGs). These ARGs can be horizontally transferred to other bacteria, raising concerns about the Inc plasmid-mediated ARG transmission from Proteus mirabilis, which poses a serious public health threat. This study aims to investigate the presence of Inc plasmid types in pig-derived Proteus mirabilis in Kunming, Yunnan, China. METHODS: Fecal samples were collected from pig farms across six districts of Kunming (Luquan, Jinning, Yiliang, Anning, Songming, and Xundian) from 2022 to 2023. Proteus mirabilis isolates were identified using IDS and 16S rRNA gene sequencing. Then, positive strains underwent antimicrobial susceptibility testing and incompatibility plasmid typing. Multi-drug-resistant isolates with positive incompatibility plasmid genes were selected for whole-genome sequencing. Resistance and Inc group data were then isolated and compared with 126 complete genome sequences from public databases. Whole-genome multi-locus sequence typing, resistance group analysis, genomic island prediction, and plasmid structural gene analysis were performed. RESULTS: A total of 30 isolates were obtained from 230 samples, yielding a prevalence of 13.04%. All isolates exhibited multi-drug resistance, with 100% resistance to cotrimoxazole, erythromycin, penicillin G, chloramphenicol, ampicillin, and streptomycin. Among these, 15 isolates tested positive for the IncQ1α plasmid repC gene. The two most multi-drug-resistant and repC-positive strains, NO. 15 and 21, were sequenced to compare genomic features on Inc groups and ARGs with public data. Genome analysis revealed that the repC gene was primarily associated with IncQ1α, with structural genes from other F-type plasmids (TraV, TraU, TraN, TraL, TraK, TraI, TraH, TraG, TraF, TraE/GumN, and TraA) also present. Strain NO. 15 carried 33 ARGs, and strain NO. 21 carried 38 ARGs, conferring resistance to tetracyclines, fluoroquinolones, aminoglycosides, sulfonamides, peptides, chloramphenicol, cephalosporins, lincomycins, macrolides, and 2-aminopyrimidines. CONCLUSION: The repC gene is primarily associated with IncQ1α, with structural genes from other F-type plasmids. A comparison with 126 public genome datasets confirmed this association.202439850143
252160.9344Insights into antimicrobial resistance among long distance migratory East Canadian High Arctic light-bellied Brent geese (Branta bernicla hrota). BACKGROUND: Antimicrobial resistance (AMR) is the most significant threat to global public health and ascertaining the role wild birds play in the epidemiology of resistance is critically important. This study investigated the prevalence of AMR Gram-negative bacteria among long-distance migratory East Canadian High Arctic (ECHA) light-bellied Brent geese found wintering on the east coast of Ireland. FINDINGS: In this study a number of bacterial species were isolated from cloacal swabs taken from ECHA light-bellied Brent geese. Nucleotide sequence analysis identified five species of Gram-negative bacteria; the dominant isolated species were Pantoea spp. (n = 5) followed by Buttiauxella agrestis (n = 2). Antimicrobial susceptibility disk diffusion results identified four of the Pantoea spp. strains, and one of the Buttiauxella agrestis strains resistant to amoxicillin-clavulanic acid. CONCLUSION: To our knowledge this is the first record of AMR bacteria isolated from long distance migratory ECHA light-bellied Brent geese. This indicates that this species may act as reservoirs and potential disseminators of resistance genes into remote natural ecosystems across their migratory range. This population of geese frequently forage (and defecate) on public amenity areas during the winter months presenting a potential human health risk.201527651892
348770.9343A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures. As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.202439006014
348580.9341Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.202133913739
637990.9341Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India. Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.202032155479
5185100.9340Genomic characterisation of nasal isolates of coagulase-negative Staphylococci from healthy medical students reveals novel Staphylococcal cassette chromosome mec elements. Coagulase-negative staphylococci (CoNS) are a diverse group of Gram-positive bacteria that are part of the normal human microbiota. Once thought to be non-pathogenic, CoNS has emerged in recent years as opportunistic pathogens of concern particularly in healthcare settings. In this study, the genomes of four methicillin-resistant CoNS isolates obtained from the nasal swabs of healthy university medical students in Malaysia were sequenced using the Illumina short-read platform. Genome sequencing enabled the identification of the four isolates as Staphylococcus warneri UTAR-CoNS1, Staphylococcus cohnii subsp. cohnii UTAR-CoNS6, Staphylococcus capitis subsp. urealyticus UTAR-CoNS20, and Staphylococcus haemolyticus UTAR-CoNS26. The genome of S. cohnnii UTAR-CoNS6 harboured the mecA methicillin-resistance gene on a Staphylococcal cassette chromosome mec (SCCmec) element similar to SCCmec type XIV (5 A) but the SCCmec cassettes identified in the other three CoNS genomes were novel and untypeable. Some of these SCCmec elements also encoded heavy metal resistance genes while the SCCmec type XIV (5 A) variant in S. cohnii UTAR-CoNS6 harboured the complete ica operon, a known virulence factor that functions in biofilm formation. In S. cohnii UTAR-CoNS6, the macrolide resistance genes msrA and mphC along with copper and cadmium resistance genes were located on a 26,630 bp plasmid, pUCNS6. This study showcased the diversity of CoNS in the nasal microbiota of medical students but the discovery of novel SCCmec elements, various antimicrobial and heavy metal resistance along with virulence genes in these isolates is of concern and warrants vigilance due to the likelihood of spread, especially to hospitalised patients.202540595841
3117110.9339Detection of antimicrobial resistance genes in urban air. To understand antibiotic resistance in pathogenic bacteria, we need to monitor environmental microbes as reservoirs of antimicrobial resistance genes (ARGs). These bacteria are present in the air and can be investigated with the whole metagenome shotgun sequencing approach. This study aimed to investigate the feasibility of a method for metagenomic analysis of microbial composition and ARGs in the outdoor air. Air samples were collected with a Harvard impactor in the PM(10) range at 50 m from a hospital in Budapest. From the DNA yielded from samples of PM(10) fraction single-end reads were generated with an Ion Torrent sequencer. During the metagenomic analysis, reads were classified taxonomically. The core bacteriome was defined. Reads were assembled to contigs and the ARG content was analyzed. The dominant genera in the core bacteriome were Bacillus, Acinetobacter, Leclercia and Paenibacillus. Among the identified ARGs best hits were vanRA, Bla1, mphL, Escherichia coli EF-Tu mutants conferring resistance to pulvomycin; BcI, FosB, and mphM. Despite the low DNA content of the samples of PM(10) fraction, the number of detected airborne ARGs was surprisingly high.202134964297
3272120.9338Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses. Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus-bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive.202439770612
1809130.9338Deciphering antibiotic resistance genes and plasmids in pathogenic bacteria from 166 hospital effluents in Shanghai, China. Although previous studies using phenotypic or metagenomic approaches have revealed the patterns of antibiotic resistance genes (ARGs) in hospital effluents in local regions, limited information is available regarding the antibiotic resistome and plasmidome in human pathogenic bacteria in hospital effluents of megacity in China. To address this knowledge gap, we analyzed effluent samples from 166 hospitals across 13 geographical districts in Shanghai, China, using both cultivation-based approaches and metagenomics. A total of 357 strains were isolated from these samples, with the predominant species being Escherichia coli (n = 61), Aeromonas hydrophila (n = 57), Klebsiella pneumoniae (n = 48), and Aeromonas caviae (n = 42). Those identified indicator bacteria were classified into biosafety level 1 (BSL-1, 60 %) and BSL-2 (40 %). We identified 1237 ARG subtypes across 22 types, predominantly including beta-lactam, tetracycline, multidrug, polymyxin, and aminoglycoside resistance genes, using culture-enriched phenotypic metagenomics. Mobile genetic elements such as plasmids, transposons (tnpA), integrons (intI1), and insertion sequences (IS91) were abundant. We recovered 135 plasmids classified into mobilizable (n = 94) and non-mobilizable (n = 41) types. Additionally, 80 metagenome-assembled genomes (MAGs) were reconstructed from the hospital effluents for the assessment of ARG transmission risks, including genes for last-line antibiotics such as bla(NDM), bla(KPC), bla(imiH), and mcr. This study is the first to comprehensively characterize and assess the risk of antimicrobial resistance levels and plasmidome in the hospital effluents of China's megacity, providing city-wide surveillance data and evidence to inform public health interventions.202539612873
7656140.9337The host-specific resistome in environmental feces of Eurasian otters (Lutra lutra) and leopard cats (Prionailurus bengalensis) revealed by metagenomic sequencing. Investigation of feces of wildlife, which is considered as reservoirs, melting pots, vectors and secondary sources of antimicrobial resistance genes (ARGs), provides insights into the risks and ecology of ARGs in the environment. Here, we investigated microbiomes, virulence factor genes (VFGs) of bacterial pathogens, and resistomes in environmental feces of Eurasian otters (Lutra lutra) and leopard cats (Prionailurus bengalensis) using shotgun metagenome sequencing. As expected, the taxonomic compositions of bacteria were significantly different between the animals. Importantly, we found that the compositions of ARGs were also significantly different between the animals. We detected ARGs including iri, tetA(P), tetB(P), floR, sulII, strA, strB, tetW and tetY. Some of them were significantly more abundant in either of the host animals, such as strA, strB and tetY in Eurasian otters, and tetA(P), tetW and iri in leopard cats. We also found that some ARGs were selectively correlated to particular VFGs-related bacteria, such as tetA(P) and tetB(P) to Clostridium, and iri to Mycobacterium. We also found that there were positive correlations between Acinetobacter and ARGs of multiple antimicrobial classes. The host-specific resistomes and VFGs-related bacteria may be due to differences in the host's gut microbiome, diet and/or habitat, but further investigation is needed. Overall, this study provided important baseline information about the resistomes of the wildlife in Korea, which may help the conservation of these endangered species and assessment of human health risks posed by ARGs and bacterial pathogens from wildlife.202235399616
3271150.9337Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea. Mass transit systems, including subways and buses, are useful environments for studying the urban microbiome, as the vast majority of populations in urban areas use public transportation. Microbial communities in urban environments include both human- and environment-associated bacteria that play roles in health and pathogen transmission. In this study, we used shotgun metagenomic sequencing to profile microbial communities sampled from various surfaces found in subway stations and bus stops within the Seoul mass transit system. The metagenomic approach and network analysis were used to investigate broad-spectrum antibiotic resistance genes (ARGs) and their co-occurrence patterns. We uncovered 598 bacterial species in 76 samples collected from various surfaces within the Seoul mass transit system. All samples were dominated by the potential human pathogen Salmonella enterica (40 %) and the human skin bacterium Cutibacterium acnes (19 %). Significantly abundant biomarkers detected in subway station samples were associated with bacteria typically found in the human oral cavity and respiratory tract, whereas biomarkers detected in bus stop samples were associated with bacteria commonly found in soil, water, and plants. Temperature and location had significant effects on microbial community structure and diversity. In total, 41 unique ARG subtypes were identified, associated with single-drug or multidrug resistance to clinically important and extensively used antibiotics, including aminoglycosides, carbapenem, glycopeptide, and sulfonamides. We revealed that Seoul subway stations and bus stops possess unique microbiomes containing potential human pathogens and ARGs. These findings provide insights for refining location-specific responses to reduce exposure to potentially causative agents of infectious diseases, improving public health.202236257123
1812160.9336Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing. According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses.202539860994
1255170.9336Emergence of quinupristin/dalfopristin resistance among livestock-associated Staphylococcus aureus ST9 clinical isolates. Quinupristin/dalfopristin (Q/D) is a valuable alternative to vancomycin for the treatment of meticillin-resistant Staphylococcus aureus (MRSA) infections. However, not long after Q/D was approved, bacteria with resistance to this newer antimicrobial agent were reported. To investigate the prevalence of Q/D resistance, a total of 1476 non-duplicate S. aureus isolates, including 775 MRSA, from a Chinese tertiary hospital were selected randomly from 2003 to 2013. Of the 775 MRSA, 3 (0.4%) were resistant to Q/D. All meticillin-susceptible S. aureus were susceptible to Q/D. The prevalence of Q/D resistance among S. aureus was 0.2% (3/1476). The three isolates with Q/D resistance had the same antimicrobial resistance profile, except for cefaclor and chloramphenicol. All three Q/D-resistant MRSA were positive for five streptogramin B resistance genes (ermA, ermB, ermC, msrA and msrB) and two streptogramin A resistance genes (vatC and vgaA) as determined by PCR and DNA sequencing. MRSA WZ1031 belonged to ST9-MRSA-SCCmecV-t899, whilst MRSA WZ414 and WZ480 belonged to ST9-MRSA-SCCmecNT(non-typeable)-t899. ST9 has been reported predominantly in livestock-associated (LA) MRSA in some Asian countries. The three patients with these MRSA isolates were not livestock handlers and did not keep close contact with livestock. The origin of these important LA-MRSA isolates causing human infections is not known. Taken together, Q/D resistance, which was caused by a combination of ermA-ermB-ermC-msrA-msrB-vatC-vgaA, was first found among S. aureus clinical isolates in China. The present study is the first report of the emergence of human infections caused by ST9 LA-MRSA isolates with Q/D resistance.201425218154
830180.9336Detection and characterisation of 16S rRNA methyltransferase-producing Pseudomonas aeruginosa from the UK and Republic of Ireland from 2003-2015. 16S rRNA methyltransferase (16S RMTase) genes confer high-level aminoglycoside resistance, reducing treatment options for multidrug-resistant Gram-negative bacteria. Pseudomonas aeruginosa isolates (n = 221) exhibiting high-level pan-aminoglycoside resistance (amikacin, gentamicin and tobramycin MICs ≥64, ≥32 and ≥32 mg/L, respectively) were screened for 16S RMTase genes to determine their occurrence among isolates submitted to a national reference laboratory from December 2003 to December 2015. 16S RMTase genes were identified using two multiplex PCRs, and whole-genome sequencing (WGS) was used to identify other antibiotic resistance genes, sequence types (STs) and the genetic environment of 16S RMTase genes. 16S RMTase genes were found in 8.6% (19/221) of isolates, with rmtB4 (47.4%; 9/19) being most common, followed by rmtD3 (21.1%; 4/19), rmtF2 (15.8%; 3/19) and single isolates harbouring rmtB1, rmtC and rmtD1. Carbapenemase genes were found in 89.5% (17/19) of 16S RMTase-positive isolates, with bla(VIM) (52.9%; 9/17) being most common. 16S RMTase genes were found in 'high-risk' clones known to harbour carbapenemase genes (ST233, ST277, ST357, ST654 and ST773). Analysis of the genetic environment of 16S RMTase genes identified that IS6100 was genetically linked to rmtB1; IS91 to rmtB4, rmtC or rmtD3; ISCR14 to rmtD1; and rmtF2 was linked to Tn3, IS91 or Tn1721. Although 16S RMTase genes explained only 8.6% of pan-aminoglycoside resistance in the P. aeruginosa isolates studied, the association of 16S RMTase genes with carbapenemase-producers and 'high-risk' clones highlights that continued surveillance is required to monitor spread as well as the importance of suppressing the emergence of dually-resistant clones in hospital settings.202235176475
1407190.9335World Health Organization priority antimicrobial resistance in Enterobacterales, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus and Enterococcus faecium healthcare-associated bloodstream infections in Brazil (ASCENSION): a prospective, multicentre, observational study. BACKGROUND: Carbapenem-resistant Enterobacterales (CRE), Acinetobacter baumannii (CRAB), Pseudomonas aeruginosa (CRPA), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE) are listed by World Health Organization (WHO) as priority antimicrobial-resistant bacteria. Data on WHO Priority Antimicrobial resistance Phenotype (WPAP) bacteria from low- and middle-income countries are scarce. In this study, we investigated the occurrence of WPAP in healthcare-associated bloodstream infections (BSI) in Brazil, an upper-middle-income country in South America. METHODS: ASCENSION was a prospective, multicentre, observational study conducted in 14 hospitals from four of five Brazilian regions. Enterobacterales, A. baumannii, P. aeruginosa, S. aureus and E. faecium BSIs in hospitalised patients were analysed. The primary outcome was the frequency of WPAP among all bacteria of interest. Secondary outcomes were incidence-density of bacteria isolates in hospitalised patients, WPAP proportions within bacterial species, and 28-day mortality. PCR for carbapenemase genes was performed in carbapenem-resistant Gram-negative bacteria. FINDINGS: Between August 15, 2022, and August 14, 2023, 1350 isolates (1220 BSI episodes) were included. WPAP accounted for 38.8% (n = 524; 95% Confidence Interval 32.0-46.1) of all isolates, with CRE (19.3%) as the most frequent, followed by CRAB (9.6%), MRSA (4.9%), VRE (2.7%), and CRPA (2.4%). Incidence-density of all and WPAP isolates were 1.91 and 0.77/1000 patients-day, respectively. Carbapenem-resistant Klebsiella pneumoniae (CRKP) was the most common CRE, corresponding to 14.2% of all BSIs. A. baumannii isolates presented the highest proportion of WPAP (87.8%). Mortality rates were higher in patients with BSIs by WPAP than non-WPAP isolates. KPC (64.4%) was the predominant carbapenemase in CRE, followed by NDM (28.4%) and KPC + NDM co-production (7.1%). OXA-23 was the most frequent in CRAB. INTERPRETATION: A high frequency of WPAP bacteria, particularly CRKP and CRAB, were found in healthcare-associated BSIs in Brazil, posing them as a major public health problem in this country. FUNDING: National Council for Scientific and Technological Development, Brazil.202539957800