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524400.9840Potentially pathogenic bacteria and antimicrobial resistance in bioaerosols from cage-housed and floor-housed poultry operations. BACKGROUND: Antibiotics are used in animal confinement buildings, such as cage-housed (CH) and floor-housed (FH) poultry operations, to lower the likeliness of disease transmission. In FH facilities, antibiotics may also be used at sub-therapeutic levels for growth promotion. Low levels of antibiotic create a selective pressure toward antimicrobial resistance (AMR) in chicken fecal bacteria. OBJECTIVE: The objective of this study was to compare bacteria and AMR genes in bioaerosols from CH and FH poultry facilities. METHODS: Bioaerosols were collected from 15 CH and 15 FH poultry operations, using stationary area samplers as well as personal sampling devices. Bacteria concentrations were determined by genus- or species-specific quantitative polymerase chain reaction (PCR) and AMR genes were detected using endpoint PCR. RESULTS: Enterococcus spp., Escherichia coli, and Staphylococcus spp. were significantly higher in bioaerosols of FH poultry operations than CH bioaerosols (P < 0.001) while Clostridium perfringens was significantly higher in area bioaerosols of CH operations than FH area bioaerosols (P < 0.05). Campylobacter spp. were detected only in bioaerosols of FH facilities. Zinc bacitracin resistance gene, bcrR, erythromycin resistance gene, ermA, and tetracycline resistance gene, tetA/C, were more prevalent in bioaerosols of FH facilities than CH bioaerosols (P < 0.01, P < 0.01, and P < 0.05, respectively). CONCLUSIONS: Most bacteria are more concentrated and most AMR genes are more prevalent in bioaerosols of FH poultry operations, where growth-promoting antibiotics may be used.201222156572
307210.9838Faecal 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
306920.9836The 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
306630.9836Staphylococci and fecal bacteria as bioaerosol components in animal housing facilities in the Zoological Garden in Chorzów. Zoos are places open for a large number of visitors, adults and children, who can admire exotic as well as indigenous animal species. The premises for animals may contain pathogenic microbes, including those exhibiting antibiotic resistance. It poses a threat to people remaining within the zoo premises, both for animal keepers who meet animals on a daily basis and visitors who infrequently have contact with animals. There are almost no studies concerning the presence on the concentration of airborne bacteria, especially staphylococci and fecal bacteria in animal shelters in the zoo. There is no data about antibiotic resistance of staphylococci in these places. The results will enable to determine the scale of the threat that indicator bacteria from the bioaerosol pose to human health within zoo premises. This study conducted in rooms for 5 animals group (giraffes, camels, elephants, kangaroos, and Colobinae (species of monkey)) in the Silesian Zoological Garden in Chorzów (Poland). The bioaerosol samples were collected using a six-stage Andersen cascade impactor to assess the concentrations and size distribution of airborne bacteria. Staphylococci were isolated from bioaerosol and tested for antibiotic resistance. In our study, the highest contamination of staphylococci and fecal bacteria was recorded in rooms for camels and elephants, and the lowest in rooms for Colobinae. At least 2/3 of bacteria in bioaerosol constituted respirable fraction that migrates into the lower respiratory tract of the people. In investigated animal rooms, the greatest bacteria contribution was recorded for bioaerosol fraction sized 1.1-3.3μm. Bacterial concentrations were particularly strong in spring and autumn, what is related to shedding fur by animals. Among the isolated staphylococci which most often occurred were Staphylococcus succinus, S. sciuri, and S. vitulinus. The highest antibiotic resistance was noted in the case of Staphylococcus epidermidis, while the lowest for S. xylosus. In addition to standard cleaning of animal rooms, periodic disinfection should be considered. Cleaning should be carried out wet, which should reduce dust, and thus the concentrations of bacteria in the air of animal enclosures.202134061267
311240.9836Farm-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
311350.9833Resistome 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
306560.9831Species diversity, virulence, and antimicrobial resistance of the nasal staphylococcal and mammaliicoccal biota of reindeer. BACKGROUND: Staphylococcus (S.) spp. and Mammaliicoccus (M.) spp., in addition to their established role as components of the human and animal microbiota, can also cause opportunistic infections. This study aimed to characterize bacteria recovered from nasal cavities of healthy adult reindeer from two farms located in Poland (15 reindeer) and Germany (15 reindeer). The research include bacteria isolation, species identification, detection of selected superantigen (SAg) genes, assessment of biofilm-forming capability in vitro, and evaluation of antimicrobial resistance. RESULTS: Seventy-four staphylococci and mammaliicocci from 14 different species were isolated from 30 nasal swabs, with one to four strains obtained from each reindeer. The most frequently identified species was S. equorum, followed by S. succinus, M. sciuri, S. xylosus, M. lentus, S. chromogenes, S. devriesei, M. vitulinus, S. auricularis, S. agnetis, S. edaphicus, S. petrasii, S. simulans, and S. warneri. A greater species diversity was observed among the reindeer from Poland compared to those from Germany. All isolated bacteria were coagulase negative and clumping factor negative and did not carry any of the 21 analyzed SAg genes. M. sciuri demonstrated the highest antimicrobial resistance (100%), followed by S. succinus (91%) and S. equorum (78%). Resistance to rifampicin was the most common (30% strains). Sixteen strains (22%) exhibited biofilm production at least 10% greater than the strong biofilm-forming S. aureus ATCC 6538. CONCLUSIONS: This study reveals a significant knowledge gap regarding the nasal microbiota of reindeer. It contributes to our understanding of staphylococcal and mammaliicoccal biota of reindeer and underscores the necessity for monitoring of microbial populations to assess their health implications for both animals and humans, particularly concerning the zoonotic transmission of bacteria.202540452044
843970.9830Comparative genomics analysis and virulence-related factors in novel Aliarcobacter faecis and Aliarcobacter lanthieri species identified as potential opportunistic pathogens. BACKGROUND: Emerging pathogenic bacteria are an increasing threat to public health. Two recently described species of the genus Aliarcobacter, A. faecis and A. lanthieri, isolated from human or livestock feces, are closely related to Aliarcobacter zoonotic pathogens (A. cryaerophilus, A. skirrowii, and A. butzleri). In this study, comparative genomics analysis was carried out to examine the virulence-related, including virulence, antibiotic, and toxin (VAT) factors in the reference strains of A. faecis and A. lanthieri that may enable them to become potentially opportunistic zoonotic pathogens. RESULTS: Our results showed that the genomes of the reference strains of both species have flagella genes (flaA, flaB, flgG, flhA, flhB, fliI, fliP, motA and cheY1) as motility and export apparatus, as well as genes encoding the Twin-arginine translocation (Tat) (tatA, tatB and tatC), type II (pulE and pulF) and III (fliF, fliN and ylqH) secretory pathways, allowing them to secrete proteins into the periplasm and host cells. Invasion and immune evasion genes (ciaB, iamA, mviN, pldA, irgA and fur2) are found in both species, while adherence genes (cadF and cj1349) are only found in A. lanthieri. Acid (clpB), heat (clpA and clpB), osmotic (mviN), and low-iron (irgA and fur2) stress resistance genes were observed in both species, although urease genes were not found in them. In addition, arcB, gyrA and gyrB were found in both species, mutations of which may mediate the resistance to quaternary ammonium compounds (QACs). Furthermore, 11 VAT genes including six virulence (cadF, ciaB, irgA, mviN, pldA, and tlyA), two antibiotic resistance [tet(O) and tet(W)] and three cytolethal distending toxin (cdtA, cdtB, and cdtC) genes were validated with the PCR assays. A. lanthieri tested positive for all 11 VAT genes. By contrast, A. faecis showed positive for ten genes except for cdtB because no PCR assay for this gene was available for this species. CONCLUSIONS: The identification of the virulence, antibiotic-resistance, and toxin genes in the genomes of A. faecis and A. lanthieri reference strains through comparative genomics analysis and PCR assays highlighted the potential zoonotic pathogenicity of these two species. However, it is necessary to extend this study to include more clinical and environmental strains to explore inter-species and strain-level genetic variations in virulence-related genes and assess their potential to be opportunistic pathogens for animals and humans.202235761183
181180.9830Abundance 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
708090.9830Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. BACKGROUND: Emergence and spread of antibiotic resistance has become a global health threat and is often linked with overuse and misuse of clinical and veterinary chemotherapeutic agents. Modern industrial-scale animal feeding operations rely extensively on veterinary pharmaceuticals, including antibiotics, to augment animal growth. Following excretion, antibiotics are transported through the environment via runoff, leaching, and land application of manure; however, airborne transport from feed yards has not been characterized. OBJECTIVES: The goal of this study was to determine the extent to which antibiotics, antibiotic resistance genes (ARG), and ruminant-associated microbes are aerially dispersed via particulate matter (PM) derived from large-scale beef cattle feed yards. METHODS: PM was collected downwind and upwind of 10 beef cattle feed yards. After extraction from PM, five veterinary antibiotics were quantified via high-performance liquid chromatography with tandem mass spectrometry, ARG were quantified via targeted quantitative polymerase chain reaction, and microbial community diversity was analyzed via 16S rRNA amplification and sequencing. RESULTS: Airborne PM derived from feed yards facilitated dispersal of several veterinary antibiotics, as well as microbial communities containing ARG. Concentrations of several antibiotics in airborne PM immediately downwind of feed yards ranged from 0.5 to 4.6 μg/g of PM. Microbial communities of PM collected downwind of feed yards were enriched with ruminant-associated taxa and were distinct when compared to upwind PM assemblages. Furthermore, genes encoding resistance to tetracycline antibiotics were significantly more abundant in PM collected downwind of feed yards as compared to upwind. CONCLUSIONS: Wind-dispersed PM from feed yards harbors antibiotics, bacteria, and ARGs.201525633846
2877100.9828Metagenomic insights into isolable bacterial communities and antimicrobial resistance in airborne dust from pig farms. This study aims to investigate bacterial communities and antimicrobial resistance (AMR) in airborne dust from pig farms. Airborne dust, pig feces and feed were collected from nine pig farms in Thailand. Airborne dust samples were collected from upwind and downwind (25 meters from pig house), and inside (in the middle of the pig house) of the selected pig house. Pig feces and feed samples were individually collected from the pen floor and feed trough from the same pig house where airborne dust was collected. A direct total bacteria count on each sampling plate was conducted and averaged. The ESKAPE pathogens together with Escherichia coli, Salmonella, and Streptococcus were examined. A total of 163 bacterial isolates were collected and tested for MICs. Pooled bacteria from the inside airborne dust samples were analyzed using Metagenomic Sequencing. The highest bacterial concentration (1.9-11.2 × 10(3) CFU/m(3)) was found inside pig houses. Staphylococcus (n = 37) and Enterococcus (n = 36) were most frequent bacterial species. Salmonella (n = 3) were exclusively isolated from feed and feces. Target bacteria showed a variety of resistance phenotypes, and the same bacterial species with the same resistance phenotype were found in airborne dust, feed and fecal from each farm. Metagenomic Sequencing analysis revealed 1,652 bacterial species across all pig farms, of which the predominant bacterial phylum was Bacillota. One hundred fifty-nine AMR genes of 12 different antibiotic classes were identified, with aminoglycoside resistance genes (24%) being the most prevalent. A total of 251 different plasmids were discovered, and the same plasmid was detected in multiple farms. In conclusion, the phenotypic and metagenomic results demonstrated that airborne dust from pig farms contained a diverse array of bacterial species and genes encoding resistance to a range of clinically important antimicrobial agents, indicating the significant role in the spread of AMR bacterial pathogens with potential hazards to human health. Policy measurements to address AMR in airborne dust from livestock farms are mandatory.202438872793
7131110.9828Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome. BACKGROUND: Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids. METHODS: In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples. RESULTS: Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later. CONCLUSIONS: Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.202336850017
2603120.9827Characterization of antimicrobial resistance genes in Enterobacteriaceae carried by suburban mesocarnivores and locally owned and stray dogs. The role of wildlife in the dissemination of antimicrobial-resistant bacteria and antimicrobial resistance genes (ARGs) in the environment is of increasing concern. We investigated the occurrence, richness and transmissibility potential of ARGs detected in the faeces of three mesocarnivore species: the coyote (Canis latrans), raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana), and of stray and owned dogs in suburban Chicago, IL, USA. Rectal swabs were collected from live-captured coyotes (n = 32), raccoons (n = 31) and Virginia opossums (n = 22). Fresh faecal samples were collected from locally owned (n = 13) and stray dogs (n = 18) and from the live-captured mesocarnivores, when available. Faecal samples and rectal swabs were enriched to select for Enterobacteriaceae and pooled by mesocarnivore species and dog type (owned or stray). Pooled enriched samples were then analysed for the presence of ARGs using shotgun sequencing. The three mesocarnivore and stray dog samples had twice as many unique ARGs compared to the owned dog sample, which was partly driven by a greater richness of beta-lactamase genes (genes conferring resistance to penicillins and cephalosporins). Raccoon and stray dog samples had the most ARGs in common, suggesting possible exposure to similar environmental sources of ARGs. In addition to identifying clinically relevant ARGs (e.g. bla(CMY) and qnrB), some ARGs were linked to the class 1 integrase gene, intI1, which may indicate anthropogenic origin. Findings from this pilot investigation suggest that the microbial communities of suburban mesocarnivores and stray dogs can host ARGs that can confer resistance to several antimicrobials used in human and veterinary medicine.202032034890
2522130.9827Identification and specificity validation of unique and antimicrobial resistance genes to trace suspected pathogenic AMR bacteria and to monitor the development of AMR in non-AMR strains in the environment and clinical settings. The detection of developing antimicrobial resistance (AMR) has become a global issue. The detection of developing antimicrobial resistance has become a global issue. The growing number of AMR bacteria poses a new threat to public health. Therefore, a less laborious and quick confirmatory test becomes important for further investigations into developing AMR in the environment and in clinical settings. This study aims to present a comprehensive analysis and validation of unique and antimicrobial-resistant strains from the WHO priority list of antimicrobial-resistant bacteria and previously reported AMR strains such as Acinetobacter baumannii, Aeromonas spp., Anaeromonas frigoriresistens, Anaeromonas gelatinfytica, Bacillus spp., Campylobacter jejuni subsp. jejuni, Enterococcus faecalis, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Klebsiella pneumonia subsp. pneumoniae, Pseudomonas aeruginosa, Salmonella enterica subsp. enterica serovar Typhimurium, Thermanaeromonas toyohensis, and Vibrio proteolyticus. Using in-house designed gene-specific primers, 18 different antibiotic resistance genes (algJ, alpB, AQU-1, CEPH-A3, ciaB, CMY-1-MOX-7, CMY-1-MOX-9, CMY-1/MOX, cphA2, cphA5, cphA7, ebpA, ECP_4655, fliC, OXA-51, RfbU, ThiU2, and tolB) from 46 strains were selected and validated. Hence, this study provides insight into the identification of strain-specific, unique antimicrobial resistance genes. Targeted amplification and verification using selected unique marker genes have been reported. Thus, the present detection and validation use a robust method for the entire experiment. Results also highlight the presence of another set of 18 antibiotic-resistant and unique genes (Aqu1, cphA2, cphA3, cphA5, cphA7, cmy1/mox7, cmy1/mox9, asaI, ascV, asoB, oxa-12, acr-2, pepA, uo65, pliI, dr0274, tapY2, and cpeT). Of these sets of genes, 15 were found to be suitable for the detection of pathogenic strains belonging to the genera Aeromonas, Pseudomonas, Helicobacter, Campylobacter, Enterococcus, Klebsiella, Acinetobacter, Salmonella, Haemophilus, and Bacillus. Thus, we have detected and verified sets of unique and antimicrobial resistance genes in bacteria on the WHO Priority List and from published reports on AMR bacteria. This study offers advantages for confirming antimicrobial resistance in all suspected AMR bacteria and monitoring the development of AMR in non-AMR bacteria, in the environment, and in clinical settings.202338058762
7726140.9827Distribution 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
3114150.9826Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles. Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6')-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.202134900133
7077160.9826Surfaces of gymnastic equipment as reservoirs of microbial pathogens with potential for transmission of bacterial infection and antimicrobial resistance. Gymnastic equipment surfaces are shared by many people, and could mediate the transfer of bacterial pathogens. To better understand this detrimental potential, investigations on the reservoirs of bacterial pathogens and antimicrobial resistance on the surfaces of gymnastic equipment were performed by analyzing the bacterial community structures, prevalence of viable bacteria, and presence of antimicrobial resistance on both indoor and outdoor gymnastic facilities. The results of high-throughput 16S rDNA amplicon sequencing showed that Gram-positive bacteria on the surfaces of indoor gymnastic equipment significantly enriched, including the opportunistic pathogen Staphylococcus strains, while Enterobacteriaceae significantly enriched on surfaces of outdoor gymnastic equipment. The analysis of α-diversities showed a higher richness and diversity for bacterial communities on the surfaces of gymnastic equipment than the environment. Analysis of β-diversities showed that the bacterial communities on the surfaces of gymnastic equipment differ significantly from environmental bacterial communities, while the bacterial communities on indoor and outdoor equipment are also significantly different. Thirty-four bacterial isolates were obtained from the surfaces of gymnastic equipment, including three multidrug Staphylococcus and one multidrug resistant Pantoea. In particular, Staphylococcus hemolyticus 5-6, isolated from the dumbbell surface, is a multidrug resistant, hemolytic, high- risk pathogen. The results of quantitative PCR targeting antibiotic resistance related genes (intI1, sul1 and bla (TEM)) showed that the abundances of sul1 and bla (TEM) genes on the surfaces of gymnastic equipment are higher than the environment, while the abundances of sul1 gene on indoor equipment are higher than outdoor equipment. These results lead to the conclusion that the surfaces of gymnastic equipment are potential dissemination pathways for highly dangerous pathogens as well as antimicrobial resistance, and the risks of indoor equipment are higher than outdoor equipment.202337152727
2587170.9825Prevalence of multi-drug resistant bacteria associated with foods and drinks in Nigeria (2015-2020): A systematic review. Foods are essential vehicles in human exposure to antibiotic resistant bacteria which serve as reservoirs for resistance genes and a rising food safety concern. Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally and poses a serious concern to human health. This study was designed to synthesize data regarding the prevalence of MDR bacteria associated with foods and drinks sold within Nigeria in order to contribute to the existing findings in this area. A comprehensive literature search on the prevalence of multi-drug resistant bacteria associated with foods and drinks in Nigeria from 2015 to 2020 was conducted using three databases; PubMed, Science Direct and Scopus. After screening and selection, 26 out of 82 articles were used for the qualitative data synthesis. Of the total of one thousand three hundred and twenty-six MDR bacteria reportedly isolated in all twenty-six articles, the highest prevalence (660) was observed in drinks, including water, while the lowest (20) was observed in the article which combined results for both protein and vegetable-based foods. Escherichia sp. had the most frequency of occurrence, appearing as MDR bacteria in ten out of the twenty-six articles. Salmonella sp. appeared as MDR in seven out of the twenty-six articles included in this study, in all seven articles where it was reported, it had the highest percentage (85.4%) prevalence as MDR bacteria. Public health personnel need to ensure critical control during the production and handling of foods and drinks, as well as create more awareness on proper hygienic practices to combat the spread of MDR bacteria becoming a growing food safety issue (Zurfluh et al., 2019; Mesbah et al., 2017; Campos et al., 2019). Foods can be contaminated by different means, including exposure to irrigation water, manure, feces or soil with pathogenic bacteria. Foods can also become contaminated as they are harvested, handled after harvest or during processing if food safety standards are not correctly applied (Meshbah et al., 2017). Food-borne diseases caused by resistant organisms are one of the most important public health problems as they contribute to the risk of development of antibiotic resistance in the food production chain (Hehempour-Baltork et al., 2019). Apart from pathogenic bacteria causing foodborne diseases, foods that are raw or not processed following standard procedures can introduce several antibiotic-resistant bacteria (ARB) to consumers (Gekemidis et al., 2018). Antibiotic resistance, though harbored in non-pathogenic bacteria, can potentially be spread through horizontal gene transfer to other species including opportunistic pathogens that are present in the environment or after consumption of ARB-contaminated foods. When ARB-contaminated foods are consumed, the spread of antibiotic resistant genes may affect the gut microbiome thereby contributing to the pool of antibiotic-resistance genes (ARG) in the human gut (Gekemidis et al, 2018). MDR bacteria have been defined as bacteria that are resistant to at least one antimicrobial agent present in three or more antimicrobial classes (Sweeny et al., 2018). There has been an increase in drug resistance in pathogens isolated from food for human consumption with species of Escherichia coli and Salmonella enterica being considered among the most important pathogens due to their ability to effect zoonotic transfer of resistant genes (Canton et al., 2018; Maneilla-Becerra et al., 2019). However, other pathogens, such as Vibrio spp., some species of Aeromonas, spores of Clostridium botulinum type F, and Campylobacter, have been linked to food-borne diseases in humans who have consumed seafood or other animal foods (Maneilla-Becerra et al., 2019). Some other resistant bacteria associated with foods include Staphylococcus aureus, Listeria spp., and Shigella spp. (Maneilla-Becerra et al., 2019) This study was therefore designed to synthesize data (2015-2020) regarding the prevalence of MDR bacteria associated with foods and drinks sold within Nigeria in order to contribute to the existing findings in this area.202135018289
3068180.9825Metagenomic 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
7175190.9825Key Contribution and Risk of Airborne Antibiotic Resistance: Total Suspended Particles or Settled Dust? The atmosphere is an important environmental medium in spreading antimicrobial resistance (AMR) in animal farming systems, yet the exposure risks associated with airborne pathways remain underexplored. This study employed metagenomic sequencing to investigate the airborne transmission of AMR in chicken farms (i.e., chicken feces, total suspended particles (TSP), and dust) and its exposure risks on the gut and nasal cavities of workers, office staff, and nearby villagers. Results revealed that TSP exhibited greater abundance, diversity, and transfer potential of antibiotic resistance genes (ARGs) compared to dust. The abundance of airborne resistome decreased with distance from the chicken house, and ARGs were estimated to spread up to 9.48 km within 1 h. While the gut resistome of workers and villagers showed limited differences, emerging tet(X) variants and high-risk dfrA remain future concerns. More nasal resistome was attributable to TSP compared to dust. Workers faced significantly higher inhalable exposures to antibiotic-resistant bacteria (ARB) and human pathogenic antibiotic-resistant bacteria (HPARB), exceeding those of office staff and villagers by an order of magnitude. We also compiled lists of high-risk and potential-risk airborne ARGs to inform monitoring. These findings highlight the need for regular air disinfection in animal farms and better protective measures for workers.202540434009