Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria. - Related Documents




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561301.0000Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria. Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.202236232576
561410.9999A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre. There are currently no standardized guidelines for genomic surveillance of One Health antimicrobial resistance (AMR). This project aimed to utilize metagenomics to identify AMR genes present in a companion animal hospital and compare these with phenotypic results from bacterial isolates from clinical specimens from the same veterinary hospital. Samples were collected from sites within a primary care companion animal veterinary hospital in London, UK. Metagenomic DNA was sequenced using Oxford Nanopore Technologies MinION. The sequencing data were analysed for AMR genes, plasmids and clinically relevant pathogen species. These data were compared to phenotypic speciation and antibiotic susceptibility tests of bacterial isolates from patients. The most common resistance genes identified were aph (n=101 times genes were detected across 48 metagenomic samples), sul (84), bla (CARB) (63), tet (58) and bla (TEM) (46). In clinical isolates, a high proportion of isolates were phenotypically resistant to β-lactams. Rooms with the greatest mean number of resistance genes identified per swab site were the medical preparation room, dog ward and surgical preparation room. Twenty-four and four plasmids typically associated with Gram-positive and Enterobacteriaceae, respectively, were identified. Sequencing reads matched with 14 out of 22 (64%) of the phenotypically isolated bacterial species. Metagenomics identified AMR genes, plasmids and species of relevance to human and animal medicine. Communal animal-handling areas harboured more AMR genes than areas animals did not frequent. When considering infection prevention and control measures, adherence to, and frequency of, cleaning schedules, alongside potentially more comprehensive disinfection of animal-handling areas, may reduce the number of potentially harmful bacteria present.202540889140
571620.9999Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.202438563788
192930.9999Research Note: Detection of antibiotic-resistance genes in commercial poultry and turkey flocks from Italy. Antibiotics are routinely used in commercial poultry farms for the treatment of economically important bacterial diseases. Repeated use of antibiotics, usually administered in the feed or drinking water, may also result in the selection of resistant bacteria in animal feces, able to transfer their antimicrobial-resistance genes (ARG), residing on mobile elements, to other microorganisms, including human pathogens. In this study, single and multiplex PCR protocols were performed to detect tetracycline-, lincomycin-, chloramphenicol-, aminoglycoside-, colistin-, vancomycin-, and carbapenem-resistance genes, starting from 38 litter samples collected from 6 poultry and 2 turkey Italian flocks. The ARG were confirmed for all investigated classes of antimicrobials, except for colistin (mcr-1, mcr-2, mcr-3,mcr-4 mcr-5) and carbapenem (IMP, OXA-48, NDM, KPC), while the vanB gene was only detected for vancomycin. The highest positivity was obtained for tetracycline (tet[L], tet[M], tet[K], tetA[P]] and aminoglycoside (aadA2) ARG, confirming the predominant use of these antimicrobials in the veterinary practice and their potential to enhance the resistance patterns also in humans as a consequence of environmental contamination. On the contrary, the dissemination by poultry of ARG for critically important antimicrobials seems to be of minor concern, suggesting a negligible environmental dissemination by these genes in the Italian poultry industry. Finally, the molecular screening performed in this study using a noninvasive sampling method represents a simple and rapid tool for monitoring the ARG patterns at the farm level.202133799114
187940.9999Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans. The emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context requiring continuous surveillance. Resistance to ciprofloxacin and cephalosporins is of particular concern. Since pigs are a relevant source of foodborne Salmonella for human beings, we studied transmissible AMR genes and MGE in a collection of 83 strains showing 9 different serovars and 15 patterns of multidrug resistant (MDR) previously isolated from pigs raised in the conventional breeding system of Northern Spain. All isolates were susceptible to ciprofloxacin and three isolates carried bla(CMY-2) or bla(CTX-M-9) genes responsible for cefotaxime resistance. Filter mating experiments showed that the two plasmids carrying bla(CTX-M-9) were conjugative while that carrying bla(CMY-2) was self-transmissible by transformation. Whole-genome sequencing and comparative analyses were performed on the isolates and plasmids. The IncC plasmid pSB109, carrying bla(CMY-2), was similar to one found in S. Reading from cattle, indicating potential horizontal transfer between serovars and animal sources. The IncHI2 plasmids pSH102 in S. Heidelberg and pSTM45 in S. Typhimurium ST34, carrying bla(CTX-M-9), shared similar backbones and two novel "complex class 1 integrons" containing different AMR and heavy metal genes. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.IMPORTANCEThe emergence of foodborne Salmonella strains carrying antimicrobial resistance (AMR) in mobile genetic elements (MGE) is a significant public health threat in a One Health context. Since pigs are a relevant source of foodborne Salmonella for humans, in this study, we investigate different aspects of AMR in a collection of 83 Salmonella showing nine different serovars and 15 patterns of multidrug resistant (MDR) isolated from pigs raised in the conventional breeding system. Our findings emphasize the importance of sequencing techniques to identify emerging AMR regions in conjugative and stable plasmids from livestock production. The presence of MGE carrying clinically relevant AMR genes raises public health concerns, requiring monitoring to mitigate the emergence of bacteria carrying AMR genes and subsequent spread through animals and food.202438695519
159250.9999Identification of ESBL-Producing Enterobacterales From Vegetable Plants: Preliminary Findings From a Small Cross-Sectional Study in a Rural Area of Madagascar. Extended-spectrum beta-lactamases (ESBL)-producing enterobacterales are considered a key indicator for antimicrobial resistance (AMR) epidemiological surveillance in animal, human, and environment compartments. In this study, we aim to investigate the presence and genetic diversity of ESBL-producing enterobacterales on vegetable plants. We isolated beta-lactam resistant enterobacterales from several vegetable plants and sequenced their whole genome. Utilising standard genomic and phylogenetic methods, we sought to (i) characterise the resistance genes and plasmid content of the plant-isolated strains, (ii) investigate their genetic structure, and (iii) determine their relationships with strains from other reservoirs. Among the 22 strains collected from vegetable plants, 6 showed resistance to beta-lactam antibiotics, with 5 of them identified as ESBL producers. Our results indicated the presence of multidrug-resistant (MDR) strains containing multiple antibiotic resistance genes (ARGs). Importantly, no host-specific lineages were identified among the plant-isolated ESBL-producing E. coli (ESBL-Ec). Instead, these strains exhibited genetic and epidemiological connections with strains isolated from animals, humans, and the environment, suggesting transfer of ESBL-Ec between plants and other sources in rural Madagascar. These preliminary findings suggest that vegetable plants are contaminated as a result of human activities, posing a potential risk of human and animal exposure to antibiotic-resistant bacteria and genes.202540528688
185760.9999Diverse Acinetobacter in retail meat: a hidden vector of novel species and antimicrobial resistance genes, including plasmid-borne bla(OXA-58), mcr-4.3 and tet(X3). Acinetobacter species, particularly Acinetobacter baumannii, are recognized pathogens in clinical settings, yet their presence in food systems, including fresh meat remains underexplored. This comprehensive study investigated the prevalence, diversity, concentration, and antimicrobial resistance of Acinetobacter spp. in 100 fresh meat samples from diverse animal sources across various packaging conditions. Acinetobacter isolates were initially characterized by MALDI-TOF MS, with comprehensive genomic characterization through whole-genome sequencing (WGS) of 116 representative isolates. Taxonomic refinement was performed using GTDB-Tk, core-genome, rpoB gene and Average Nucleotide Identity (ANI) phylogenomic approaches. Antimicrobial resistance genes (ARGs), and their plasmidic locations, were identified, and antimicrobial susceptibility profiles were determined for 33 A. baumannii isolates. Acinetobacter spp. were detected in 74 % of samples, with turkey meat showing the highest occurrence. The counts of this bacterium ranged from < 0.23 to 3.13 log(10) CFU/g. A total of 20 know species and 2 putative novel Acinetobacter species were identified by genomic analysis. Moreover, 16 novel A. baumannii sequence types (STs) were identified. ARG profiling revealed a complex resistome, including plasmid-located ARGs spanning multiple antibiotic classes. Critical findings include the presence of plasmid-borne bla(OXA-58), mcr-4.3, and tet(X3) genes. This study expands our understanding of Acinetobacter spp. diversity and reveals fresh meat as a significant vector for this genus, including species associated with human infections. Moreover, the detection of diverse resistance genes, including some associated with plasmids and conferring resistance to critically important antibiotics, underscores the potential public health implications of meat as a transmission pathway for these bacteria.202540513431
186370.9999Genomic surveillance of extended-spectrum cephalosporin-resistant Escherichia coli isolated from poultry in the UK from 2016 to 2020. INTRODUCTION: Surveillance is vital for monitoring the increasing risk of antimicrobial resistance (AMR) in bacteria leading to failures in humans and animals to treat infections. In a One Health context, AMR bacteria from livestock and food can transfer through the food chain to humans, and vice versa, which can be characterized in detail through genomics. We investigated the critical aspects of AMR and the dynamics of AMR in poultry in the UK. METHODS: In this study, we performed whole genome sequencing for genomic characterization of 761 extended-spectrum cephalosporinases (ESCs) harboring Escherichia coli isolated from poultry caeca and meat through EU harmonized monitoring of AMR in zoonotic and commensal bacteria from 2016 and 2018 and UK national monitoring in 2020. RESULTS: The most common ESC in 2016 and 2018 was blaCTX-M-1; however, 2020 had a greater diversity of ESCs with blaCTX-M-55 dominant in chickens and blaCTX-M-15 more prevalent in turkeys. Co-resistance to sulphonamides, tetracycline, and trimethoprim was widespread, and there were several positive correlations between the sequence types (STs) and ESC genes. We identified certain AMR genotypes and STs that were frequent each year but not as successful in subsequent years, e.g., ST350 harboring blaCTX-M-1, sul2, and tetA-v4.Phylogenetic comparison of isolates prevalent in our panel with global ones from the same STs available in public databases showed that isolates from the UK generally clustered together, suggesting greater within-country than between-country transmission. DISCUSSION: We conclude that future genomic surveillance of indicator organisms will be invaluable as it will enable detailed comparisons of AMR between and within neighboring countries, potentially identifying the most successful sequence types, plasmids, or emerging threats.202338352060
283580.9998Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination. State of art metagenomics were used to investigate the microbial population, antibiotic resistance genes and plasmids of medical interest in wastewater used for urban agriculture in Ouagadougou (Burkina Faso). Wastewater samples were collected from three canals near agricultural fields in three neighbourhoods. Assessment of microbial population diversity revealed different microbial patterns among the different samples. Sequencing reads from the wastewaters revealed different functional specializations of microbial communities, with the predominance of carbohydrates and proteins metabolism functions. Eleven pathogen-specific and 56 orthologous virulence factor genes were detected in the wastewater samples. These virulence factors are usually found in human pathogens that cause gastroenteritis and/or diarrhoea. A wide range of antibiotic resistance genes was identified; 81 are transmissible by mobile genetic elements. These included seven different extended spectrum β-lactamase genes encoding synthesis of four enzyme families, including two metallo-β-lactamases (bla(AIM-1) and bla(GES-21)). Ten different incompatibility groups of Enterobacteriaceae plasmid replicons (ColE, FIB, FIC, FII, P, Q, R, U, Y, and A/C), and 30 plasmid replicon types from Gram-positive bacteria. All are implicated in the wide distribution of antibiotic resistance genes. We conclude that wastewater used for urban agriculture in the city represents a high risk for spreading bacteria and antimicrobial resistance among humans and animals.201930253312
557090.9998Monitoring the Spread of Multidrug-Resistant Escherichia coli Throughout the Broiler Production Cycle. The extensive use of antimicrobials in broiler production is changing the bird microbiota, fostering drug-resistant bacteria, and complicating therapeutic interventions, making the problem of multidrug resistance global. The monitoring of antimicrobial virulence and resistance genes are tools that have come to assist the breeding of these animals, directing possible treatments as already used in human medicine and collecting data to demonstrate possible dissemination of multidrug-resistant strains that may cause damage to industry and public health. This work aimed to monitor broiler farms in southern Brazil, isolating samples of E. coli and classifying them according to the profile of resistance to antimicrobials of interest to human and animal health. We also monitored the profile of virulence genes and conducted an epidemiological survey of possible risk factors that contribute to this selection of multidrug-resistant isolates. Monitoring was carried out on farms in the three southern states of the country, collecting samples of poultry litter, cloacal swabs, and beetles of the species Alphitobius diaperinus, isolating E. coli from each of these samples. These were evaluated by testing their susceptibility to antimicrobials of animal and human interest; detecting whether the samples were extended-spectrum β-lactamase enzyme (ESBL) producers; and when positive, selected for genotypic tests to identify resistant genes (CTX-M, TEM, and SHV) and virulence. Among the antimicrobials tested, enrofloxacin and ciprofloxacin demonstrated some of the highest frequencies of resistance in the isolated strains, with significant statistical results. The use of these antimicrobials increased the likelihood of resistance by over three times and was associated with a 1.5-fold higher probability of multidrug resistance. Of all isolates, 95% were multidrug-resistant, raising concerns for production and public health. Among 231 ESBL-positive samples, the CTX-M1 group predominated.202539858355
2043100.9998Antimicrobial Resistance Genotypes and Mobile Genetic Elements of Poultry-Derived Escherichia coli: A Retrospective Genomic Study from the United States. The presence of antibiotic resistance in commensal bacteria may be an influential factor in the persistence of resistance in pathogens. This is especially critical for Escherichia coli that consumers may be exposed to through the consumption of uncooked meat. In this study, E. coli isolates previously recovered from poultry in the US between 2001 and 2012 were whole-genome sequenced to identify their antibiotic resistance genes and mobile genetic elements. The genomes of 98 E. coli isolates from poultry carcass rinsates and 2 isolates from poultry diagnostic samples with multidrug resistance or potential extended-spectrum β-lactam (ESBL)-producing phenotypes as well as the genetic variabilities among the E. coli were assessed. All E. coli isolates were positive for at least one antibiotic resistance gene and plasmid replicon, with 37 resistance genes and 27 plasmid replicons detected among the isolates. While no ESBL genes were detected, bla(CMY-2) was the most common β-lactamase gene, and bla(TEM) and bla(CARB-2) were also identified. Most isolates (95%) harbored at least one intact phage, and as many as seven intact phages were identified in one isolate. These results show the occurrence of antibiotic resistance genes and mobile genetic elements in these 100 poultry-associated E. coli isolates, which may be responsible for the resistance phenotypes exhibited by the isolates. This retrospective study also enables comparisons of resistance genes and mobile genetic elements from more recent E. coli isolates associated with poultry to aid in understanding the trends of both antibiotic resistance phenotypes and genotypes in the poultry setting over time.202540872236
1926110.9998Whole genome sequencing revealed high occurrence of antimicrobial resistance genes in bacteria isolated from poultry manure. BACKGROUND: Global demand for food has driven expansion and intensification of livestock production, particularly in developing nations where antibiotic use is often routine. Waste from poultry production, including manure, is commonly utilized as fertilizers in agroecosystems, risking environmental contamination with potentially zoonotic bacteria and antimicrobial resistance genes (ARGs). METHODS: Here, 33 bacterial isolates were recovered from broiler (n = 17) and layer (n = 16) chicken manure by aerobic culture using Luria Bertani agar. Antimicrobial susceptibility testing (AST) was performed using disc diffusion method. MALDI-ToF and 16S rRNA sequencing were used to identify and compare a subset of antibiotic-resistant isolates (n = 13). Comparison of whole genome sequence assemblies and phenotypic assays were used to assess capacity for biofilm formation, heavy metal tolerance and virulence. RESULTS: AST by disc diffusion revealed all isolates were resistant to a minimum of three antibiotics, with resistance to ampicillin, co-trimoxazole, fluoroquinolones, tetracyclines, streptomycin, rifampicin and/or chloramphenicol detected. Stutzerimonas sp. and Acinetobacter sp. were the common genera observed in this study. Genome sequencing of each selected isolate revealed carriage of multiple ARGs capable of conferring resistance to many antimicrobials commonly employed in poultry production and human medicine, including tetracyclines, quinolones, macrolides, sulfonamide and cephalosporins. CONCLUSIONS: The high occurrence of ARGs in studied bacterial isolates confirms that poultry manure could act as a source of genetic material that could be transferred to commensal microbiota and opportunistic pathogens of humans. Understanding the complex resistome interplay between humans, animals, and the environment requires a One Health approach, with implications for agricultural settings and public health.202539880102
2534120.9998Prevalence, antibiotic resistance, and virulence gene profile of Escherichia coli strains shared between food and other sources in Africa: A systematic review. BACKGROUND AND AIM: Foodborne diseases caused by Escherichia coli are prevalent globally. Treatment is challenging due to antibiotic resistance in bacteria, except for foodborne infections due to Shiga toxin-producing E. coli, for which treatment is symptomatic. Several studies have been conducted in Africa on antibiotic resistance of E. coli isolated from several sources. The prevalence and distribution of resistant pathogenic E. coli isolated from food, human, and animal sources and environmental samples and their virulence gene profiles were systematically reviewed. MATERIALS AND METHODS: Bibliographic searches were performed using four databases. Research articles published between 2000 and 2022 on antibiotic susceptibility and virulence gene profile of E. coli isolated from food and other sources were selected. RESULTS: In total, 64 articles were selected from 14 African countries: 45% of the studies were conducted on food, 34% on animal samples, 21% on human disease surveillance, and 13% on environmental samples. According to these studies, E. coli is resistant to ~50 antimicrobial agents, multidrug-resistant, and can transmit at least 37 types of virulence genes. Polymerase chain reaction was used to characterize E. coli and determine virulence genes. CONCLUSION: A significant variation in epidemiological data was noticed within countries, authors, and sources (settings). These results can be used as an updated database for monitoring E. coli resistance in Africa. More studies using state-of-the-art equipment are needed to determine all resistance and virulence genes in pathogenic E. coli isolated in Africa.202338023276
1964130.9998Antimicrobial resistance of pet-derived bacteria in China, 2000-2020. With the rapid growth of the pet industry in China, bacterial infectious diseases in pets have increased, highlighting the need to monitor antimicrobial resistance (AMR) in pet-derived bacteria to improve the diagnosis and treatment. Before the establishment of the China Antimicrobial Resistance Surveillance Network for Pets (CARPet) in 2021, a comprehensive analysis of such data in China was lacking. Our review of 38 point-prevalence surveys conducted between 2000 and 2020 revealed increasing trends in AMR among pet-derived Escherichia coli, Klebsiella pneumoniae, Staphylococcus spp., Enterococcus spp., and other bacterial pathogens in China. Notable resistance to β-lactams and fluoroquinolones, which are largely used in both pets and livestock animals, was observed. For example, resistance rates for ampicillin and ciprofloxacin in E. coli frequently exceeded 50.0%, with up to 41.3% of the isolates producing extended-spectrum β-lactamases. The emergence of carbapenem-resistant K. pneumoniae and E. coli, carrying bla(NDM) and bla(OXA) genes, highlighted the need for vigilant monitoring. The detection rate of SCCmec (Staphylococcal Cassette Chromosome mec), a genetic element associated with methicillin resistance, in Staphylococcus pseudintermedius isolated from pets in China was found to be over 40.0%. The resistance rate of E. faecalis to vancomycin was 2.1% (5/223) in East China, which was higher than the detection rate of human-derived vancomycin-resistant Enterococcus (0.1%, 12/11,215). Establishing the national AMR surveillance network CARPet was crucial, focusing on representative cities, diverse clinical samples, and including both commonly used antimicrobial agents in veterinary practice and critically important antimicrobial agents for human medicine, such as carbapenems, tigecycline, and vancomycin.202540135877
2837140.9998Molecular evidence of the close relatedness of clinical, gull and wastewater isolates of quinolone-resistant Escherichia coli. Escherichia coli with reduced susceptibility to quinolones isolated from different environmental sources (urban wastewater treatment plants, n=61; hospital effluent, n=10; urban streams, n=9; gulls, n=18; birds of prey, n=17) and from hospitalised patients (n=28) were compared based on multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). The habitats with the most diversified genotypes of quinolone-resistant E. coli, corresponding to the highest genetic diversity (H'), were wastewater and gulls. In addition, genetically distinct populations were observed in clinical samples and birds of prey, suggesting the influence of the habitat or selective pressures on quinolone-resistant E. coli. The close genetic relatedness between isolates of clinical origin and from gulls and wastewater suggests the existence of potential routes of propagation between these sources. The most common sequence types were ST131 and ST10, with ST131 being highly specific to patients, although distributed in all of the other habitats except birds of prey. The prevalence of antimicrobial resistance was significantly higher in isolates from patients and gulls than from other sources (P<0.01), suggesting that the effect of selective pressures met by isolates subjected to strong human impacts. The evidence presented suggests the potential circulation of bacteria between the environmental and clinical compartments, with gulls being a relevant vector of bacteria and resistance genes.201527842875
1591150.9998Influence of agricultural practice on mobile bla genes: IncI1-bearing CTX-M, SHV, CMY and TEM in Escherichia coli from intensive farming soils. Many calls have been made to address antibiotic resistance in an environmental perspective. With this study, we showed the widespread presence of high-level antibiotic resistant isolates on a collection of non-susceptible Gram-negative bacteria (n = 232) recovered from soils. Bacteria were selected using amoxicillin, cefotaxime and imipenem, from sites representing different agricultural practices (extensive, intensive and organic). Striking levels of non-susceptibility were noticed in intensive soils for norfloxacin (74%), streptomycin (50.7%) and tetracycline (46.6%); indeed, the exposure to intensive agricultural practices constituted a risk factor for non-susceptibility to many antibiotics, multidrug resistance and production of extended-spectrum β-lactamases (ESBL). Analyses of non-susceptibility highlighted that environmental and clinical bacteria from the same species might not share the same intrinsic resistance patterns, raising concerns for therapy choices in environment-borne infections. The multiple sequence-type IncI1-driven spread of penicillinases (blaTEM-1, blaTEM-135), ESBL (blaSHV-12 and blaCTX-M-1) and plasmid-mediated AmpC β-lactamases (blaCMY-2), produced by isolates that share their molecular features with isolates from humans and animals, suggests contamination of agricultural soils. This is also the first appearance of IncI1/ST28-harbouring blaCTX-M-1, which should be monitored to prevent their establishment as successfully dispersed plasmids. This research may help disclose paths of contamination by mobile antibiotic resistance determinants and the risks for their dissemination.201626279315
1865160.9998Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment. Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which bla(CTX-M) was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.202540245502
5729170.9998Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6')Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.202235298535
2836180.9998Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment. OBJECTIVES: Multidrug-resistant Enterobacteriaceae pose a significant threat to public health. We aimed to study the impact of sewage treatment effluent on antibiotic resistance reservoirs in a river. METHODS: River sediment samples were taken from downstream and upstream of a waste water treatment plant (WWTP) in 2009 and 2011. Third-generation cephalosporin (3GC)-resistant Enterobacteriaceae were enumerated. PCR-based techniques were used to elucidate mechanisms of resistance, with a new two-step PCR-based assay developed to investigate bla(CTX-M-15) mobilization. Conjugation experiments and incompatibility replicon typing were used to investigate plasmid ecology. RESULTS: We report the first examples of bla(CTX-M-15) in UK river sediment; the prevalence of bla(CTX-M-15) was dramatically increased downstream of the WWTP. Ten novel genetic contexts for this gene were identified, carried in pathogens such as Escherichia coli ST131 as well as indigenous aquatic bacteria such as Aeromonas media. The bla(CTX-M-15) -gene was readily transferable to other Gram-negative bacteria. We also report the first finding of an imipenem-resistant E. coli in a UK river. CONCLUSIONS: The high diversity and host range of novel genetic contexts proves that evolution of novel combinations of resistance genes is occurring at high frequency and has to date been significantly underestimated. We have identified a worrying reservoir of highly resistant enteric bacteria in the environment that poses a threat to human and animal health.201424797064
1593190.9998Epidemiological Description and Detection of Antimicrobial Resistance in Various Aquatic Sites in Marseille, France. Antibiotic resistance is a worldwide public health concern and has been associated with reports of elevated mortality. According to the One Health concept, antibiotic resistance genes are transferrable to organisms, and organisms are shared among humans, animals, and the environment. Consequently, aquatic environments are a possible reservoir of bacteria harboring antibiotic resistance genes. In our study, we screened water and wastewater samples for antibiotic resistance genes by culturing samples on different types of agar media. Then, we performed real-time PCR to detect the presence of genes conferring resistance to beta lactams and colistin, followed by standard PCR and gene sequencing for verification. We mainly isolated Enterobacteriaceae from all samples. In water samples, 36 Gram-negative bacterial strains were isolated and identified. We found three extended-spectrum β-lactamase (ESBL)-producing bacteria-Escherichia coli and Enterobacter cloacae strains-harboring the CTX-M and TEM groups. In wastewater samples, we isolated 114 Gram-negative bacterial strains, mainly E. coli, Klebsiella pneumoniae, Citrobacter freundii and Proteus mirabilis strains. Forty-two bacterial strains were ESBL-producing bacteria, and they harbored at least one gene belonging to the CTX-M, SHV, and TEM groups. We also detected carbapenem-resistant genes, including NDM, KPC, and OXA-48, in four isolates of E. coli. This short epidemiological study allowed us to identify new antibiotic resistance genes present in bacterial strains isolated from water in Marseille. This type of surveillance shows the importance of tracking bacterial resistance in aquatic environments. IMPORTANCE Antibiotic-resistant bacteria are involved in serious infections in humans. The dissemination of these bacteria in water, which is in close contact with human activities, is a serious problem, especially under the concept of One Health. This study was done to survey and localize the circulation of bacterial strains, along with their antibiotic resistance genes, in the aquatic environment in Marseille, France. The importance of this study is to monitor the frequency of these circulating bacteria by creating and surveying water treatments.202336976002