Whole genome analysis reveals the distribution and diversity of plasmid reservoirs of NDM and MCR in commercial chicken farms in China. - Related Documents




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185401.0000Whole genome analysis reveals the distribution and diversity of plasmid reservoirs of NDM and MCR in commercial chicken farms in China. The increase in multidrug-resistant (MDR) Enterobacteriaceae presents a significant challenge to clinical treatment, particularly in infections where carbapenems and colistin serve as the last-resort antimicrobial agents. In this study, we isolated 119 non-repetitive gram-negative bacteria from MacConkey medium supplemented with imipenem and colistin. The isolates were dominated by Klebsiella pneumoniae (58.0%, n = 69) and Escherichia coli (31.1%, n = 37). The predominant sequence types (STs) of E. coli were ST226, ST1286, and ST11738, whereas K. pneumoniae displayed ST152, ST395, and ST709 as major types. Genomic analysis identified mcr-1/3/8/9 in 44 strains and bla(NDM) in 63 strains across various species. IncX3 (n = 57) and IncFII (n = 5) were the most common bla(NDM-5)-carrying plasmid types. Several plasmid replicons were associated with mcr genes, including IncI2, IncX4, and novel plasmids. Remarkably, we discovered four combinations of bla(NDM) and mcr co-occurrence in 28 isolates, including bla(NDM-5)/mcr-1, bla(NDM-5)/mcr-3, bla(NDM-5)/mcr-8, and bla(NDM-5)/mcr-9. Our findings reveal that chicken farms are significant reservoirs for both bla(NDM) and mcr genes, with frequent co-occurrence of these resistance determinants. The presence of these genes alongside other resistance factors, such as blaESBL, highlights a critical public health risk. This study underscores the need for enhanced surveillance and intervention strategies to mitigate the spread of MDR pathogens from agricultural environments to clinical settings.IMPORTANCEThis study reveals that commercial poultry farms in China serve as critical reservoirs for MDR gram-negative bacteria harboring carbapenemase (bla(NDM)) and mobilized colistin resistance (mcr) genes. By analyzing 119 isolates, we uncovered extensive genetic diversity and plasmid-mediated co-occurrence of these resistance determinants, enabling bacteria to evade nearly all available treatments. Alarmingly, the horizontal transfer of resistance genes via highly mobile plasmids facilitates their spread across microbial communities and potentially into clinical settings. These findings underscore the urgent need to address antibiotic overuse in agriculture and strengthen surveillance under the One Health framework. The persistence of MDR pathogens in poultry environments highlights a significant risk for zoonotic transmission, emphasizing the necessity of coordinated interventions to curb the global antimicrobial resistance crisis.202540488461
163710.9998Genomic surveillance of antimicrobial resistance in bovine fecal samples from Lebanon. Antimicrobial resistance (AMR) threatens human and animal health worldwide, driven by the spread of extended-spectrum β-lactamase (ESBL)-producing, and carbapenem-resistant Gram-negative bacteria. In Lebanon, inadequate surveillance and antibiotic misuse worsen the issue. Animal fecal material is an important reservoir of resistance genes and mobile elements. This study aims to address AMR in bovine feces. To achieve this, bovine fecal samples were collected from 24 farms in Lebanon. Sixty-two ESBL-producing bacteria were recovered on CHROMagar ESBL and whole-genome sequencing followed by in silico typing was used to determine the resistance genes, virulence factors, and mobile genetic elements. Disk diffusion assay revealed the prevalence of multidrug-resistant (MDR) Gram-negative bacteria (33/62) with Escherichia coli being the most common (37/62). Resistance to amoxicillin, ceftriaxone, and cefotaxime was detected in all 37 E. coli isolates, with one also exhibiting resistance to colistin. β-lactam resistance was primarily associated with bla(CTX-M-15) and bla(TEM-1B), while colistin resistance was linked to mcr-1.1 on an IncHI2A/IncFIC multi-replicon plasmid. Plasmid typing identified 22 replicons, the most common being IncFIB and IncFII. Virulence factor analysis identified enterotoxin-encoding genes in one E. coli isolate, suggesting a potentially pathogenic strain with diarrheagenic properties among the recovered isolates. The findings of this study revealed highly resistant Gram-negative bacteria with plasmid-mediated resistance to critical antibiotics such as colistin, emphasizing the risks posed to human and livestock health. Comprehensive surveillance and responsible antibiotic use, guided by an integrated One Health approach, are essential steps to effectively tackle the interconnected challenges of AMR.202540482361
152620.9998Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon. BACKGROUND: The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE). METHODS: Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays. RESULTS: We detected 18 different β-lactamases, including four carbapenemases (bla(NDM-1), bla(NDM-5), bla(NDM-7), bla(OXA-48)) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200 kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes. CONCLUSION: Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.202337871361
184230.9998Emergence of mcr-9.1 in Extended-Spectrum-β-Lactamase-Producing Clinical Enterobacteriaceae in Pretoria, South Africa: Global Evolutionary Phylogenomics, Resistome, and Mobilome. Extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae are critical-priority pathogens that cause substantial fatalities. With the emergence of mobile mcr genes mediating resistance to colistin in Enterobacteriaceae, clinicians are now left with few therapeutic options. Eleven clinical Enterobacteriaceae strains with resistance to cephems and/or colistin were genomically analyzed to determine their resistomes, mobilomes, and evolutionary relationships to global strains. The global phylogenomics of mcr genes and mcr-9.1-bearing genomes were further analyzed. Ten isolates were ESBL positive. The isolates were multidrug resistant and phylogenetically related to global clones but distant from local strains. Multiple resistance genes, including bla (CTX-M-15) bla (TEM-1), and mcr-9.1, were found in single isolates; ISEc9, IS19, and Tn3 transposons bracketed bla (CTX-M-15) and bla (TEM-1) Common plasmid types included IncF, IncH, and ColRNAI. mcr-9 was of close sequence identity to mcr-3, mcr-5, mcr-7, mcr-8, and mcr-10. Genomes bearing mcr-9.1 clustered into six main phyletic groups (A to F), with those of this study belonging to clade B. Enterobacter species and Salmonella species are the main hosts of mcr-9.1 globally, although diverse promiscuous plasmids disseminate mcr-9.1 across different bacterial species. Emergence of mcr-9.1 in ESBL-producing Enterobacteriaceae in South Africa is worrying, due to the restricted therapeutic options. Intensive One Health molecular surveillance might discover other mcr alleles and inform infection management and antibiotic choices.IMPORTANCE Colistin is currently the last-resort antibiotic for difficult-to-treat bacterial infections. However, colistin resistance genes that can move from bacteria to bacteria have emerged, threatening the safe treatment of many bacterial infections. One of these genes, mcr-9.1, has emerged in South Africa in bacteria that are multidrug resistant, further limiting treatment options for clinicians. In this work, we show that this new gene is disseminating worldwide through Enterobacter and Salmonella species through multiple plasmids. This worrying observation requires urgent action to prevent further escalation of this gene in South Africa and Africa.202032430406
276140.9998First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment. The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n = 2), healthcare facility wastewater (n = 2), wastewater treatment plant influent (n = 1) and integrated constructed wetland influent (piggery farm waste) (n = 1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases, bla(OXA-48) (n = 2) and bla(NDM-1) (n = 1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.202336906027
163850.9998First national study on genomic profiling of Escherichia coli in United Arab Emirates (UAE) aquatic environments shows diverse Quinolone and Cephalosporin resistance. Antimicrobial resistance (AMR) is a serious threat to human, animal and plant health, and over recent years the role of the aquatic environment as a hotspot and dissemination route for resistant bacteria has been increasingly recognised. The United Arab Emirates (UAE) has identified AMR as a critical area of concern; however, limited studies have been conducted regarding the presence of AMR in aquatic environments in the region. This study addresses this gap by conducting a national surveillance to better understand the prevalence of aquatic AMR. We investigated the phenotypic and genotypic resistances in Escherichia coli (E. coli) isolates (n= 256) from sewage impacted and unimpacted coastal waters and artificial lakes across the UAE. Multidrug resistance was observed in 34.2% of isolates, with 22.7% exhibiting resistance to 3(rd) and 4(th) generation cephalosporins, cefotaxime and ceftazidime, including 16.6% displaying an extended-spectrum β-lactamase (ESBL) phenotype. Resistance to fluoroquinolones, macrolides, and carbapenems was also detected. Whole-genome sequencing (n=92) revealed a high prevalence of the fimH virulence gene, as well as conjugative plasmids (IncF, IncA/C and IncY) carrying resistance determinants. Notably, qnrS1 and bla(CTX-M-15) resistance genes were identified in 39% of sequenced isolates, while the bla(NDM-5) gene was detected for the first time in a single isolate. These findings underscore the need for harmonised AMR surveillance and a regional monitoring framework to assess the environmental dissemination of AMR bacteria in a One Health context.202540969202
168060.9998Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic. The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % K. pneumoniae isolates were phenotypically resistant to colistin, no mobile colistin resistance (mcr) genes were detected. Among carbapenem-resistant isolates, bla(NDM) and bla(OXA-48)-like were the most prevalent genetic determinants and were significantly overrepresented among K. pneumoniae. Furthermore, 84.78% of K. pneumoniae isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (qnrS and qnrB) were detected among the bacterial species and were significantly more prevalent among K. pneumoniae. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR.202438494251
185370.9998Dissemination dynamics of colistin resistance genes mcr-9 and mcr-10 across diverse Inc plasmid backbones. BACKGROUND: The polymyxin antibiotic colistin is used as a final line of treatment for life threatening infections caused by multidrug resistant and carbapenem-resistant Gram-negative bacteria. Mobile colistin resistance genes mcr-9 and mcr-10 are increasingly detected in Enterobacteriaceae but their epidemiology is poorly understood. METHODS: The genetic characteristics of mcr-9 and mcr-10, being the only mobile colistin resistance genes detected in a local population of Enterobacter species isolated from bloodstream infections in Dartmouth Hitchcock Medical Center, USA, were elucidated and contextualized against a global dataset of mcr-9/10-bearing plasmids using genomic and phylogenetic tools. RESULTS: Seven out of 59 Enterobacter isolates carry either an mcr-9 or mcr-10 on a plasmid with distinct single and multiple replicon configurations, including IncFIB(pECLA), IncFIB(K), IncFIA(HI1)-IncFIB(K), IncFIB(pECLA)--IncFII(pECLA) and IncFIB(K)--IncFII(pECLA), whereas two genomes harbor mcr-9 on their chromosome. Global contextualization reveals that allelic variants of mcr-9 and mcr-10 are widely disseminated across diverse Inc-type plasmids, transcending geographic and taxonomic boundaries. Plasmid-borne genes conferring resistance to other antimicrobial agents, such as aminoglycoside, tetracycline and trimethoprim, tend to co-occur with mcr-9.1 and mcr-9.2 alleles. CONCLUSIONS: Findings from this study enhance our understanding of the plasmid backgrounds of mcr-9 and mcr-10, their associated antimicrobial resistance gene carriage and co-occurrence. This knowledge may be critical to inform scalable and effective public health interventions aimed at preserving the efficacy of colistin.202540999001
87780.9998Drug resistance analysis of three types of avian-origin carbapenem-resistant Enterobacteriaceae in Shandong Province, China. Animal-derived Enterobacteriaceae bacteria such as Escherichia coli (E. coli), Proteus mirabilis (P. mirabilis), and Klebsiella pneumoniae (K. pneumoniae) are important food-borne zoonotic bacilli that exist widely in the broiler-breeding industry. Although carbapenem antibiotics are considered to be the last line of defense against multidrug-resistant bacteria, carbapenem-resistant Enterobacteriaceae (CRE) break through them. In our study, we therefore, examined the prevalence of CRE and characteristics of antimicrobial resistance in 6 conventional broiler-fattening farms in Shandong Province, China. Our study revealed isolation rates of 3.57% (6/168) for carbapenem-resistant E. coli, 10% (5/50) for carbapenem-resistant P. mirabilis, and 3.03% (1/33) for carbapenem-resistant K. pneumoniae. All 12 CRE bacterial strains showed varying degrees of resistance to 27 antibiotics in 8 classes and were multidrug-resistant. The rate of the strains containing bla(NDM) genes, at 91.67% (11/12), was especially high. Among other results, the carrying rate of integrons in CRE bacteria was 91.67% (11/12), and 2 strains carried both class I and class II integrons, which accelerated the lateral transmission of resistant bacteria. Our first-ever finding of the 3 CRE bacteria E. coli, P. mirabilis, and K. pneumoniae on the same broiler farm suggests that poultry-derived CRE strains may pose a risk to humans. Moreover, our findings from surveillance can inform current understandings of the prevalence and characteristics of multidrug-resistant CRE in Shandong Province and, in turn, help to curb threats to food safety and public health and better prevent and control infectious zoonotic diseases.202336682131
184390.9998Chromosome-Based blaOXA-48-Like Variants in Shewanella Species Isolates from Food-Producing Animals, Fish, and the Aquatic Environment. Carbapenems are considered last-resort antibiotics in health care. Increasing reports of carbapenemase-producing bacteria in food-producing animals and in the environment indicate the importance of this phenomenon in public health. Surveillance for carbapenemase genes and carbapenemase-producing bacteria in Dutch food-producing animals, environmental freshwater, and imported ornamental fish revealed several chromosome-based bla(OXA-48)-like variants in Shewanella spp., including two new alleles, bla(OXA-514) and bla(OXA-515) Carbapenemase genes were not associated with mobile genetic elements or Enterobacteriaceae.201727855066
1630100.9997One Health study of mobile colistin resistance (mcr) in Salmonella enterica in Canada, 2017-2022. Colistin is a last-resort treatment for highly drug-resistant bacterial infections. Of 47,184 Salmonella isolates collected from 2017 to 2022 in Canada from human and animal/food sources, mobile colistin resistance (mcr) variants conferring colistin resistance were detected exclusively in humans (n = 15). These variants were mcr-1.1 (n = 7), mcr-3.1 (n = 5), mcr-3.2 (n = 2), and mcr-1.2 (n = 1). The most common mcr-containing serotypes were I 4,[5],12:i:- (n = 8) and Typhimurium (n = 3). The proportion of Salmonella carrying mcr genes remains low in Canada (0.03%). IMPORTANCE: Colistin can be used in combination with other drugs as salvage therapy for extensively drug-resistant infections. If mobile colistin resistance (mcr) becomes widely disseminated in Enterobacterales, colistin will no longer be an option for salvage therapy in otherwise untreatable infections. While colistin is not commonly used to treat human Salmonella infections, Salmonella represents an important reservoir of mcr genes that may be transmitted to other gram-negative bacteria. Our aim was to determine the occurrence of mcr genes in Salmonella isolates collected from humans, food animals, and retail meats in Canada.202540387317
1907110.9997Nationwide surveillance of carbapenem-resistant Gram-negative pathogens in the Lebanese environment. Gram-negative ESKAPE pathogens with carbapenem resistance pose a significant health threat. Despite extensive research on the spread of these pathogens within Lebanese hospital settings, their emergence in environmental settings remains understudied. This study aimed to explore the environmental spread of carbapenem resistance among Gram-negative bacteria isolated from environmental samples in nine districts across Lebanon. A total of 250 samples were collected from wild animals, sewage, water, and soil between June 2022 and September 2023. Samples were streaked on MacConkey agar plates supplemented with 2 mg/L meropenem. Bacterial species were identified primarily using API20E. Antimicrobial susceptibility profiles were determined by the disk diffusion method and the Vitek 2 compact system. Meropenem-resistant Gram-negative bacteria were further characterized by whole-genome sequencing, and each of the bacterial species, sequence types, resistance genes, and plasmids was detected by sequence data analysis. We successfully isolated 130 carbapenem-resistant isolates from various samples, 67 of which belonged to the ESKAPE pathogens list and showed a multidrug-resistant (MDR) profile. The distribution of the latter was as follows: Escherichia coli (65.67%), Acinetobacter baumannii (16.42%), Pseudomonas aeruginosa (11.94%), and Klebsiella pneumoniae (5.97%). Several carbapenem resistance genes were detected, with a prevalence of blaNDM-5 in Escherichia coli and Klebsiella pneumoniae, blaIMP-1 and mexAB-OprM efflux pumps in Pseudomonas aeruginosa, and blaOXA-23 in Acinetobacter baumannii. Our findings revealed a widespread distribution of carbapenem-resistant ESKAPE bacteria in Lebanon, underscoring the significant public health risk posed by these pathogens. This highlights the urgent need to address the dissemination of antibiotic resistance in Lebanese environmental settings. IMPORTANCE: The emergence of antimicrobial resistance (AMR) extremely burdens public health and increases morbid and mortal threats in Lebanon. While the majority of the studies in our country target antimicrobial resistance in clinical settings, fewer studies focus on antimicrobial resistance dissemination in the environment. The significance of our research is that it sheds light on the environment as a less explored yet equally crucial sector in the spread of AMR. Here, we isolated carbapenemase-producing bacteria (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) that were categorized as multidrug resistant (MDR) from diverse environmental sources in multiple provinces across Lebanon. The finding of carbapenem-resistant bacteria carrying plasmids represents a potential risk due to the possible spread of resistance genes via horizontal gene transfer across the environment and hospital settings. This highly recommends the implementation of regular surveillance to monitor the spread of antimicrobial resistance among environmental bacteria, which consequently leads to its spread within communities and thus poses a great threat to human health.202540492734
1686120.9997Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates. The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.201829883490
1913130.9997Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase bla(NDM) and bla(KPC) resistance genes in hospital wastewater. Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; bla(TEM) in 33.1%, bla(CTX-M) in 25.4%, bla(KPC) in 25.4%, bla(NDM) 8.8%, bla(SHV) in 5.3%, and bla(OXA-48) in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase bla(KPC) was found in six Citrobacter spp. and E. coli, while bla(NDM) was detected in two distinct Enterobacter spp. and E. coli. Notably, bla(NDM-1) was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase bla(KPC) and bla(NDM). We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains. IMPORTANCE: The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as bla(KPC) and bla(NDM) within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.202439012101
1858140.9997Molecular Characteristics of Antimicrobial Resistance and Virulence in Klebsiella pneumoniae Strains Isolated from Goose Farms in Hainan, China. We retrospectively investigated 326 samples that were collected from goose farms in Hainan Province, China, in 2017. A total of 33 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates were identified from 326 samples, and the 33 CRKP isolates were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. All of these 33 CRKP isolates possessed bla(NDM-5), and a single isolate coharbored mcr-1 and bla(NDM-5), while 4 isolates carried multiple virulence and metal tolerance gene clusters. One CRKP strain (CMG-35-2) was selected for long sequence reading. A hybrid plasmid carrying the virulence, resistance, and metal resistance gene in the strain was found. It possessed 2 backbones [IncFIB(K)-IncFII(K)] within a single plasmid that were closely related to K. pneumoniae plasmids from a human-associated habitat in the United States and from a human isolate in Hong Kong. A mouse abdominal infection model indicated that that strain was of the moderate virulence phenotype. This study revealed that K. pneumoniae on goose farms is an important reservoir for bla(NDM-5) and these bacteria are represented by a diversity of sequence types. The heterozygous multiple drug resistance genes carried on plasmids highlighted the genetic complexity of CRKP and the urgent need for continued active surveillance. IMPORTANCE CRKP is one of the most important pathogens, which can cause infection not only in humans but also in waterfowl. The discovery of bla(NDM-5)-producing K. pneumoniae in waterfowl farms in recent years suggests that waterfowl are an important reservoir for bla(NDM-5)-producing Enterobacteriaceae. However, there are few studies on the spread of bla(NDM-5)-producing bacteria in waterfowl farms. Our study showed that the IncX3 plasmid carrying bla(NDM-5) in goose farms is widely present in K. pneumoniae isolates and a large number of resistance genes are accumulated in it. We found a transferable IncFIB-FII hybrid plasmid that combines virulence, resistance, and metal resistance genes, which allow transfer of these traits between bacteria in different regions. The results of this study contribute to a better understanding of the prevalence and transmission of carbapenem-resistant K. pneumoniae in goose farms.202235389252
878150.9997Environmental Spread of New Delhi Metallo-β-Lactamase-1-Producing Multidrug-Resistant Bacteria in Dhaka, Bangladesh. Resistance to carbapenem antibiotics through the production of New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an emerging challenge in the treatment of bacterial infections. To monitor the possible source of the spread of these organisms in Dhaka, Bangladesh, we conducted a comparative analysis of wastewater samples from hospital-adjacent areas (HAR) and from community areas (COM), as well as public tap water samples, for the occurrence and characteristics of NDM-1-producing bacteria. Of 72 HAR samples tested, 51 (71%) samples were positive for NDM-1-producing bacteria, as evidenced by phenotypic tests and the presence of the bla(NDM-1) gene, compared to 5 of 41 (12.1%) samples from COM samples (P < 0.001). All tap water samples were negative for NDM-1-producing bacteria. Klebsiella pneumoniae (44%) was the predominant bacterial species among bla(NDM-1)-positive isolates, followed by Escherichia coli (29%), Acinetobacter spp. (15%), and Enterobacter spp. (9%). These bacteria were also positive for one or more other antibiotic resistance genes, including bla(CTX-M-1) (80%), bla(CTX-M-15) (63%), bla(TEM) (76%), bla(SHV) (33%), bla(CMY-2) (16%), bla(OXA-48-like) (2%), bla(OXA-1) (53%), and bla(OXA-47-like) (60%) genes. Around 40% of the isolates contained a qnr gene, while 50% had 16S rRNA methylase genes. The majority of isolates hosted multiple plasmids, and plasmids of 30 to 50 MDa carrying bla(NDM-1) were self-transmissible. Our results highlight a number of issues related to the characteristics and source of spread of multidrug-resistant bacteria as a potential public health threat. In view of the existing practice of discharging untreated liquid waste into the environment, hospitals in Dhaka city contribute to the potential dissemination of NDM-1-producing bacteria into the community.IMPORTANCE Infections caused by carbapenemase-producing Enterobacteriaceae are extremely difficult to manage due to their marked resistance to a wide range of antibiotics. NDM-1 is the most recently described carbapenemase, and the bla(NDM-1) gene, which encodes NDM-1, is located on self-transmissible plasmids that also carry a considerable number of other antibiotic resistance genes. The present study shows a high prevalence of NDM-1-producing organisms in the wastewater samples from hospital-adjacent areas as a potential source for the spread of these organisms to community areas in Dhaka, Bangladesh. The study also examines the characteristics of the isolates and their potential to horizontally transmit the resistance determinants. The significance of our research is in identifying the mode of spread of multiple-antibiotic-resistant organisms, which will allow the development of containment measures, leading to broader impacts in reducing their spread to the community.201728526792
5612160.9997Epidemiological factors associated with the prevalence of mobile genetic elements, and antimicrobial resistance patterns in Klebsiella pneumoniae of farm environments in Bangladesh. Farm environments serve as reservoirs for antibiotic-resistant bacteria and mobile genetic elements (MGEs), spreading resistance genes. Klebsiella pneumoniae, a nosocomial opportunistic pathogen, often acquires resistance through MGEs. This study examined the prevalence, resistance patterns, and factors associated with MGEs in K. pneumoniae isolates, focusing on environmental and management practices. 48 pooled samples were collected from environmental niches in three major districts of Bangladesh including Dhaka, Barisal, and Sylhet and analyzed using standard microbiological techniques and PCR. Antibiotic susceptibility was assessed per CLSI (2020) guidelines, and multidrug-resistant (MDR) strains were identified. Genotypic resistance patterns and mobile genetic elements (MGEs), including class 1 integrons and plasmids, were detected via PCR. Fisher's exact test evaluated factors associated with MGEs. Overall, 66.66% tested positive for K. pneumoniae. Regarding resistance patterns, the highest resistance was observed to ertapenem (90.6%) and ampicillin (84%), while complete sensitivity was noted to several antibiotics, including amikacin and tigecycline. Among the tested isolates, 53.12% were identified as MDR. Genotypic analysis revealed that bla(CTX-M), bla(NDM-5,)bla(Oxa-1) and bla(Oxa-48) were the most prevalent. Additionally, the presence of MGEs including class 1 integron and IncQ type plasmid were significantly associated with factors such as poor sanitation, antibiotic misuse, and high cattle density, highlighting critical areas for intervention. This study revealed that MDR K. pneumoniae circulates in food animals' farm environments in Bangladesh, with environmental factors strongly linked to the presence of MGEs. Farm niches, particularly soil, act as key reservoirs of MGEs and resistance genes. Importantly, these also carry serious implications for human health, as resistance genes may transfer to clinical settings, exacerbating the burden of AMR. Strengthening environmental and agricultural policies through a One Health approach is essential to mitigate the public health threat posed by antimicrobial resistance.202540619416
1869170.9997An update on the prevalence of colistin and carbapenem-resistant Gram-negative bacteria in aquaculture: an emerging threat to public health. Aquaculture has been recognized as a hotspot for the emergence and spread of antimicrobial resistance genes conferring resistance to clinically important antibiotics. This review gives insights into studies investigating the prevalence of colistin and carbapenem resistance (CCR) among Gram-negative bacilli in aquaculture. Overall, a high incidence of CCR has been reported in aquatic farms in several countries, with CCR being more prevalent among opportunistic human pathogens such as Acinetobacter nosocomialis, Shewanella algae, Photobacterium damselae, Vibrio spp., Aeromonas spp., as well as members of Enterobacteriaceae family. A high proportion of isolates in these studies exhibited wide-spectrum profiles of antimicrobial resistance, highlighting their multidrug-resistance properties (MDR). Several mobile colistin resistance genes (including, mcr-1, mcr-1.1, mcr-2, mcr-2.1, mcr-3, mcr-3.1, mcr-4.1, mcr-4.3, mcr-5.1, mcr-6.1, mcr-7.1, mcr-8.1, and mcr-10.1) and carbapenemase encoding genes (including, blaOXA-48, blaOXA-55, blaNDM, blaKPC, blaIMI, blaAIM, blaVIM, and blaIMP) have been detected in aquatic farms in different countries. The majority of these were carried on MDR Incompatibility (Inc) plasmids including IncA/C, and IncX4, which have been associated with a wide host range of different sources. Thus, there is a risk for the possible spread of resistance genes between fish, their environments, and humans. These findings highlight the need to monitor and regulate the usage of antimicrobials in aquaculture. A multisectoral and transdisciplinary (One Health) approach is urgently needed to reduce the spread of resistant bacteria and/or resistance genes originating in aquaculture and avoid their global reach.202438059867
1727180.9997Coexistence and genomics characterization of mcr-1 and extended-spectrum-β-lactamase-producing Escherichia coli, an emerging extensively drug-resistant bacteria from sheep in China. The emergence of pathogens harboring multiple resistance genes poses a great threat to global public health. However, the coexistence of mobile resistance genes that provide resistance to both third-generation cephalosporins and colistin in sheep-origin Escherichia coli has not been previously investigated in China. This study is the first to characterize five E. coli isolates from sheep in Shaanxi province that harbor both Extended-Spectrum β-Lactamase (ESBL) and mcr-1 resistance genes. The isolates were identified and characterized by Illumina sequencing, nanopore sequencing, bioinformatic analysis, conjugation experiments, and antimicrobial susceptibility testing. Genetic analysis revealed that bla(CTX-M-55) gene, mediated by the IS26, was located on the IncFIB-IncFIC plasmid, while the mcr-1 gene was located on the IncI2(Delta) plasmid. Notably, two copies of bla(CTX-M-55) gene were also identified on the chromosome of one isolate (SX45), facilitated by the ISEcp1 insertion sequence. Additionally, the plasmid pSX23-2 was identified as a complex plasmid derived through homologous recombination of pMG337 from E. coli (MK878890) and pZY-1 from Citrobacter freundii (CP055248). Data mining of publicly available databases revealed that isolates carrying both bla(CTX-M-55) and mcr-1 genes have been found in humans, animals, and the environment, indicating the widespread presence of these critical resistance genes across different niches. Antimicrobial susceptibility testing showed that the five isolates were resistant to a nearly all tested antibiotics, except meropenem. Conjugative transfer experiments demonstrated that the IncFIB-IncFIC and IncI2(Delta) plasmids carrying mcr-1 and bla(CTX-M-55) were capable of transferring between different sequence types (STs) of sheep-origin E. coli, including ST10, ST162, and ST457. This finding suggests the potential for wide dissemination of these resistance markers among diverse E. coli strains. Overall, the characterization of these ESBL and mcr-1 co-harboring isolates enhances our understanding of the spread of these resistance genes in sheep-origin E. coli. Global surveillance of these isolates, particularly within the One Health framework, is essential to monitor and mitigate the risks posed by the dissemination of these resistance genes across various settings.202439426540
1726190.9997Molecular epidemiology and population genomics of tet(X4), bla(NDM) or mcr-1 positive Escherichia coli from migratory birds in southeast coast of China. The emergence of multidrug-resistant (MDR) bacteria harboring tet(X4), bla(NDM) or mcr-1 posed a serious threat to public health. Wild birds, especially migratory birds, were considered as one of important transmission vectors for antibiotic resistance genes (ARGs) globally, however, few studies were performed on the genomic epidemiology of critical resistance genes among them. Isolates harboring tet(X4), mcr-1 or bla(NDM) from migratory birds were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assays, whole genome sequencing and bioinformatics analysis. A total of 14 tet(X4)-bearing E. coli, 4 bla(NDM)-bearing E. coli and 23 mcr-1-bearing E. coli isolates were recovered from 1060 fecal samples of migratory birds. All isolates were MDR bacteria and most plasmids carrying tet(X4), bla(NDM) or mcr-1 were conjugative. We first identified an E. coli of migratory bird origin carrying bla(NDM-4), which was located on a conjugative IncHI2 plasmid and embedded on a novel MDR region flanked by IS26 that could generate the circular intermediate. The emergency of E. coli isolates co-harboring mcr-1 and bla(NDM-5) in migratory birds indicated the coexistence of ARGs in migratory birds was a novel threat. This study revealed the prevalence and molecular characteristics of three important ARGs in migratory birds, provided evidence that migratory birds were potential vectors of novel resistance genes and highlighted the monitoring of ARGs in migratory birds should be strengthened to prevent the spread of ARGs in a One Health strategy.202236084501