Shelter dogs as reservoirs of international clones of Escherichia coli carrying mcr-1.1 and bla(CTX-M) resistance genes in Lima, Peru. - Related Documents




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174201.0000Shelter dogs as reservoirs of international clones of Escherichia coli carrying mcr-1.1 and bla(CTX-M) resistance genes in Lima, Peru. Antimicrobial resistance (AMR) poses a critical public health threat worldwide, particularly at the human-animal interface where cross-transmission of critical priority Enterobacterales, such as Escherichia coli, have become increasingly reported. Worryingly, E. coli encoding extended-spectrum β-lactamases (ESBLs) has been documented in companion animals worldwide. Conversely, the presence of mcr genes, which confer resistance to polymyxins, in bacteria from pets remains more infrequent. In this study, we sequenced and reported on the first genomic data of E. coli strains carrying mcr-1 and/or bla(CTX-M) genes isolated from rectal swabs of stray dogs in a shelter in the city of Lima, Peru. Antimicrobial susceptibility revealed that E. coli strains exhibited a multidrug resistance profile. In addition to mcr-1 and bla(CTX-M) genes, other clinically relevant resistance determinants were identified, with notably presence of bla(TEM-176) and the novel bla(SCO-2) variant. The association of mcr-1.1 and IncI2 plasmid was confirmed. Several virulence genes were detected, classifying strains as putative extraintestinal pathogenic E. coli. Multilocus sequence typing prediction recognized diverse sequence types (ST), including ST155, ST189, ST657, ST746, ST1140, ST3014, and ST7188. This study represents the first report of mcr-positive E. coli in dogs from Peru, emphasizing the need for continuous surveillance and genomic characterization to better understand the transmission dynamics of these critical resistance genes at the human-animal interface. Furthermore, our results provide evidence that stray, and shelter dogs could be a reservoir for the spread of WHO priority pathogens, and/or polymyxin and β-lactam resistance genes, which is a public health and One Health concern that requires appropriate management strategies.202540339258
163710.9997Genomic 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
174320.9997International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil. CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried bla(CTX-M) -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.202032239649
172730.9997Coexistence 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
189140.9997Emergence of plasmid-mediated fosfomycin resistance among Escherichia coli harboring fosA4, tet(X4), and mcr-1 genes in wild birds. Fosfomycin represents a last-line reserve antibiotic for the treatment of infections caused by multidrug-resistant (MDR) bacteria. Nevertheless, the advent of plasmid-mediated fosfomycin resistance among bacteria from humans and food animals incurs great concern. This study reports the detection and genomic portrait of the plasmid-mediated fosfomycin resistance gene, fosA4, amid Escherichia coli from wild birds co-harboring plasmid-mediated tigecycline resistance gene, tet(X4), and colistin resistance gene, mcr-1. A total of 100 samples from fecal droppings of wild birds in the urban parks in Faisalabad, Pakistan were subjected for the isolation and characterization of fosfomycin-resistant E. coli. The fosA4 gene was identified in 11 (11%) of the E. coli isolates, and all exhibited an MDR phenotype. Genome sequencing confirmed that all the fosA4-positive isolates also co-harbored the mobile tigecycline resistance tet(X4) gene on a large MDR IncFII plasmid. One isolate PKF8 belonging to ST48 also co-carried the colistin resistance gene mcr-1 on the IncHI2 plasmid. To the extent of our knowledge, this is the first discovery of E. coli isolates in wild birds co-harboring the mcr-1, fosA4, and tet(X4) genes. The emergence of these pivotal antimicrobial resistance genes in wild birds native to South Asia with their close association to humans and animals is alarming. Our findings highlight the urgent need for further surveillance of bacterial resistance to last-resort antibiotics in the clinics, animal farming, and environment with the One Health approach. IMPORTANCE: The global spread of the plasmid-mediated fosfomycin resistance gene fosA4 bearing Escherichia coli strains incurs a public health concern. However, research focusing on the pervasiveness of fosA4-positive isolates in wild birds is still rare, and to the best of our knowledge, this is the first documentation from South Asia highlighting the concurrent presence of the fosA4, mcr-1, and tet(X4) genes within E. coli isolates recovered from fecal samples of wild birds in Pakistan. This co-existence of ARGs along with phylogenetic analysis revealed that MDR plasmids carried by E. coli isolates have the ability to spread horizontally between wild birds, food animals, and humans. Co-existence of fosA4, tet(X4), and mcr-1-carrying plasmids is worrying and warrants further investigation.202540079598
172550.9997Letter to the Editor: Escherichia fergusonii Harboring IncHI2 Plasmid Containing mcr-1 Gene-A Novel Reservoir for Colistin Resistance in Brazil. Emergence of colistin-resistant bacteria harboring mobile colistin resistance genes (mcr genes) pose a threat for food-producing animals and humans. In this article, we aim to highlight the emergence of Escherichia fergusonii as an important new reservoir to mcr-1-harboring plasmid in poultry production. Three strains closely related were isolated from cloacal swabs. Their genome contains four plasmids, including a 182,869 bp IncHI2 plasmid harboring the colistin resistance gene mcr-1. These results will contribute to our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii.202133001761
263760.9997Potentially Pathogenic Multidrug-Resistant Escherichia coli in Lamb Meat. Extended-spectrum cephalosporin (ESC) resistance remains a threat since ESC are important antimicrobials used to treat infections in humans and animals. Escherichia coli is an important source of ESC-resistance genes, such as those encoding extended-spectrum β-lactamases (ESBLs). E. coli is a common commensal of lambs. Reports that contaminated food can be a source of ESC-resistant bacteria in humans and that ESBL-producing E. coli are found in sheep in Brazil led us to survey their presence in retail lamb meat. Twenty-five samples intended for human consumption were screened for ESC-resistant E. coli, and the isolates were characterized. IncI1-bla(CTX-M-8) and IncHI2-bla(CTX-M-2) were the main plasmids responsible for ESC resistance. The plasmids harbored common ESBL genes in Enterobacteriaceae from food-producing animals in Brazil. IncI1-bla(CTX-M-14) and IncF-bla(CTX-M-55) plasmids, associated with human infections, were also detected. Few CTX-M-producing E. coli have been clustered by typing methods, and some may be genetically pathogenic. The findings indicate the presence of diverse strains of E. coli, harboring important ESBL genes, in lamb meat in Brazil. Surveillance of ESC-resistant bacteria could reduce the spread of antimicrobial resistance through the food chain.202133417827
163870.9997First 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
158980.9997Clonal Complexes 23, 10, 131 and 38 as Genetic Markers of the Environmental Spread of Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli. In accordance with the global action plan on antimicrobial resistance adopted by the World Health Assembly in 2015, there is a need to develop surveillance programs for antimicrobial resistant bacteria. In this context, we have analyzed the clonal diversity of Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from aquatic environments and human and food samples in Spain, with the aim of determining possible clonal complexes (CCs) that act as markers of the potential risk of transmission of these resistant bacteria. The phylogenetic groups, sequence types (STs) and CCs were determined by different Polymerase Chain Reaction (PCR) and Multilocus Sequence Typing (MLST) techniques. Phylogroup A was prevalent and was mainly present in food and water strains, while human strains were mostly associated with phylogroup B2. According to the observed prevalence in the different niches, CC23 and CC10 are proposed as markers of phylogroups A and C, related with the spread of bla(CTX-M1) and bla(CTX-M15) genes. Similarly, CC131 and CC38 could be associated to the dissemination of pathogenic strains (phylogroups B2 and D) carrying mainly bla(CTX-M14) and bla(CTX-M15) genes. Some strains isolated from wastewater treatment plants (WWTPs) showed identical profiles to those isolated from other environments, highlighting the importance that water acquires in the dissemination of bacterial resistance. In conclusion, the detection of these genetic markers in different environments could be considered as an alert in the spread of ESBL.202236358120
160790.9997mcr-1 colistin resistance gene sharing between Escherichia coli from cohabiting dogs and humans, Lisbon, Portugal, 2018 to 2020. BackgroundThe emergence of colistin resistance is a One Health antimicrobial resistance challenge worldwide. The close contact between companion animals and humans creates opportunities for transmission and dissemination of colistin-resistant bacteria.AimTo detect potential animal reservoirs of colistin-resistant Escherichia coli and investigate the possible sharing of these bacteria between dogs, cats and their cohabiting humans in the community in Lisbon, Portugal.MethodsA prospective longitudinal study was performed from 2018 to 2020. Faecal samples from dogs and cats either healthy or diagnosed with a skin and soft tissue or urinary tract infection, and their cohabiting humans were screened for the presence of colistin-resistant E. coli. All isolates were tested by broth microdilution against colistin and 12 other antimicrobials. Colistin-resistant isolates were screened for 30 resistance genes, including plasmid-mediated colistin resistance genes (mcr-1 to mcr-9), and typed by multilocus sequence typing. Genetic relatedness between animal and human isolates was analysed by whole genome sequencing.ResultsColistin-resistant E. coli strains harbouring the mcr-1 gene were recovered from faecal samples of companion animals (8/102; 7.8%) and humans (4/125; 3.2%). No difference between control and infection group was detected. Indistinguishable multidrug-resistant E. coli ST744 strains harbouring the mcr-1 gene were found in humans and their dogs in two households.ConclusionsThe identification of identical E. coli strains containing the plasmid-mediated mcr-1 gene in companion animals and humans in daily close contact is of concern. These results demonstrate the importance of the animal-human unit as possible disseminators of clinically important resistance genes in the community setting.202236330821
1842100.9997Emergence 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
1726110.9997Molecular 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
1612120.9997Carriage of antimicrobial resistant Escherichia coli in dogs: Prevalence, associated risk factors and molecular characteristics. Resistance to antimicrobials, in particular that mediated by extended spectrum β-lactamases (ESBL) and AmpC β-lactamases are frequently reported in bacteria causing canine disease as well as in commensal bacteria, which could be a potential health risk for humans they come into contact with. This cross-sectional study aimed to estimate the prevalence and investigate the molecular characteristics of ESBL and plasmid encoded AmpC (pAmpC)-producing E. coli in the mainland UK vet-visiting canine population and, using responses from detailed questionnaires identify factors associated with their carriage. Faecal samples were cultured for antimicrobial resistant (AMR), ESBL and pAmpC-producing E. coli. A subset of ESBL and pAmpC-producing isolates were subjected to multi-locus sequence typing and DNA microarray analyses. Multivariable logistic regression analysis was used to construct models to identify risk factors associated with multidrug resistant (MDR, resistance to three or more antimicrobial classes), fluoroquinolone resistant, ESBL and AmpC-producing E. coli. AMR E.coli were isolated from 44.8% (n=260) of samples, with 1.9% and 7.1% of samples carrying ESBL and pAmpC-producing E. coli, respectively. MDR E. coli were identified in 18.3% of samples. Recent use of antimicrobials and being fed raw poultry were both identified as risk factors in the outcomes investigated. A number of virulence and resistance genes were identified, including genes associated with extra-intestinal and enteropathogenic E. coli genotypes. Considering the close contact that people have with dogs, the high levels of AMR E. coli in canine faeces may be a potential reservoir of AMR bacteria or resistance determinants.201728110781
1527130.9996Emergence of an Escherichia coli strain co-harbouring mcr-1 and bla(NDM-9) from a urinary tract infection in Taiwan. OBJECTIVES: Multidrug-resistant bacteria have become a serious threat worldwide. In particular, the coexistence of carbapenemase genes and mcr-1 leaves few available treatment options. Here we report a multidrug-resistant Escherichia coli isolate harbouring both mcr-1 and bla(NDM-9) from a patient with a urinary tract infection. METHODS: Antimicrobial susceptibility and resistance genes of the E. coli isolate were characterised. Furthermore, the assembled genome sequences of mcr-1- and bla(NDM-9)-carrying plasmids were determined and comparative genetic analysis with closely related plasmids was carried out. RESULTS: Three contigs were assembled comprising the E. coli chromosome and two plasmids harbouring mcr-1 (p5CRE51-MCR-1) and bla(NDM-9) (p5CRE51-NDM-9), respectively. Whole-genome sequencing revealed that the two antimicrobial resistance genes are located on individual plasmids. CONCLUSIONS: The emergence of coexistence of carbapenemase genes and mcr-1 in Enterobacteriaceae highlights a serious threat to antimicrobial therapy.201930312830
1636140.9996Widespread high-risk clones of multidrug-resistant extended-spectrum β-lactamase-producing Escherichia coli B2-ST131 and F-ST648 in public aquatic environments. Aquatic environments are considered a reservoir for the dissemination of multidrug-resistant (MDR) bacteria, principally Escherichia coli, with the consequent spread of acquired antimicrobial resistance genes (ARGs). Widespread high-risk clones of MDR E. coli are responsible for human infections worldwide. This study aimed to characterise, through whole-genome sequencing (WGS), isolates of MDR E. coli harbouring ARGs obtained from public aquatic environments in Brazil. MDR E. coli isolates were obtained from rivers, streams and lakes that presented different Water Quality Index records and were submitted to WGS. The resistome, mobilome and virulome showed a great diversity of ARGs, plasmids and virulence genes, respectively. In addition, mutations in the quinolone resistance-determining regions of GyrA, ParC and ParE as well as several metal resistance genes (MRGs) and antibacterial biocide resistance genes (ABGs) were detected. Typing and subtyping of MDR E. coli revealed different lineages, with two belonging to widespread high-risk clones (i.e. B2-ST131-fimH30 and F-ST648-fimH27), which are grouped by core genome multilocus sequence typing (cgMLST) in clusters with E. coli lineages obtained from different sources distributed worldwide. MDR bacteria carrying MRGs and ABGs have emerged as a global human and environmental health problem. Detection of widespread high-risk clones calls for attention to the dissemination of fluoroquinolone-resistant QnrS1- and CTX-M-producing E. coli lineages associated with human infections in public aquatic environments.202032479889
1887150.9996Complete Genetic Analysis of Plasmids Carrying mcr-1 and Other Resistance Genes in Avian Pathogenic Escherichia coli Isolates from Diseased Chickens in Anhui Province in China. Antimicrobial resistance associated with colistin has emerged as a significant concern worldwide, threatening the use of one of the most important antimicrobials for treating human disease. This study aimed to investigate the prevalence of colistin-resistant avian-pathogenic Escherichia coli (APEC) and shed light on the possibility of transmission of mcr-1 (mobilized colistin resistance)-positive APEC. A total of 72 APEC isolates from Anhui Province in China were collected between March 2017 and December 2018 and screened for the mcr-1 gene. Antimicrobial susceptibility testing was performed using the broth dilution method. Pulsed-field gel electrophoresis, Southern blot analysis, and conjugation assay were performed to determine the location and conjugative ability of the mcr-1 gene. Whole-genome sequencing and analysis were performed using Illumina MiSeq and Nanopore MinION platforms. Three APEC isolates (AH25, AH62, and AH65) were found to be positive for the mcr-1 gene and showed multidrug resistance. The mcr-1 genes were located on IncI2 plasmids, and conjugation assays revealed that these plasmids were transferrable. Notably, strains AH62 and AH65, both belonging to ST1788, were collected from different places but carried the same drug resistance genes and shared highly similar plasmids. This study highlights the potential for a possible epidemic of mcr-1-positive APEC and the urgent need for continuous active monitoring.IMPORTANCE In this study, three plasmids carrying mcr-1 were isolated and characterized from APEC isolates from Anhui Province in China. The mcr-1 genes were located on IncI2 plasmids, and these plasmids were transferrable. These three IncI2 plasmids had high homology with the plasmids harbored by pathogenic bacteria isolated from other species. This finding showed that IncI2 plasmids poses a risk for the exchange of genetic material between different niches. Although colistin has been banned for use in food-producing animals in China, the coexistence of the broad-spectrum β-lactamase and mcr-1 genes on a plasmid can also lead to the stable existence of mcr-1 genes. The findings illustrated the need to improve the monitoring of drug resistance in poultry systems so as to curb the transmission or persistence of multidrug-resistant bacteria.202133853876
1854160.9996Whole 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
1526170.9996Carbapenem 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
1729180.9996Plasmid-Borne and Chromosomal ESBL/AmpC Genes in Escherichia coli and Klebsiella pneumoniae in Global Food Products. Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular Escherichia coli and Klebsiella pneumoniae, with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Products originated from 35 countries from six continents and represented four food categories: vegetables (n = 60), fruits and berries (n = 50), meat (n = 60), and seafood (n = 30). Additionally, subsamples (n = 40) were taken from broiler meat. Samples were screened for ESBL/AmpC-producing Enterobacteriaceae and whole genome sequenced to identify resistance and virulence genes and sequence types (STs). To accurately identify plasmids harboring resistance and virulence genes, a hybrid sequence analysis combining long- and short-read sequencing was employed. Sequences were compared to previously published plasmids to identify potential epidemic plasmid types. Altogether, 14 out of 200 samples were positive for ESBL/AmpC-producing E. coli and/or K. pneumoniae. Positive samples were recovered from meat (18%; 11/60) and vegetables (5%; 3/60) but were not found from seafood or fruit. ESBL/AmpC-producing E. coli and/or K. pneumoniae was found in 90% (36/40) of broiler meat subsamples. Whole genome sequencing of selected isolates (n = 21) revealed a wide collection of STs, plasmid replicons, and genes conferring multidrug resistance. bla (CTX-M-15)-producing K. pneumoniae ST307 was identified in vegetable (n = 1) and meat (n = 1) samples. Successful IncFII plasmid type was recovered from vegetable and both IncFII and IncI1-Iγ types from meat samples. Hybrid sequence analysis also revealed chromosomally located beta-lactamase genes in two of the isolates and indicated similarity of food-derived plasmids to other livestock-associated sources and also to plasmids obtained from human clinical samples from various countries, such as IncI type plasmid harboring bla (TEM-52C) from a human urine sample obtained in the Netherlands which was highly similar to a plasmid obtained from broiler meat in this study. Results indicate certain foods contain bacteria with multidrug resistance and pose a possible risk to public health, emphasizing the importance of surveillance and the need for further studies on epidemiology of epidemic plasmids.202133613476
1902190.9996Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients. INTRODUCTION: In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates. METHODS: The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination. RESULTS: The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the bla(KPC-2), bla(NDM-5), bla(OXA-1), bla(OXA-48), and bla(OXA-181) β-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the β-lactamase gene clusters in plasmid contigs that carried the same AMR genes. DISCUSSION: Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.202337323902