Dissemination of Blandm-5 in Escherichia Coli via the Incx3 Plasmid From Different Regions in China

Abstract Background: Recently, the spread of NDM-5-producing Escherichia coli has become a severe challenge in clinical therapy, which necessitates reliable detection and surveillance methods. However, limited information is available regarding the prevalence and dissemination of the blaNDM-5 gene in Escherichia coli in China. Therefore, we investigated the dissemination of the blaNDM-5 gene in carbapenem-resistant Escherichia coli isolates from different regions in China.Methods: A total of 1,180 carbapenem-resistant enterobacteriaceae strains were obtained from patients admitted to the 20 sentinel hospitals in eight cities. Strains positive for blaNDM-5 were detected using the Vitek 2 compact system, 16S rRNA gene sequencing, PCR, the S1-pulsed-field gel electrophoresis assay, and Southern blot hybridization. The horizontal-transfer capability of the blaNDM gene was assessed by filter mating with a standard E. coli J53 azide-resistant strain as the recipient. Genotyping, susceptibility testing, and whole genome sequencing were performed. Results: Seven strains of blaNDM-5-positive E.coli was detected in 1180 clinical strains from different regions in China. The blaNDM-5-carrying strains showed resistance to multiple tested antibiotics and belonged to two widespread sequence types, ST167 and ST405. Antimicrobial resistance genes including blaCTX-M, blaOXA, blaCMY, and two novel blaTEM variants (blaTEM-230 and blaTEM-231) were also identified. Southern blotting located the blaNDM-5 gene on 46-kb IncX3 plasmids in all isolates, which showed only two single nucleotide differences between EJN003 and the other strains. Conclusions: This study further confirms the increasing occurrence of blaNDM-5-carrying IncX3 plasmids and the dissemination of carbapenem resistance in E. coli isolates via the plasmid from different parts in China, which warrants stringent surveillance and control measures.

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Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01345-16 ◽

2016 ◽

Vol 60 (11) ◽

pp. 6795-6805 ◽

Cited By ~ 32

Author(s):

Amit Ranjan ◽

Sabiha Shaik ◽

Agnismita Mondal ◽

Nishant Nandanwar ◽

Arif Hussain ◽

...

Keyword(s):

Escherichia Coli ◽

Effective Means ◽

Genomic Analysis ◽

Virulence Gene ◽

Carbapenem Resistance ◽

Control Measures ◽

Large Sample Size ◽

Gene Repertoire ◽

Content Type ◽

E Coli

ABSTRACTThe global dissemination and increasing incidence of carbapenem-resistant, Gram-negative organisms have resulted in acute public health concerns. Here, we present a retrospective multicenter study on molecular characterization of metallo-β-lactamase (MBL)-producing clinicalEscherichia coliisolates recovered from extraintestinal infections in two hospitals in Pune, India. We screened a large sample size of 510E. coliisolates for MBL production wherein we profiled their molecular determinants, antimicrobial resistance phenotypes, functional virulence properties, genomic features, and transmission dynamics. Approximately 8% of these isolates were MBL producers, the majority of which were of the NDM-1 (69%) type, followed by NDM-5 (19%), NDM-4 (5.5%), and NDM-7 (5.5%). MBL producers were resistant to all antibiotics tested except for colistin, fosfomycin, and chloramphenicol, which were effective to various extents. Plasmids were found to be an effective means of dissemination of NDM genes and other resistance traits. All MBL producers adhered to and invaded bladder epithelial (T24) cells and demonstrated significant serum resistance. Genomic analysis of MBL-producingE. coliisolates revealed higher resistance but a moderate virulence gene repertoire. A subset of NDM-1-positiveE. coliisolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. A majority of MBL-producingE. colistrains revealed unique genotypes, suggesting that they were clonally unrelated. Overall, the coexistence of virulence and carbapenem resistance in clinicalE. coliisolates is of serious concern. Moreover, the emergence of NDM-1 among the globally dominantE. coliST101 isolates warrants stringent surveillance and control measures.

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High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh

Antibiotics ◽

10.3390/antibiotics9110796 ◽

2020 ◽

Vol 9 (11) ◽

pp. 796

Author(s):

Razib Mazumder ◽

Ahmed Abdullah ◽

Dilruba Ahmed ◽

Arif Hussain

Keyword(s):

Escherichia Coli ◽

Carbapenem Resistance ◽

Multidrug Resistant ◽

Control Measures ◽

E Coli ◽

Infection Control Measures ◽

Extended Spectrum ◽

Virulence Potential ◽

High Prevalence ◽

High Virulence

The emergence of multidrug-resistant (MDR) Escherichia coli (E. coli) clonal lineages with high virulence potential is alarming. Lack of sufficient data on molecular epidemiology of such pathogens from countries with high infection burden, such as Bangladesh, hinders management and infection control measures. In this study, we assessed the population structure, virulence potential and antimicrobial susceptibility of clinical E. coli isolates from Dhaka, Bangladesh. A high prevalence of MDR (69%) and extended-spectrum β-lactamase production (ESBL) (51%) was found. Most E. coli isolates were susceptible to amikacin (95%), meropenem (94%) and nitrofurantoin (89%) antibiotics. A high prevalence of ST131 (22%) and ST95 (9%) followed by ST69 (4%) and ST73 (3%) was observed. Phylogroups B2 (46%), B1 (16%), D (10%) and F (9%) were prominent. blaCTX-M-15 (52%) and blaNDM-1 (5%) were the most prevalent ESBL and carbapenem resistance genes, respectively. Moreover, the predominant pathotype identified was extraintestinal pathogenic E. coli (ExPEC) (41%) followed by enteric pathogens (11%). In conclusion, our results suggest the transmission of clonal E. coli groups amidst diverse E. coli population that are associated with high virulence potential and MDR phenotype. This is of high concern and mandates more efforts towards molecular surveillance of antimicrobial resistance (AMR) in clinically significant pathogens.

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Emergence of IncHI2 Plasmid-Harboring blaNDM-5 from Porcine Escherichia coli Isolates in Guangdong, China

Pathogens ◽

10.3390/pathogens10080954 ◽

2021 ◽

Vol 10 (8) ◽

pp. 954

Author(s):

Zhenbao Ma ◽

Zhenling Zeng ◽

Jiao Liu ◽

Chang Liu ◽

Yu Pan ◽

...

Keyword(s):

Escherichia Coli ◽

Susceptibility Testing ◽

Carbapenem Resistance ◽

Guangdong Province ◽

Whole Genome Sequence ◽

Molecular Characteristics ◽

E Coli ◽

Carbapenem Resistant ◽

Genetic Feature ◽

Plasmid Backbone

Carbapenem resistance has posed potential harmful risks to human and animals. The objectives of this study were to understand the prevalence of blaNDM-5 in pigs and investigate the molecular characteristics of NDM-5-producing Escherichia coli isolates in Guangdong province in China. Carbapenem-resistant E. coli isolates were isolated from pigs and obtained using MacConkey plates containing 0.5 mg/L meropenem. Conjugation assay and antimicrobial susceptibility testing were conducted for the isolates and their transconjugants. Whole-genome sequence (WGS) was used to analyze the plasmid genetic feature. A total of five blaNDM-5-carrying E. coli isolates were obtained in the present investigations. They belonged to five ST types. The blaNDM-5 genes were found to be in IncX3 and IncHI2 plasmid. The IncX3 plasmid was 46,161 bp in size and identical to other reports. IncHI2 plasmid was 246,593 bp in size and similar to other IncHI2-ST3 plasmids. It consisted of a typical IncHI2 plasmid backbone region and a multiresistance region (MRR). The blaNDM-5 was closely associated with the IS3000-ISAba125-blaNDM-5-bleMBL-trpF-tat-IS26 unit. We first reported the blaNDM-5-carrying IncHI2 in E. coli isolates recovered from pigs and revealed the molecular characterization. Continued surveillance for the dissemination of blaNDM-5 among food-producing animals is required.

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Genomic characterization of carbapenem resistant Escherichia coli from multiple hospitals in Nanjing, China: focusing on frequent co-occurrence of blaNDM and blaKPC-2

10.21203/rs.3.rs-37813/v2 ◽

2020 ◽

Author(s):

Xiaoli Cao ◽

Jie Zheng ◽

Li Cheng ◽

Wanqing Zhou ◽

Zhifeng Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Control Measures ◽

Potential Threat ◽

E Coli ◽

Infection Control Measures ◽

Carbapenem Resistant ◽

Plasmid Replicon ◽

Drum Tower Hospital ◽

Genomic Characterization

Abstract Background: The increasing emergence of carbapenem resistant Escherichia coli (CREC) poses a potential threat to public health, hence genomic characterization of isolates is needed for a better understanding of its transmission and implementation of infection control measures. Materials and methods：Eleven CREC isolates were collected in 2015 from 6 hospitals in Nanjing, China, and analyzed using whole genome sequencing. Resistance determinants, virulence elements, multi-locus sequence type (MLST), serotypes, phylogeny and fimH types were determined. Results: All of the CREC carried at least one carbapenemase. NDM-5 (n=9) was the most frequent carbapenemase, followed by KPC-2 (n=3) and NDM-1 (n=2); three isolates produced NDM-5 and KPC-2. Ten out of the 11 isolates co-carried blaCTX-M variants. MLST analysis found 7 distinct STs, including ST410 (n=2), ST3489 (n=1), ST156 (n=1), ST683 (n=1), ST297 (n=1), ST167 (n=1), and ST361 (n=1). Six distinct serotypes and 8 Fim types were identified. A great diversity of plasmid profiles was observed with plasmid replicon IncX3 being the most frequent (n=11). Phylogenetic analysis showed great diversity between the 11 CREC isolates and also between 6 additional isolates co-carrying blaNDM and blaKPC which were selected from the strains collection of Nanjing Drum Tower Hospital for comparison. Conjugation assays demonstrated that blaNDM was transferable. Conclusion: NDM is the major carbapenemase among CREC, with NDM-5 being the main variant which can be horizontally disseminated by IncX3 plasmids. These isolates displayed genetic diversity by MLST, Fim typing and serotyping. We herein provided the first report on emergence of NDM-5 producing E. coli ST297, ST683, ST3489, and NDM-1 producing E. coli ST361.

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Characterization of plasmid-mediated quinolone resistance by the qnrS gene in Escherichia coli isolated from healthy chickens and pigs

Veterinární Medicína ◽

10.17221/108/2009-vetmed ◽

2009 ◽

Vol 54 (No. 10) ◽

pp. 473-482 ◽

Cited By ~ 10

Author(s):

H.-C. Kuo ◽

C.-C. Chou ◽

C. Tu ◽

S.-R. Gong ◽

C.-L. Han ◽

...

Keyword(s):

Escherichia Coli ◽

Blot Hybridization ◽

Southern Blot Hybridization ◽

Quinolone Resistance ◽

E Coli ◽

Sequence Variations ◽

Southern Blot Hybridization Analysis ◽

Ciprofloxacin Resistance ◽

Polymerase Chain

The prevalence of qnr and qepA genes in 660 Escherichia coli isolates was investigated in healthy animals from 30 pig farms and 30 chicken farms in Taiwan from January 2005 to February 2006 by the polymerase chain reaction. The qnrS gene, but not qnrA, qnrB, and qepA were detected in 12/360 pig isolates (3.33%) and in 6/300 chicken isolates (2%). Southern blot hybridization analysis indicated that qnrS was located on plasmids ranging in size from 50–165 kb. Eleven of the 18 qnrS positive isolates which showed a high ciprofloxacin resistance phenotype (minimum inhibitory concentration ≥ 8 mg/l) also had amino acid sequence variations in chromosomal quinolone resistance-determining regions of gyrA and parC. Only two qnrS-positive isolates carried the aac(6’)-Ib-crvariant that mediates FQ acetylation. For the high percentage resistance of cephalosporins, the blaCTX-M gene was also examined in qnrS-positive isolates. The blaCTX-M gene was detected in fifteen isolates (15/18, 83.3%) of which 12 isolates were blaCTX-M-1 and three isolates were blCTX-M-15. This study demonstrated a close linkage between the qnrS gene and blaCTX-M-1, suggesting CTX-M and Qnr-based mechanisms might be co-emerging in E. coli strains isolated from healthy chickens and pigs under selective pressure of quinolone and cephalosporine administration.

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Characteristics of Cefotaxime-Resistant Escherichia coli from Wild Birds in The Netherlands

Applied and Environmental Microbiology ◽

10.1128/aem.01880-13 ◽

2013 ◽

Vol 79 (24) ◽

pp. 7556-7561 ◽

Cited By ~ 39

Author(s):

Kees Veldman ◽

Peter van Tulden ◽

Arie Kant ◽

Joop Testerink ◽

Dik Mevius

Keyword(s):

Escherichia Coli ◽

The Netherlands ◽

Blot Hybridization ◽

Bird Species ◽

Southern Blot Hybridization ◽

Wild Birds ◽

Content Type ◽

E Coli ◽

Associated Species ◽

Wide Dissemination

ABSTRACTCloacal swabs from carcasses of Dutch wild birds obtained in 2010 and 2011 were selectively cultured on media with cefotaxime to screen for the presence of extended-spectrum β-lactamase (ESBL)/AmpC-producingEscherichia coli. Subsequently, all cefotaxime-resistantE. coliisolates were tested by broth microdilution and microarray. The presence of ESBL/AmpC and coexisting plasmid-mediated quinolone resistance (PMQR) genes was confirmed by PCR and sequencing. To determine the size of plasmids and the location of ESBL and PMQR genes, S1 pulsed-field gel electrophoresis (PFGE) was performed on transformants, followed by Southern blot hybridization. The study included 414 cloacal swabs originating from 55 different bird species. Cefotaxime-resistantE. coliisolates were identified in 65 birds (15.7%) from 21 different species. In all, 65 cefotaxime-resistantE. coliESBL/AmpC genes were detected, mainly comprising variants ofblaCTX-MandblaCMY-2. Furthermore, PMQR genes [aac(6′)-lb-cr,qnrB1, andqnrS1] coincided in seven cefotaxime-resistantE. coliisolates. Overall, replicon typing of the ESBL/AmpC-carrying plasmids demonstrated the predominant presence of IncI1 (n= 31) and variants of IncF (n= 18). Our results indicate a wide dissemination of ESBL and AmpC genes in wild birds from The Netherlands, especially among aquatic-associated species (waterfowl, gulls, and waders). The identified genes and plasmids reflect the genes found predominantly in livestock animals as well as in humans.

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Clinical and Microbiological Characteristics of a Community-Acquired Carbapenem-Resistant Escherichia coli ST410 Isolate Harbouring blaNDM-5-Encoding IncX3-Type Plasmid From Blood

Frontiers in Medicine ◽

10.3389/fmed.2021.658058 ◽

2021 ◽

Vol 8 ◽

Author(s):

Ji-Na Gu ◽

Lin Chen ◽

Xing-Bei Weng ◽

Xiao-Yan Yang ◽

Dan-Mei Pan

Keyword(s):

Escherichia Coli ◽

Antimicrobial Susceptibility ◽

Screening Test ◽

Faecal Sample ◽

Sequence Data ◽

Control Measures ◽

Whole Genome Sequence ◽

E Coli ◽

Carbapenem Resistant ◽

Microbiological Characteristics

Objectives: The aim of this research was to investigate the clinical and microbiological characteristics of a case of community-acquired carbapenem-resistant Escherichia coli isolated from a patient with a bloodstream infection in China.Methods:Escherichia coli Huamei202001 was recovered from the first blood culture from a patient hospitalised in China. An antimicrobial susceptibility test was performed, and the genome was sequenced on an Illumina HiSeq X 10 platform with a 150-bp paired-end approach. The generated sequence reads were assembled using Unicycler, and the whole genome sequence data were analysed using bioinformatics tools. Moreover, the patient and her main family members obtained a faecal sample screening test for CRE, the positive strain was further isolated and the identification and antimicrobial susceptibility testing was performed.Results:Escherichia coli Huamei202001 belonged to sequence type 410. In addition, a blaNDM-5-encoding IncX3-type plasmid was responsible for the spreading of carbapenem resistance. Only the patient was detected as having a positive faecal sample screening test for CRE. Strain Fec01 was identified as E. coli, and the antibiotic susceptibility profile was the same as that of E. coli Huamei202001.Conclusions:Escherichia coli Huamei202001 is defined as community-acquired carbapenem-resistant Enterobacteriaceae. The clone ST410 that harbours the blaNDM-5-encoding IncX3-type plasmid is causing new high-risk clones globally. Thus, infection control measures should be strengthened to curb the dissemination of IncX3.

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Genomic characterization of carbapenem resistant Escherichia coli from multiple hospitals in Nanjing, China: focusing on frequent co-occurrence of blaNDM and blaKPC-2

10.21203/rs.3.rs-37813/v1 ◽

2020 ◽

Author(s):

Xiaoli Cao ◽

Jie Zheng ◽

Li Cheng ◽

Wanqing Zhou ◽

Zhifeng Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Control Measures ◽

Potential Threat ◽

E Coli ◽

Infection Control Measures ◽

Carbapenem Resistant ◽

Plasmid Replicon ◽

Drum Tower Hospital ◽

Genomic Characterization

Abstract Background The increasing emergence of carbapenem resistant Escherichia coli (CREC) poses a potential threat to public health, hence genomic characterization of isolates is needed for a better understanding of its transmission and implementation of infection control measures. Materials and methods Eleven CREC isolates were collected in 2015 from 6 hospitals in Nanjing, China, and analyzed using whole genome sequencing. Resistance determinants, virulence elements, multi-locus sequence type (MLST), serotypes, phylogeny and fimH types were determined. Results All of the CREC carried at least one carbapenemase. NDM-5 (n = 9) was the most frequent carbapenemase, followed by KPC-2 (n = 3) and NDM-1 (n = 2); three isolates produced NDM-5 and KPC-2. Ten out of the 11 isolates co-carried blaCTX-M variants. MLST analysis found 7 distinct STs, including ST410 (n = 2), ST3489 (n = 1), ST156 (n = 1), ST683 (n = 1), ST297 (n = 1), ST167 (n = 1), and ST361 (n = 1). Six distinct serotypes and 8 Fim types were identified. A great diversity of plasmid profiles was observed with plasmid replicon IncX3 being the most frequent (n = 11). Phylogenetic analysis showed great diversity between the 11 CREC isolates and also between 6 additional isolates co-carrying blaNDM and blaKPC which were selected from the strains collection of Nanjing Drum Tower Hospital for comparison. Conjugation assays demonstrated that blaNDM was transferable. Conclusion NDM is the major carbapenemase among CREC, with NDM-5 being the main variant which can be horizontally disseminated by IncX3 plasmids. These isolates displayed genetic diversity by MLST, Fim typing and serotyping. We herein provided the first report on emergence of NDM-5 producing E. coli ST297, ST683, ST3489, and NDM-1 producing E. coli ST361.

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Activity of Cefiderocol, Ceftazidime-Avibactam, and Eravacycline against Carbapenem-Resistant Escherichia coli Isolates from the United States and International Sites in Relation to Clonal Background, Resistance Genes, Coresistance, and Region

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00797-20 ◽

2020 ◽

Vol 64 (10) ◽

Cited By ~ 1

Author(s):

Brian D. Johnston ◽

Paul Thuras ◽

Stephen B. Porter ◽

Melissa Anacker ◽

Brittany VonBank ◽

...

Keyword(s):

Escherichia Coli ◽

Carbapenem Resistance ◽

The United States ◽

Asia Pacific ◽

Beta Lactamase ◽

Content Type ◽

Beta Lactamases ◽

E Coli ◽

Carbapenem Resistant ◽

Primary Agent

ABSTRACT Emerging carbapenem resistance in Escherichia coli, including sequence type 131 (ST131), the leading cause of extraintestinal E. coli infections globally, threatens therapeutic efficacy. Accordingly, we determined broth microdilution MICs for three distinctive newer agents, i.e., cefiderocol (CFDC), ceftazidime-avibactam (CZA), and eravacycline (ERV), plus 11 comparators, against 343 carbapenem-resistant (CR) clinical E. coli isolates, then compared susceptibility results with bacterial characteristics and region. The collection comprised 203 U.S. isolates (2002 to 2017) and 141 isolates from 17 countries in Europe, Latin America, and the Asia-West Pacific region (2003 to 2017). Isolates were characterized for phylogenetic group, resistance-associated sequence types (STs) and subsets thereof, and relevant beta-lactamase-encoding genes. CFDC, CZA, and ERV exhibited the highest percent susceptible (82% to 98%) after tigecycline (TGC) (99%); avibactam improved CZA's activity over that of CAZ (11% susceptible). Percent susceptible varied by phylogroup and ST for CFDC and CZA (greatest in phylogroups B2, D, and F, and in ST131, ST405, and ST648). Susceptibility also varied by resistance genotype, being higher with the Klebsiella pneumoniae carbapenemase (KPC) for CZA, lower with metallo-beta-lactamases for CFDC and CZA, and higher with the beta-lactamase CTX-M for ERV. Percent susceptible also varied by global region for CZA (lower in Asia-Pacific) and by U.S. region for ERV (lower in the South and Southeast). Although resistance to comparators often predicted reduced susceptibility to a primary agent (especially CFDC and CZA), even among comparator-resistant isolates the primary-agent-susceptible fraction usually exceeded 50%. These findings clarify the likely utility of CFDC, CZA, and ERV against CR E. coli in relation to multiple bacterial characteristics and geographical region.

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Activity of Imipenem-Relebactam against Carbapenem-Resistant Escherichia coli Isolates from the United States in Relation to Clonal Background, Resistance Genes, Coresistance, and Region

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02408-19 ◽

2020 ◽

Vol 64 (5) ◽

Cited By ~ 2

Author(s):

Brian D. Johnston ◽

Paul Thuras ◽

Stephen B. Porter ◽

Melissa Anacker ◽

Brittany VonBank ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Carbapenem Resistance ◽

The United States ◽

Resistance Mechanisms ◽

Beta Lactamase ◽

Content Type ◽

E Coli ◽

Highly Active ◽

Carbapenem Resistant

ABSTRACT Imipenem-relebactam (I-R) is a recently developed carbapenem–beta-lactamase inhibitor combination agent that can overcome carbapenem resistance, which has now emerged in Escherichia coli, including sequence type 131 (ST131) and its fluoroquinolone-resistant H30R subclone, the leading cause of extraintestinal E. coli infections globally. To clarify the likely utility of I-R for carbapenem-resistant (CR) E. coli infections in the United States, we characterized 203 recent CR clinical E. coli isolates from across the United States (years 2002 to 2017) for phylogroup, clonal group (including ST131, H30R, and the CTX-M-15-associated H30Rx subset within H30R), relevant beta-lactamase genes, and broth microdilution MICs for I-R and 11 comparator agents. Overall, I-R was highly active (89% susceptible), more so than all comparators except tigecycline and colistin (both 99% susceptible). I-R’s activity varied significantly in relation to phylogroup, clonal background, resistance genotype, and region. It was greatest among phylogroup B2, ST131-H30R, H30Rx, Klebsiella pneumoniae carbapenemase (KPC)-positive, and northeast U.S. isolates and lowest among phylogroup C, New Delhi metallo-β-lactamase (NDM)-positive, and southeast U.S. isolates. Relebactam improved imipenem’s activity against CR isolates within each phylogroup—especially groups A, B1, and B2—and particularly against isolates containing KPC. I-R remained substantially active against isolates coresistant to comparator agents, albeit somewhat less so than against the corresponding susceptible isolates. These findings suggest that I-R should be useful for treating most CR E. coli infections in the United States, largely independent of coresistance, although this likely will vary in relation to the local prevalence of specific E. coli lineages and carbapenem resistance mechanisms.

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