Genomic Characterization of ESBL-producing Escherichia coli Isolates Belonging to a Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Human Diarrheagenic Isolates, Meat, Poultry and Wildlife

Different surveillance studies (2005-2015) on the presence of ESBL-producing E. coli in the northwest Spain revealed that eae-positive isolates of serotype O153:H10 were periodically detected in meat (of beef, chicken and pork), and also implicated in human diarrhea. This study aimed: i) to characterize the degree of relatedness between human and animal isolates; ii) to know if this was a geographically restricted or disseminated genetic lineage. Thirty-two isolates were conventionally typified as O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1, being 21 of those CTX-M-32 or SHV-12 producers. PFGE comparison of their macrorestriction profiles showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like. Besides, the core genome investigation based on the cgMLST scheme from Enterobase, proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of clonal group O153:H10-A-ST10 (CH11-54) would be playing a successful role in spreading ESBLs (CTX-M-32) in our region within different hosts, including wildlife. It would be potentially implicated in human diarrhea via food (meat) transmission. Importantly, we proved genomic evidence of a related hybrid aEPEC/ExPEC in other countries.

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Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic Samples

Antibiotics ◽

10.3390/antibiotics9040192 ◽

2020 ◽

Vol 9 (4) ◽

pp. 192 ◽

Cited By ~ 3

Author(s):

Dafne Díaz-Jiménez ◽

Isidro García-Meniño ◽

Alexandra Herrera ◽

Vanesa García ◽

Ana María López-Beceiro ◽

...

Keyword(s):

Escherichia Coli ◽

Core Genome ◽

Animal Origin ◽

Human Consumption ◽

Surveillance Studies ◽

Genomic Characterization ◽

Close Relatedness ◽

Stable Combination ◽

Genomic Relatedness

Different surveillance studies (2005–2015) in northwest Spain revealed the presence of eae-positive isolates of Escherichia coli O153:H10 in meat for human consumption, poultry farm, wildlife and human diarrheagenic samples. The aim of this study was to explore the genetic and genomic relatedness between human and animal/meat isolates, as well as the mechanism of its persistence. We also wanted to know whether it was a geographically restricted lineage, or whether it was also reported elsewhere. Conventional typing showed that 32 isolates were O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1. Amongst these, 21 were CTX-M-32 or SHV-12 producers. The PFGE XbaI-macrorestriction comparison showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like plasmids. The core genome investigation based on the cgMLST scheme from EnteroBase proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of the clonal group O153:H10-A-ST10 (CH11-54) is circulating in our region within different hosts, including wildlife. It seems implicated in human diarrhea via meat transmission, and in the spreading of ESBL genes (mainly of CTX-M-32 type). We found genomic evidence of a related hybrid aEPEC/ExPEC in at least one other country.

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Detection of Multiple-Antimicrobial Resistance and Characterization of the Implicated Genes in Escherichia coli Isolates from Foods of Animal Origin in Tunis

Journal of Food Protection ◽

10.4315/0362-028x-72.5.1082 ◽

2009 ◽

Vol 72 (5) ◽

pp. 1082-1088 ◽

Cited By ~ 20

Author(s):

AHLEM JOUINI ◽

KARIM BEN SLAMA ◽

YOLANDA SÁENZ ◽

NAOUEL KLIBI ◽

DANIELA COSTA ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Food Samples ◽

Animal Origin ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Class 1 ◽

Agar Dilution

Phenotypic and genotypic characterization of antimicrobial resistance was conducted for 98 Escherichia coli isolates recovered from 40 food samples of animal origin (poultry, sheep, beef, fish, and others) obtained in supermarkets and local butcheries in Tunis during 2004 and 2005. Susceptibility to 15 antimicrobial agents was tested by disk diffusion and agar dilution methods, the mechanisms of resistance were evaluated using PCR and sequencing methods, and the clonal relationship among isolates was evaluated using pulsed-field gel electrophoresis. High resistance was detected to tetracycline, sulphonamides, nalidixic acid, ampicillin, streptomycin, and trimethoprim-sulfamethoxazole (29 to 43% of isolates), but all isolates were susceptible to cefotaxime, ceftazidime, cefoxitin, azthreonam, and amikacin. One-third of the isolates had multiresistant phenotypes (resistance to at least five different families of antimicrobial agents). Different variants of blaTEM, tet, sul, dfrA, aadA, and aac(3) genes were detected in most of the strains resistant to ampicillin, tetracycline, sulphonamide, trimethoprim, streptomycin, and gentamicin, respectively. The presence of class 1 and class 2 integrons was studied in 15 sulphonamide-resistant unrelated E. coli strains, and 14 of these strains harbored class 1 integrons with five different arrangements of gene cassettes, and a class 2 integron with the dfrA1 + sat + aadA1 arrangement was found in one strain. This study revealed the high diversity of antimicrobial resistance genes, some of them included in integrons, in E. coli isolates of food origin.

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Genomic Characterization of a Proteus sp. Strain of Animal Origin Co-Carrying blaNDM-1 and lnu(G)

Antibiotics ◽

10.3390/antibiotics10111411 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1411

Author(s):

Ying Li ◽

Yichuan Qiu ◽

Junping She ◽

Xu Wang ◽

Xiaoyi Dai ◽

...

Keyword(s):

Resistance Genes ◽

Treatment Options ◽

Antibiotic Resistance Genes ◽

Animal Origin ◽

Global Public Health ◽

Carbapenem Resistant ◽

Extensive Drug Resistance ◽

Genetic Features ◽

Genomic Characterization

The emergence of carbapenem-resistant Proteus represents a serious threat to global public health due to limited antibiotic treatment options. Here, we characterize a Proteus isolate NMG38-2 of swine origin that exhibits extensive drug resistance, including carbapenems. Whole-genome sequencing based on Illumina and MinION platforms showed that NMG38-2 contains 24 acquired antibiotic resistance genes and three plasmids, among which, pNDM_NMG38-2, a pPvSC3-like plasmid, is transferable and co-carries blaNDM-1 and lnu(G). Sequence analysis of pPvSC3-like plasmids showed that they share a conserved backbone but have a diverse accessory module with complex chimera structures bearing abundant resistance genes, which are facilitated by transposons and/or homologous recombination. The acquisition of blaNDM-1 in pNDM_NMG38-2 was due to the ISCR1-mediated integration event. Comprehensive analysis of the lnu(G)-bearing cassettes carried by bacterial plasmids or chromosomes revealed a diversification of its genetic contexts, with Tn6260 and ISPst2 elements being the leading contributors to the dissemination of lnu(G) in Enterococcus and Enterobacteriaceae, respectively. In conclusion, this study provides a better understanding of the genetic features of pPvSC3-like plasmids, which represent a novel plasmid group as a vehicle mediating the dissemination of blaNDM-1 among bacteria species. Moreover, our results highlight the central roles of Tn6260 and ISPst2 in the spread of lnu(G).

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Genomic Characterization of MDR Escherichia coli Harboring blaOXA-48 on the IncL/M-type Plasmid Isolated from Blood Stream Infection

BioMed Research International ◽

10.1155/2018/3036143 ◽

2018 ◽

Vol 2018 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

S. Alousi ◽

T. Salloum ◽

H. Arabaghian ◽

G. M. Matar ◽

G. F. Araj ◽

...

Keyword(s):

Escherichia Coli ◽

Blood Stream Infection ◽

Genomic Analysis ◽

Blood Stream ◽

Population Movements ◽

E Coli ◽

Resistance Determinants ◽

Genomic Characterization ◽

Hospital Acquired

Escherichia coli is responsible for a wide variety of community and hospital acquired extraintestinal infections, and the emergence of ESBL resistant isolates is a major clinical concern. In this study, we characterized the genomic attributes of an OXA-48 and CTX-M-3 producing E. coli EC-IMP153. Whole-genome initial assembly produced 146 contigs with a combined 5,504,170 bp in size and a G+C content of 50.5%. wgSNPs-based phylogenetic comparison with 36 publically available genomes was also performed. Comprehensive genomic analysis showed that EC-IMP153 belonged to sequence type ST-405 and harbored several resistance determinants including the β-lactam resistance genes blaOXA-48, blaCTX-M-3, blaTEM-1B, blaOXA-1, and blaCMY-70, aminoglycoside fyuA and aac(3)IId, tetracycline tet(A) and tet(R), and fluoroquinolone gyrA, parC, and mfd resistance determinants. Plasmids with the following incompatibility groups were detected in silico and confirmed using PBRT: IncI1-α, IncL, IncW, Col (BS512), and IncF. To our knowledge this is the first in-depth genomic analysis of an OXA-48 producing E. coli ST-405 isolated from a patient in Lebanon and linked to a blood stream infection. Continuous monitoring is necessary to better understand the continued diffusion of such pathogens, especially in view of the population movements triggered by unrest in the Middle East.

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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 extended-spectrum and CMY-2 ß-lactamases, and associated virulence genes in Escherichia coli from food of animal origin in México

British Food Journal ◽

10.1108/bfj-02-2018-0104 ◽

2018 ◽

Vol 120 (7) ◽

pp. 1457-1473 ◽

Cited By ~ 1

Author(s):

Edwin Barrios-Villa ◽

Gerardo Cortés-Cortés ◽

Patricia Lozano Zarain ◽

Sergio Romero-Romero ◽

Norarizbeth Lara Flores ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Food Samples ◽

Animal Origin ◽

Content Type ◽

E Coli ◽

Extended Spectrum ◽

Food Of Animal Origin ◽

Cephalosporin Resistance

Purpose Broad-spectrum cephalosporin resistance is rapidly increasing in Escherichia coli, representing a food safety problem. The purpose of this paper is to characterize eight extended-spectrum-ß-lactamase (ESBL) and acquired AmpC ß-lactamase-producing E. coli isolates and virotypes associated, obtained from chicken and pork food samples in Puebla, Mexico. Design/methodology/approach Samples (36 from chicken and 10 from pork) were cultured on Levine agar plates supplemented with cefotaxime (2 mg/L) for isolation of cefotaxime-resistant (CTXR) E. coli. CTXR-E. coli isolates were detected in 33 of 46 samples (72 percent), and one isolate/sample was characterized (28 from chicken and 5 from pork), for ESBL production, phylogenetic group, sequence typing, resistance and virulence genes by PCR and sequencing. Findings Results showed 16 ESBL-E. coli (35 percent) (12/16 belonging to phylogroup B1) and 8 CMY-2-E. coli (17 percent). ESBL detected were as follows (number of isolates): CTX-M-2 (8); CTX-M-1 (2); CTX-M-15 (1); SHV-2a (4) and TEM-52c (1). In total, 20 different sequence types (STs) were identified among the ESBL- or CMY-2-producing E. coli strains, which included four new ones. The CTX-M-15 β-lactamase was detected in one E. coli ST617-ST10 Cplx-B1 strain that also carried ibeA gene. One CMY-2-positive strain of lineage ST224-B2 was detected and it carried the qnrA1 gene. Originality/value In this study, a ST131-based virotyping scheme for strains from food of animal origin was established since this kind of strains constitutes an important vehicle of virulent ESBL- and CMY-2-producing E. coli isolates, which could be transmitted to humans by direct contact or through the food chain.

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Genomic characterization of 16S rRNA methyltransferase-producing Escherichia coli isolates from the Parisian area, France

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa105 ◽

2020 ◽

Vol 75 (7) ◽

pp. 1726-1735 ◽

Cited By ~ 2

Author(s):

François Caméléna ◽

Florence Morel ◽

Manel Merimèche ◽

Jean-Winoc Decousser ◽

Hervé Jacquier ◽

...

Keyword(s):

Escherichia Coli ◽

16S Rrna ◽

Genomic Diversity ◽

Health Concern ◽

M Gene ◽

Genetic Environment ◽

E Coli ◽

Genomic Characterization ◽

High Level

Abstract Background The resistance to all aminoglycosides (AGs) conferred by 16S rRNA methyltransferase enzymes (16S-RMTases) is a major public health concern. Objectives To characterize the resistance genotype, its genetic environment and plasmid support, and the phylogenetic relatedness of 16S-RMTase-producing Escherichia coli from France. Methods We screened 137 E. coli isolates resistant to all clinically relevant AGs from nine Parisian hospitals for 16S-RMTases. WGS was performed on clinical isolates with high-level AG resistance (MIC ≥256 mg/L) and their transformants. Results Thirty of the 137 AG-resistant E. coli produced 16S-RMTases: 11 ArmA, 18 RmtB and 1 RmtC. The 16S-RMTase producers were also resistant to third-generation cephalosporins (90% due to a blaCTX-M gene), co-trimoxazole, fluoroquinolones and carbapenems (blaNDM and blaVIM genes) in 97%, 83%, 70% and 10% of cases, respectively. Phylogenomic diversity was high in ArmA producers, with 10 different STs, but a similar genetic environment, with the Tn1548 transposon carried by a plasmid closely related to pCTX-M-3 in 6/11 isolates. Conversely, RmtB producers belonged to 12 STs, the most frequent being ST405 and ST complex (STc) 10 (four and four isolates, respectively). The rmtB gene was carried by IncF plasmids in 10 isolates and was found in different genetic environments. The rmtC gene was carried by the pNDM-US plasmid. Conclusions ArmA and RmtB are the predominant 16S-RMTases in France, but their spread follows two different patterns: (i) dissemination of a conserved genetic support carrying armA in E. coli with high levels of genomic diversity; and (ii) various genetic environments surrounding rmtB in clonally related E. coli.

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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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Genomic Characterization of Clinical Listeria monocytogenes Isolates in Beijing, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.751003 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaoai Zhang ◽

Yuzhu Liu ◽

Penghang Zhang ◽

Yanlin Niu ◽

Qian Chen ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Common Core ◽

Core Genome ◽

The United States ◽

Multidrug Resistant ◽

Human Pathogen ◽

Genomic Characterization ◽

Beijing China ◽

Insight Into

Listeria monocytogenes is a foodborne human pathogen that affects public health worldwide. Whole-genome sequencing (WGS) can classify L. monocytogenes isolates and identify virulence islands and resistance genes potentially influencing infectivity. Herein, WGS was used to assess 151 L. monocytogenes isolates from 120 cases of clinical infection in Beijing, China, between 2014 and 2018. Most isolates were either serogroup 1/2a,3a or serogroup 1/2b,3b,7, with 25 multilocus sequence typing (MLST) types (STs) represented, of which ST8, ST87, and ST5 were the most common. Core-genome MLST (cgMLST) grouped the 151 isolates into 116 cgMLST types. The discriminatory power of cgMLST was greater than other subtypes, revealing that isolates from the same patient were highly related (only differing at one allele). Eighty-six isolates formed 30 complexes with ≤ 7 cgMLST alleles between neighboring isolates, suggesting possible outbreaks. Compared with isolates in the United States, ST8, ST121, ST619, ST87, and ST155 isolates were grouped into unified clades. All 151 isolates were positive for common virulence-associated loci, and 26 lineage I isolates harbored the pathogenicity island 3 (LIPI-3) locus, while 42 lineage I isolates harbored the complete LIPI-4 locus. Eleven ST619 isolates had both LIPI-3 and LIPI-4. Among the 151 isolates, 13 were resistant to at least one antibiotic, and no multidrug-resistant isolates were identified. Resistance phenotypes correlated with genotypes, apart from two meropenem resistance isolates. The findings provided insight into the nature of L. monocytogenes strains currently causing clinical disease in Beijing, and WGS analysis indicated possible outbreaks.

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Multidrug Resistance and the Predominance of blaCTX-M in Extended Spectrum Beta-Lactamase-Producing Enterobacteriaceae of Animal and Water Origin

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000495409 ◽

2018 ◽

Vol 28 (4) ◽

pp. 201-206 ◽

Cited By ~ 1

Author(s):

Bilel Hassen ◽

Senda Sghaier ◽

Mohamed Salah Abbassi ◽

Mohamed Amine Ferjani ◽

Meriam Ben Said ◽

...

Keyword(s):

Wastewater Treatment Plants ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum ◽

Water Origin ◽

Class 1 ◽

Synergy Test ◽

Animal Isolates

The aim of this work was the genetic characterization of cefotaxime-resistant enterobacteria from animals (53 samples), the surface water of rivers (17 samples), and wastewater treatment plants (43 samples) in Tunisia. A total of 48 (42.4%) cefotaxime-resistant isolates were recovered. An extended spectrum beta-lactamase (ESBL) phenotype with a positive double-disk synergy test (DDST) was exhibited by 34 (70.8%) and 14 (29.1%) isolates from water and animal origins, respectively. Isolates from water were identified as: Escherichia coli (n = 17), Hafnia spp. (n = 13), Citrobacter spp. (n = 1), Enterobacter cloacae (n = 1), Klebsiella pneumoniae (n = 1), and K. oxytoca (n = 1). Animal isolates were identified as: E. coli (n = 11), E. cloacae (n = 1), Hafnia spp. (n = 1), and K. pneumoniae (n = 1). PCR investigation of blaCTX-M, blaTEM, and blaSHV genes showed that amongst the 48 isolates with a positive DDST, 41 (87.5%) carried the blaCTX-M gene, 1 isolate harbored the blaSHV gene, and 1 isolate coharbored blaCTX-M with blaSHV genes. The class 1 and 2 integrons were detected in 27 (56.2%) and 1 (2%) isolates, respectively. Our study showed a significant occurrence of ESBL-producing enterobacteria in animals and aquatic environments with a predominance of blaCTX-M genes.

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