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Moniruzzaman M, Hussain MT, Ali S, Hossain M, Hossain MS, Alam MAU, Galib FC, Islam MT, Paul P, Islam MS, Siddiqee MH, Mondal D, Parveen S, Mahmud ZH. Multidrug-resistant Escherichia coli isolated from patients and surrounding hospital environments in Bangladesh: A molecular approach for the determination of pathogenicity and resistance. Heliyon 2023; 9:e22109. [PMID: 38027708 PMCID: PMC10679508 DOI: 10.1016/j.heliyon.2023.e22109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 09/08/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Extended spectrum β-lactamase producing Escherichia coli (ESBL E. coli) is a primary concern for hospital and community healthcare settings, often linked to an increased incidence of nosocomial infections. This study investigated the characteristics of ESBL E. coli isolated from hospital environments and clinical samples. In total, 117 ESBL E. coli isolates were obtained. The isolates were subjected to molecular analysis for the presence of resistance and virulence genes, antibiotic susceptibility testing, quantitative adherence assay, ERIC-PCR for phylogenetic analysis and whole genome sequencing of four highly drug resistant isolates. Out of the 117 isolates, 68.4% were positive for blaCTX-M, 39.3% for blaTEM, 30.8% for blaNDM-1, 13.7% for blaOXA and 1.7% for blaSHV gene. Upon screening for diarrheagenic genes, no isolates were found to harbour any of the tested genes. In the case of extraintestinal pathogenic E. coli (ExPEC) virulence factors, 7.6%, 11%, 5.9%, 4.3% and 21.2% of isolates harbored the focG, kpsMII, sfaS, afa and iutA genes, respectively. At a temperature of 25°C, 14.5% of isolates exhibited strong biofilm formation with 21.4% and 28.2% exhibiting moderate and weak biofilm formation respectively, whereas 35.9% were non-biofilm formers. On the other hand at 37°C, 2.6% of isolates showed strong biofilm formation with 3.4% and 31.6% showing moderate and weak biofilm formation respectively, whereas, 62.4% were non-biofilm formers. Regarding antibiotic susceptibility testing, all isolates were found to be multidrug-resistant (MDR), with 30 isolates being highly drug resistant. ERIC-PCR resulted in 12 clusters, with cluster E-10 containing the maximum number of isolates. Hierarchical clustering and correlation analysis revealed associations between environmental and clinical isolates, indicating likely transmission and dissemination from the hospital environment to the patients. The whole genome sequencing of four highly drug resistant ExPEC isolates showed the presence of various antimicrobial resistance genes, virulence factors and mobile genetic elements, with isolates harbouring the plasmid incompatibility group IncF (FII, FIB, FIA). The sequenced isolates were identified as human pathogens with a 93.3% average score. This study suggests that ESBL producing E. coli are prevalent in the healthcare settings of Bangladesh, acting as a potential reservoir for AMR bacteria. This information may have a profound effect on treatment, and improvements in public healthcare policies are a necessity to combat the increased incidences of hospital-acquired infections in the country.
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Affiliation(s)
- M. Moniruzzaman
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Mohammed Tanveer Hussain
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Microbiology Program, Department of Mathematics and Natural Sciences, BRAC University, Mohakhali-66, Dhaka, Bangladesh
| | - Sobur Ali
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Monir Hossain
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Md. Sakib Hossain
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mohammad Atique Ul Alam
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Faisal Chowdhury Galib
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Md. Tamzid Islam
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, USA
| | - Partha Paul
- BCSIR Rajshahi Laboratories, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Md. Shafiqul Islam
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mahbubul H. Siddiqee
- Microbiology Program, Department of Mathematics and Natural Sciences, BRAC University, Mohakhali-66, Dhaka, Bangladesh
| | - Dinesh Mondal
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Shahana Parveen
- Emerging Infections, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Zahid Hayat Mahmud
- Laboratory of Environmental Health, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
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Afolayan AO, Aboderin AO, Oaikhena AO, Odih EE, Ogunleye VO, Adeyemo AT, Adeyemo AT, Bejide OS, Underwood A, Argimón S, Abrudan M, Egwuenu A, Ihekweazu C, Aanensen DM, Okeke IN. An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals. Microb Genom 2022; 8:mgen000863. [PMID: 36748556 PMCID: PMC9837563 DOI: 10.1099/mgen.0.000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/15/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016-2018 bloodstream E. coli isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum β-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely Klebsiella origin, identical to those of avian pathogenic E. coli Sanji, and serotyped in silico as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of E. coli isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.
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Affiliation(s)
- Ayorinde O. Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Adeyemi T. Adeyemo
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria
| | - Abolaji T. Adeyemo
- Department of Medical Microbiology and Parasitology, University of Osun Teaching Hospital, Osogbo, Osun State, Nigeria
| | - Oyeniyi S. Bejide
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | | | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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Patel MA, Pandey A, Patel AC, Patel SS, Chauhan HC, Shrimali MD, Patel PA, Mohapatra SK, Chandel BS. Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India. Front Microbiol 2022; 13:996214. [PMID: 36312963 PMCID: PMC9614321 DOI: 10.3389/fmicb.2022.996214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, blaTEM (63.88%) was found to be the predominant genotype, followed by blaSHV (30.55%) and blaOXA (28.70%). In the blaCTX-M group, a higher occurrence was observed in blaCTX-M-9 (23.14%), followed by blaCTX-M-2 (24.07%) and blaCTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3”)-lb, aph(6)-ld, and Aph(3’)-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.
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Affiliation(s)
- Mitul A. Patel
- Department of Biotechnology, Sankalchand Patel University, Visnagar, India
- *Correspondence: Mitul A. Patel,
| | - Aparna Pandey
- Department of Biochemistry, Dental College, Sankalchand Patel University, Visnagar, India
| | - A. C. Patel
- Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - S. S. Patel
- Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - H. C. Chauhan
- Department of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - M. D. Shrimali
- Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - Pankaj A. Patel
- Department of Physiology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - S. K. Mohapatra
- Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
| | - B. S. Chandel
- Department of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, India
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Jain P, Bepari AK, Sen PK, Rafe T, Imtiaz R, Hossain M, Reza HM. High prevalence of multiple antibiotic resistance in clinical E. coli isolates from Bangladesh and prediction of molecular resistance determinants using WGS of an XDR isolate. Sci Rep 2021; 11:22859. [PMID: 34819576 PMCID: PMC8613203 DOI: 10.1038/s41598-021-02251-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 12/04/2022] Open
Abstract
Multi-drug-resistance (MDR) is a severe public health concern worldwide, and its containment is more challenging in developing countries due to poor antimicrobial resistance (AMR) surveillance and irrational use of antibiotics. The current study investigated 100 clinical E. coli isolates and revealed that 98% of them were MDR. PCR analysis using 25 selected isolates showed the predominance of metallo-β-lactamase gene blaNDM (80%) and ESBL genes blaOXA (48%) and blaCTX-M-15 (32%). The AmpC gene was detected in 68% of the isolates, while 32% was tetC positive. Notably, 34% of the isolates were resistant to carbapenem. Whole genome sequence (WGS) analysis of an extensively drug-resistant (XDR) isolate (L16) revealed the presence of the notorious sequence type 131 responsible for multi-drug-resistant infections, multiple antibiotic resistance genes (ARGs), virulence genes, and mobile genetic elements that pose risks to environmental transmission. Our results indicate that MDR is alarmingly increasing in Bangladesh that critically limits the treatment option against infections and contributes to further aggravation to the prevailing situation of MDR worldwide. The findings of this study will be valuable in designing sustainable strategies to contain MDR in the region.
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Affiliation(s)
- Preeti Jain
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Asim Kumar Bepari
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Prosengit Kumer Sen
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Tanzir Rafe
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Rashed Imtiaz
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Maqsud Hossain
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh.
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Genomic characterization of an extensively drug-resistant chicken-borne Salmonella Indiana isolate carrying an IncHI2-IncHI2A plasmid. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bibbolino G, Di Lella FM, Oliva A, Lichtner M, Del Borgo C, Raponi G, Trancassini M, Mengoni F, Arcari G, Antonelli G, Carattoli A. Molecular epidemiology of NDM-5-producing Escherichia coli high-risk clones identified in two Italian hospitals in 2017-2019. Diagn Microbiol Infect Dis 2021; 100:115399. [PMID: 34030105 DOI: 10.1016/j.diagmicrobio.2021.115399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/09/2021] [Accepted: 04/12/2021] [Indexed: 01/01/2023]
Abstract
Between November 2018 and October 2019, carbapenem-resistant Enterobacterales carrying New Delhi Metallo-β-lactamase (NDM) caused one of the largest and persistent outbreaks occurred in Italy and intensified surveillance measures have been taken in all Italian hospitals. In this study we analyzed NDM-5- producing Escherichia coli identified in 2 hospitals of the Lazio region in Italy. Epidemiological and microbiological data demonstrated that in 2018-2019 the NDM-5-producing high-risk E. coli ST167 clone circulated in patients from both hospitals. In 2019, another NDM-5-producing E. coli clone, identified by MLST as ST617 was introduced in one of the 2 hospitals and caused an outbreak. This study describes an application of genomics as a useful method to discern endemic and outbreak clones when applied to strains of the same species (E. coli) with the same resistance determinant (NDM-5) and the relevance of screening patients admitted in critical units for carbapenemase producers to prevent outbreaks.
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Affiliation(s)
- Giulia Bibbolino
- Dept. Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | | | - Alessandra Oliva
- Dept. of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Miriam Lichtner
- Dept. of Public Health and Infectious Diseases, Sapienza University of Rome, Infectious Disease Unit, SM Goretti Hospital, Latina, Italy
| | | | - Giammarco Raponi
- Dept. of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Trancassini
- Dept. of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Fabio Mengoni
- Dept. of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Gabriele Arcari
- Dept. Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Dept. Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany. J Clin Microbiol 2021; 59:JCM.02238-20. [PMID: 33361340 DOI: 10.1128/jcm.02238-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/04/2020] [Indexed: 01/05/2023] Open
Abstract
A series of clinical NDM-5-producing Escherichia coli isolates obtained from two surveillance networks for carbapenem-producing Enterobacterales from 2018 to 2019, namely, Switzerland (NARA) and Germany (SurvCARE), were analyzed. The 33 NDM-5-producing E. coli isolates were highly resistant to β-lactams, including novel β-lactam/β-lactamase inhibitor combinations (ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam), and remained susceptible to fosfomycin, colistin, and tigecycline. These isolates were assigned to different sequence types (STs) and indicated a predominance of isolates exhibiting ST167 in Switzerland and Germany (n = 10) (phylogenetic group C), followed by ST405 (n = 4) (phylogenetic group E), ST1284 (n = 4) (phylogenetic group C), and ST361 (n = 4) (phylogenetic group C). The bla NDM-5 gene was predominantly present on an IncF-type plasmid (n = 29) and, to a lesser extent, on the narrow-host-range IncX3 plasmid (n = 4). Sequence analyses of eight NDM-5 plasmids indicated that NDM-5-encoding F-type plasmids varied in size between 86 and 132 kb. The two IncX3 plasmids pCH8NDM5 and pD12NDM5 were 46 and 45 kb in size, respectively. The highly conserved bla NDM-5 genetic surrounding structures (ΔISAba125-bla NDM-5-ble MBL-trpT-dsbD-IS26) of both the F-type and IncX3 plasmids suggested a common genetic origin. The emergence of the NDM-5 carbapenemase was evidenced in particular for the E. coli ST167 clone, which is a successful epidemic clone known to be associated with both multiresistance and virulence traits and is therefore of high public health concern. The occurrence of clonally related NDM-5-producing E. coli isolates in Switzerland and Germany further indicates the international spread of this multidrug-resistant superbug at least throughout Europe.
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Hammerum AM, Porsbo LJ, Hansen F, Roer L, Kaya H, Henius A, Møller KL, Justesen US, Søes L, Røder BL, Thomsen PK, Wang M, Søndergaard TS, Holzknecht BJ, Østergaard C, Kjerulf A, Kristensen B, Hasman H. Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019. ACTA ACUST UNITED AC 2020; 25. [PMID: 32400363 PMCID: PMC7219033 DOI: 10.2807/1560-7917.es.2020.25.18.1900742] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background Carbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark. Aim Molecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019. Methods For the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST). Results In total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark. Conclusion Import of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.
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Affiliation(s)
- Anette M Hammerum
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Lone Jannok Porsbo
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Hansen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Louise Roer
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Henius
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | | | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Lillian Søes
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Bent L Røder
- Department of Clinical Microbiology, Zealand University Hospital, Slagelse, Denmark
| | - Philip K Thomsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Mikala Wang
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Claus Østergaard
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark
| | - Anne Kjerulf
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Brian Kristensen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Hasman
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
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Identification of an extensively drug-resistant Escherichia coli clinical strain harboring mcr-1 and bla NDM-1 in Korea. J Antibiot (Tokyo) 2020; 73:852-858. [PMID: 32665613 DOI: 10.1038/s41429-020-0350-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The development of colistin resistance in carbapenem-resistant strains poses a serious public health problem. In this study, we collected 249 carbapenem-resistant Escherichia coli isolates from patients in Seoul in 2018, and screened all isolates for colistin resistance and for the presence of mobile colistin resistance (mcr) genes. Colistin-resistant strains were further analyzed using multilocus sequence typing, antimicrobial susceptibility testing, detection of antibiotic resistance determinants, plasmid transconjugation, and whole-genome sequencing. Three of the 249 carbapenem-resistant isolates were resistant to colistin, and mcr-1 was detected in one isolate (SECR18-0888), which belonged to sequence type 156 and was resistant to all antibiotics tested except tigecycline. The mcr-1.1 gene was located on an ~62 kb self-transferable IncI2 plasmid along with the blaCTX-M-55 gene, and the blaNDM-1, blaTEM, qepA1, and rmtB genes were additionally detected in SECR18-0888. As an extensively drug-resistant E. coli strain producing MCR-1 and NDM-1 was identified in Korea for the first time, continued monitoring of colistin resistance in carbapenem-resistant Enterobacteriaceae should be reinforced.
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Novel Insights and Features of the NDM-5-Producing Escherichia coli Sequence Type 167 High-Risk Clone. mSphere 2020; 5:5/2/e00269-20. [PMID: 32350092 PMCID: PMC7193042 DOI: 10.1128/msphere.00269-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli sequence type 167 (ST167), producing the metallo beta-lactamase NDM-5, has been isolated as a colonizer of patients recovered at the University Hospital Policlinico Umberto I of Rome. Phylogenesis and comparative analysis of the genomes of these strains were performed against 343 ST167 genomes available from the EnteroBase database. These analyses revealed that resistance plasmids, integrative conjugative elements (ICEs), carrying the yersiniabactin virulence trait and capsular synthesis gene clusters had variable compositions and distributions within different strains of the ST167 clone. A novel capsular synthesis gene cluster, highly similar to the K48 cluster previously described only for Klebsiella pneumoniae, was identified in phylogenetically related strains of the ST167 clone.IMPORTANCE Global dissemination of some E. coli high-risk clones has been described in the last decades. The most widespread was the ST131 clone, associated with extended-spectrum-beta-lactamase (ESBL) production. Genomics of ST131 demonstrated that one clade within the ST emerged in the early 2000s, followed by a rapid, global expansion. The E. coli ST167 clone is emerging throughout the world, being frequently reported for its association with carbapenem resistance. Our study shows that virulence features are differently represented within the ST167 population. One clade shows the K48 capsular synthesis gene cluster of K. pneumoniae, not previously described for E. coli, and is populated by NDM-5-producing strains. The combination of resistance and virulence may sustain the global expansion of this specific ST167 clade.
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Navarro-Garcia F, Ruiz-Perez F, Cataldi Á, Larzábal M. Type VI Secretion System in Pathogenic Escherichia coli: Structure, Role in Virulence, and Acquisition. Front Microbiol 2019; 10:1965. [PMID: 31543869 PMCID: PMC6730261 DOI: 10.3389/fmicb.2019.01965] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/09/2019] [Indexed: 12/18/2022] Open
Abstract
Bacterial pathogens utilize a myriad of mechanisms to invade mammalian hosts, damage tissue sites, and evade the immune system. One essential strategy of Gram-negative bacteria is the secretion of virulence factors through both inner and outer membranes to reach a potential target. Most secretion systems are harbored in mobile elements including transposons, plasmids, pathogenicity islands, and phages, and Escherichia coli is one of the more versatile bacteria adopting this genetic information by horizontal gene transfer. Additionally, E. coli is a bacterial species with members of the commensal intestinal microbiota and pathogens associated with numerous types of infections such as intestinal, urinary, and systemic in humans and other animals. T6SS cluster plasticity suggests evolutionarily divergent systems were acquired horizontally. T6SS is a secretion nanomachine that is extended through the bacterial double membrane; from this apparatus, substrates are conveyed straight from the cytoplasm of the bacterium into a target cell or to the extracellular space. This nanomachine consists of three main complexes: proteins in the inner membrane that are T4SS component-like, the baseplate complex, and the tail complex, which are formed by components evolutionarily related to contractile bacteriophage tails. Advances in the T6SS understanding include the functional and structural characterization of at least 13 subunits (so-called core components), which are thought to comprise the minimal apparatus. So far, the main role of T6SS is on bacterial competition by using it to kill neighboring non-immune bacteria for which antibacterial proteins are secreted directly into the periplasm of the bacterial target after cell-cell contact. Interestingly, a few T6SSs have been associated directly to pathogenesis, e.g., roles in biofilm formation and macrophage survival. Here, we focus on the advances on T6SS from the perspective of E. coli pathotypes with emphasis in the secretion apparatus architecture, the mechanisms of pathogenicity of effector proteins, and the events of lateral gene transfer that led to its spread.
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Affiliation(s)
- Fernando Navarro-Garcia
- Department of Cell Biology, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City, Mexico
| | - Fernando Ruiz-Perez
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Ángel Cataldi
- Laboratorio de Escherichia coli, Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA-CONICET, Buenos Aires, Argentina
| | - Mariano Larzábal
- Laboratorio de Escherichia coli, Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA-CONICET, Buenos Aires, Argentina
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