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Tewari R, Ganaie F, Venugopal N, Mitra S, Shome R, Shome BR. Occurrence and characterization of genetic determinants of β-lactam-resistance in Escherichia coli clinical isolates. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105257. [PMID: 35219866 DOI: 10.1016/j.meegid.2022.105257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
β-lactamase mediated resistance in Escherichia coli is a significant problem that requires immediate attention. Herein, we aim to characterize and understand the dynamics of the genetic determinants of β-lactam resistance (i.e. ESBL, AmpC, and MBL) in E. coli. Out of 203 E. coli isolates, genetic determinants of β-lactam resistance were identified in 50% (n = 101) of isolates. ESBL, AmpC, and MBL resistance determinants were detected in 78%, 40%, and 18% of isolates, respectively with blaCTX-M group 4 (48%), blaCMY (40%), and blaSIM (33%) as the most prevalent β-lactam resistance genes. Among these isolates, 45% harbored plasmid replicon types, with L/M (40%) and Y (33%) as the most dominant replicon types. Integrons were detected in 40% of such isolates, with Class-1 and Class-3 representing 62% and 55%, respectively. Overall, we observed high rate of genetic determinants of β-lactam-resistance in E. coli isolates recovered from patients in clinical settings. The co-occurrence of antimicrobial resistance genes and mobile genetic elements in a high percentage of isolates is a major concern and relates to complex resistance mechanisms. To combat the serious threat of antimicrobial resistance, it is imperative to develop strategies for robust surveillance and understand the molecular basis of resistance acquisition and transmission.
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Affiliation(s)
- Rituparna Tewari
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India; Department of Microbiology, Jain University, Bangalore, India.
| | - Feroze Ganaie
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India; Department of Medicine, Division of Pulmonary/ Allergy/Critical Care, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nimita Venugopal
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India; Department of Microbiology, Jain University, Bangalore, India
| | - Susweta Mitra
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India; School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Rajeswari Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India
| | - Bibek R Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India.
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Moffat J, Chalmers G, Reid-Smith R, Mulvey MR, Agunos A, Calvert J, Cormier A, Ricker N, Weese JS, Boerlin P. Resistance to extended-spectrum cephalosporins in Escherichia coli and other Enterobacterales from Canadian turkeys. PLoS One 2020; 15:e0236442. [PMID: 32925914 PMCID: PMC7489564 DOI: 10.1371/journal.pone.0236442] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/05/2020] [Indexed: 12/26/2022] Open
Abstract
The goal of this study was to determine the frequency of resistance to extended-spectrum cephalosporins (ESCs) in Escherichia coli and other Enterobacterales from turkeys in Canada and characterize the associated resistance determinants. Pooled fecal samples were collected in 77 turkey farms across British Columbia, Québec, and Ontario. Isolates were obtained with and without selective enrichment cultures and compared to isolates from diagnostic submissions of suspected colibacillosis cases in Ontario. Isolates were identified using MALDI-TOF and susceptibility to ESCs was assessed by disk diffusion. The presence of blaCMY, blaCTX-M, blaTEM, and blaSHV was tested by PCR. Transformation experiments were used to characterize blaCMY plasmids. Genome sequencing with short and long reads was performed on a representative sample of blaCTX-M-positive isolates to assess isolates relatedness and characterize blaCTX-M plasmids. For the positive enrichment cultures (67% of total samples), 93% (587/610) were identified as E. coli, with only a few other Enterobacterales species identified. The frequency of ESC resistance was low in E. coli isolates from diagnostic submission (4%) and fecal samples without selective enrichment (5%). Of the ESC-resistant Enterobacterales isolates from selective enrichments, 71%, 18%, 14%, and 8% were positive for blaCMY, blaTEM,blaCTX-M, and blaSHV, respectively. IncI1 followed by IncK were the main incompatibility groups identified for blaCMY plasmids. The blaCTX-M-1 gene was found repeatedly on IncI1 plasmids of the pMLST type 3, while blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65 were associated with a variety of IncF plasmids. Clonal spread of strains carrying blaCTX-M genes between turkey farms was observed, as well as the presence of an epidemic blaCTX-M-1 plasmid in unrelated E. coli strains. In conclusion, Enterobacterales resistant to ESCs were still widespread at low concentration in turkey feces two years after the cessation of ceftiofur use. Although blaCMY-2 is the main ESC resistance determinant in E. coli from Canadian turkeys, blaCTX-M genes also occur which are often carried by multidrug resistance plasmids. Both clonal spread and horizontal gene transfer are involved in parallel in the spread of blaCTX-M genes in Enterobacterales from Canadian turkeys.
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Affiliation(s)
- Jonathan Moffat
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Richard Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Michael R. Mulvey
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Agnes Agunos
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Julie Calvert
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Ashley Cormier
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - J. Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Dziri O, Dziri R, Maraoub A, Chouchani C. First Report of SHV-148-Type ESBL and CMY-42-Type AmpC β-Lactamase in Klebsiella pneumoniae Clinical Isolates in Tunisia. Microb Drug Resist 2018; 24:1483-1488. [PMID: 29927719 DOI: 10.1089/mdr.2018.0073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extended-spectrum beta-lactamase producing Enterobacteriaceae present a real problem worldwide. We aimed to investigate the molecular mechanisms of resistance to antibiotics among Klebsiella pneumoniae clinical isolates collected from a Hospital in the southeast of Tunisia. Eighteen cephalosporin-resistant K. pneumoniae were recovered between April 2015 and August 2016. Molecular characterization of antimicrobial resistance encoding genes was performed by PCR and sequencing. Results revealed several types of Ambler class A β-lactamase encoding genes among our isolates: [blaCTXM-15 (15), blaSHV-28 (6), blaSHV-1 (2), blaSHV-148 (1), blaSHV-61 (1), blaSHV-76 (1), blaSHV-186 (1), blaTEM-1 (8)]. The association of blaOXA-1 was observed in nine isolates. However, the class C β-lactamase encoding genes were detected in four isolates [blaCMY-4 (2), blaCMY-42 (1), blaACT-35 (1)]. Molecular typing of K. pneumoniae isolates by pulsed-field gel electrophoresis showed 16 unrelated pulsotypes proving a high diversity among our isolates. Our study provides new epidemiological information showing a huge diversity of β-lactamase encoding genes among our isolates. In fact, this is the first report of SHV-76, SHV-148, and SHV-186 in Tunisia. This is also the first report of CMY-42 and ACT-35 producing K. pneumoniae in our country.
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Affiliation(s)
- Olfa Dziri
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar , Tunis, Tunisia
| | - Raoudha Dziri
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar , Tunis, Tunisia
| | - Abderrahmen Maraoub
- 2 Hôpital régional Sadok Mkaddem de Djerba, Avenue Habib Bourguiba Houmet Souk Djerba , Tunis, Tunisia
| | - Chedly Chouchani
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar , Tunis, Tunisia
- 3 Laboratoire de Recherche Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage , Technopôle de Borj-Cedria, Hammam-Lif, Tunisia
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Jena J, Debata NK, Sahoo RK, Gaur M, Subudhi E. Genetic diversity study of various β-lactamase-producing multidrug-resistant Escherichia coli isolates from a tertiary care hospital using ERIC-PCR. Indian J Med Res 2017; 146:S23-S29. [PMID: 29205192 PMCID: PMC5735567 DOI: 10.4103/ijmr.ijmr_575_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES The prevalence of multidrug-resistant (MDR) Escherichia coli isolates producing β-lactamase enzyme is a growing problem across the globe. Strain typing is an epidemiologically important tool not only for detecting the cross transmission of nosocomial pathogens but also for determining the source of infection. The present study was conducted to understand the clonal relationship among various β-lactamase-producing MDR E. coli isolates using enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR). METHODS A total of 41 MDR E. coli isolates were randomly collected from various clinical samples and processed. Isolated organisms were tested for antibiotics resistance pattern. Phenotypic detection of metallo β-lactamases (MBL) was carried out by the imipenem-ethylenediaminetetraacetic acid disc diffusion/double-disc synergy test. AmpC enzyme production was tested by a modified three-dimensional extract test. RESULTS Almost all isolates were found sensitive to colistin. A high percentage of drug resistance was observed in these isolates against ceftazidime (100%), cefotaxime (100%), cefepime (100%), ofloxacin (97.56%), amoxicillin/clavulanic acid (97.56%) and norfloxacin (85.36%). Of the 41 isolates, ESBL producers were found to be predominant, i.e., 22 (53.65%), followed by AmpC (6, 14.63%) and MBL (5, 12.19%). INTERPRETATION & CONCLUSIONS At 60 per cent similarity cut-off value, the dendrogram analysis showed that there were a total of 14 unique clusters of ERIC (CL-1 - CL-14) within the 41 E. coli isolates, which revealed the genetic diversity existing between them.
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Affiliation(s)
- Jayanti Jena
- Department of Microbiology, Institute of Medical Sciences & SUM Hospital, Bhubaneswar, India
| | - Nagen Kumar Debata
- Department of Microbiology, Institute of Medical Sciences & SUM Hospital, Bhubaneswar, India
| | - Rajesh Kumar Sahoo
- Centre of Biotechnology, Siksha 'O' Anusandhan University, Bhubaneswar, India
| | - Mahendra Gaur
- Centre of Biotechnology, Siksha 'O' Anusandhan University, Bhubaneswar, India
| | - Enketeswara Subudhi
- Centre of Biotechnology, Siksha 'O' Anusandhan University, Bhubaneswar, India
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