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Khan A, Saraf VS, Siddiqui F, Batool T, Noreen Z, Javed S, Ahmad A, Alonazi WB, Ibrahim M, Pucciarelli S, Bokhari H. Multidrug resistance among uropathogenic clonal group A E. Coli isolates from Pakistani women with uncomplicated urinary tract infections. BMC Microbiol 2024; 24:74. [PMID: 38454332 PMCID: PMC10919050 DOI: 10.1186/s12866-024-03221-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE Multi-drug resistance (MDR) has notably increased in community acquired uropathogens causing urinary tract infections (UTIs), predominantly Escherichia coli. Uropathogenic E. coli causes 80% of uncomplicated community acquired UTIs, particularly in pre-menopausal women. Considering this high prevalence and the potential to spread antimicrobial resistant genes, the current study was conducted to investigate the presence of clinically important strains of E. coli in Pakistani women having uncomplicated cystitis and pyelonephritis. Women belonging to low-income groups were exclusively included in the study. Seventy-four isolates from urine samples were processed, phylotyped, and screened for the presence of two Single Nucleotide Polymorphisms (SNPs) particularly associated with a clinically important clonal group A of E. coli (CgA) followed by antibiotic susceptibility testing and genome sequence analysis. RESULTS Phylogroup B2 was most prevalent in patients and 44% of isolates were positive for the presence of CgA specific SNPs in Fumarate hydratase and DNA gyrase subunit B genes. Antibiotic susceptibility testing showed widespread resistance to trimethoprim-sulfamethoxazole and extended-spectrum beta-lactamase production. The infection analysis revealed the phylogroup B2 to be more pathogenic as compared to the other groups. The genome sequence of E. coli strain U17 revealed genes encoding virulence, multidrug resistance, and host colonization mechanisms. CONCLUSIONS Our research findings not only validate the significant occurrence of multidrug-resistant clonal group A E. coli (CgA) in premenopausal Pakistani women suffering from cystitis and pyelonephritis but also reveal the presence of genes associated withvirulence, and drug efflux pumps. The detection of highly pathogenic, antimicrobial-resistant phylogroup B2 and CgA E. coli strains is likely to help in understanding the epidemiology of the pathogen and may ultimately help to reduce the impact of these strains on human health. Furthermore, the findings of this study will particularly help to reduce the prevalence of uncomplicated UTIs and the cost associated with their treatment in women belonging to low-income groups.
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Affiliation(s)
- Ayesha Khan
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Health Services Academy, Opposite NIH, Islamabad, Pakistan
| | - Viqar Sayeed Saraf
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Fariha Siddiqui
- Department of Biosciences, Shifa Tameer e Millat University, Islamabad, Pakistan
| | - Tahira Batool
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zobia Noreen
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sundus Javed
- Microbiology and Public Health Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aftab Ahmad
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Ibrahim
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan.
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan.
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, Camerino, 62032, Italy
| | - Habib Bokhari
- Department of Microbiology, Kohsar University Murree, Rawalpindi, Punjab, Pakistan.
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Moazeni S, Askari Badouei M, Hashemitabar G, Rezatofighi SE, Mahmoodi F. Detection and characterization of potentially hybrid enteroaggregative Escherichia coli (EAEC) strains isolated from urinary tract infection. Braz J Microbiol 2024; 55:1-9. [PMID: 38036848 PMCID: PMC10920591 DOI: 10.1007/s42770-023-01195-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) have the potential to receive the virulence markers of intestinal pathotypes and transform into various important hybrid pathotypes. This study aimed to investigate the frequency and characteristics of hybrid enteroaggregative E. coli (EAEC)/UPEC strains. Out of 202 UPEC strains, nine (4.5%) were detected as hybrid EAEC/UPEC. These strains carried one to four iron uptake systems. Among nine investigated pathogenicity islands (PAIs), PAI IV536, PAI II536, and PAI ICFT073 were found in 9 (100%), 3 (33.3%), and 1 (11.1%) strains, respectively. The chuA and sitA genes were detected in 5 (55.5%) and 3 (33.3%) hybrid strains, respectively. Six hybrid strains were found to be typical extraintestinal pathogenic E. coli (ExPEC) according to their virulence traits. Most of the hybrid strains belonged to the phylogenetic group E (6/9). Among the hybrid strains, seven (7/9) were able to form biofilm and adhere to cells; however, only two strains penetrated into the HeLa cells. Our findings reveal some of the virulence characteristics of hybrid strains that lead to fitness and infection in the urinary tract. These strains, with virulence factors of intestinal and non-intestinal pathotypes, may become emerging pathogens in clinical settings; therefore, further studies are needed to reveal their pathogenicity mechanisms and so that preventive measures can be taken.
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Affiliation(s)
- Shima Moazeni
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Askari Badouei
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Gholamreza Hashemitabar
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Fahimeh Mahmoodi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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3
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Koley S, Ghosh A, Mukherjee M. Occurrence of Imipenem-Resistant Uropathogenic Escherichia coli in Pregnant Women: An Insight into Their Virulence Profile and Clonal Structure. Curr Microbiol 2024; 81:56. [PMID: 38193903 DOI: 10.1007/s00284-023-03576-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Uropathogenic Escherichia coli (UPEC) is the predominant pathogen in Urinary Tract Infection (UTI) in pregnant and non-pregnant women. Limited studies were initiated to explore UPEC from pregnant women with respect to imipenem resistance, pathogenicity, and their clonal lineage. In this study, imipenem resistance, phylogenetic background, virulence-associated genes, and clonal characteristics in UPECs isolated from pregnant and non-pregnant cohorts were investigated. E. coli was identified biochemically from urine culture-positive samples from pregnant and non-pregnant women. Carbapenem (meropenem, ertapenem, imipenem) susceptibility was determined by Kirby-Bauer disk diffusion test. The pathogenic determinants were identified by PCR. MEGA 11 was used to interpret clonal lineages from MLST. GraphPad Prism 8.0 and SPSS 26.0 were used for statistical interpretation. Results indicated highest resistance against imipenem compared to meropenem and ertapenem in UPECs isolated from pregnant (UPECp; 63.89%) and non-pregnant (UPECnp; 87.88%) women. Although phylogroup E was predominant in both imipenem-resistant isolates, acquisition of virulence factors was higher among UPECnp than UPECp. Akin to this observation, the presence of PAI III536 and PAI IV536 was statistically significant (p < 0.05) in the former. MLST analysis revealed similar clonal lineages between UPECnp and UPECp, which showed an overall occurrence of ST405 followed by ST101, ST410, ST131, and ST1195 in UPECnp and ST167 in UPECp, respectively, with frequent occurrence of CC131, CC405. Therefore, imipenem-resistant UPECp although discrete with respect to their virulence determinants when compared to UPECnp shared similar STs and CCs, which implied common evolutionary history. Thus, empiric treatment must be restricted in UTIs to especially protect maternal and fetal health.
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Affiliation(s)
- Snehashis Koley
- Department of Biochemistry and Medical Biotechnology, School of Tropical Medicine, 108, C.R. Avenue, Kolkata, West Bengal, 700073, India
| | - Arunita Ghosh
- Department of Biochemistry and Medical Biotechnology, School of Tropical Medicine, 108, C.R. Avenue, Kolkata, West Bengal, 700073, India
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Mandira Mukherjee
- Department of Biochemistry and Medical Biotechnology, School of Tropical Medicine, 108, C.R. Avenue, Kolkata, West Bengal, 700073, India.
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4
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Baker M, Zhang X, Maciel-Guerra A, Babaarslan K, Dong Y, Wang W, Hu Y, Renney D, Liu L, Li H, Hossain M, Heeb S, Tong Z, Pearcy N, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China. Nat Commun 2024; 15:206. [PMID: 38182559 PMCID: PMC10770378 DOI: 10.1038/s41467-023-44272-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd. and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, Shandong, 266000, P.R. China
| | - Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - David Renney
- Nimrod Veterinary Products Limited, 2, Wychwood Court, Cotswold Business Village, Moreton-in-Marsh, GL56 0JQ, London, UK
| | - Longhai Liu
- Shandong Kaijia Food Co. Ltd, Weifang, P. R. China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, No. 9, Zhenghe Road, Luolong District, Luoyang City, Henan Province, Luolong, 471000, P. R. China
| | - Nicole Pearcy
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- School of Life Sciences, University of Nottingham, East Drive, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, No. 168, Jinfeng Street, Hunnan District, Shenyang City, Liaoning Province, 110072, P. R. China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao City, Shandong Province, 266109, P. R. China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing City, 100193, P. R. China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, I06125, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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Qiu L, Chirman D, Clark JR, Xing Y, Hernandez Santos H, Vaughan EE, Maresso AW. Vaccines against extraintestinal pathogenic Escherichia coli (ExPEC): progress and challenges. Gut Microbes 2024; 16:2359691. [PMID: 38825856 PMCID: PMC11152113 DOI: 10.1080/19490976.2024.2359691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a principal global health crisis projected to cause 10 million deaths annually worldwide by 2050. While the Gram-negative bacteria Escherichia coli is commonly found as a commensal microbe in the human gut, some strains are dangerously pathogenic, contributing to the highest AMR-associated mortality. Strains of E. coli that can translocate from the gastrointestinal tract to distal sites, called extraintestinal E. coli (ExPEC), are particularly problematic and predominantly afflict women, the elderly, and immunocompromised populations. Despite nearly 40 years of clinical trials, there is still no vaccine against ExPEC. One reason for this is the remarkable diversity in the ExPEC pangenome across pathotypes, clades, and strains, with hundreds of genes associated with pathogenesis including toxins, adhesins, and nutrient acquisition systems. Further, ExPEC is intimately associated with human mucosal surfaces and has evolved creative strategies to avoid the immune system. This review summarizes previous and ongoing preclinical and clinical ExPEC vaccine research efforts to help identify key gaps in knowledge and remaining challenges.
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Affiliation(s)
- Ling Qiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dylan Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Haroldo Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Ellen E. Vaughan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
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6
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Guibert F, Espinoza K, Taboada-Blanco C, Alonso CA, Oporto R, Castillo AK, Rojo-Bezares B, López M, Sáenz Y, Pons MJ, Ruiz J. Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli. Int Microbiol 2023:10.1007/s10123-023-00445-y. [PMID: 37995017 DOI: 10.1007/s10123-023-00445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023]
Abstract
This study aimed to analyze Escherichia coli from marketed meat samples in Peru. Sixty-six E. coli isolates were recovered from 21 meat samples (14 chicken, 7 beef), and antimicrobial resistance levels and the presence of mechanisms of antibiotic resistance, as well as clonal relationships and phylogeny of colistin-resistant isolates, were established. High levels of antimicrobial resistance were detected, with 93.9% of isolates being multi-drug resistant (MDR) and 76.2% of samples possessing colistin-resistant E. coli; of these, 6 samples from 6 chicken samples presenting mcr-1-producer E. coli. Colistin-resistant isolates were classified into 22 clonal groups, while phylogroup A (15 isolates) was the most common. Extended-spectrum β-lactamase- and pAmpC-producing E. coli were found in 18 and 8 samples respectively, with blaCTX-M-55 (28 isolates; 16 samples) and blaCIT (8 isolates; 7 samples) being the most common of each type. Additionally, blaCTX-M-15, blaCTX-M-65, blaSHV-27, blaOXA-5/10-like, blaDHA, blaEBC and narrow-spectrum blaTEM were detected. In addition, 5 blaCTX-M remained unidentified, and no sought ESBL-encoding gene was detected in other 6 ESBL-producer isolates. The tetA, tetE and tetX genes were found in tigecycline-resistant isolates. This study highlights the presence of MDR E. coli in Peruvian food-chain. The high relevance of CTX-M-55, the dissemination through the food-chain of pAmpC, as well as the high frequency of unrelated colistin-resistant isolates is reported.
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Affiliation(s)
- Fernando Guibert
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Kathya Espinoza
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Clara Taboada-Blanco
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Carla A Alonso
- Servicio de Análisis Clínicos, Laboratorio de Microbiología, Hospital San Pedro, Logroño, Spain
| | - Rosario Oporto
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Angie K Castillo
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Maria J Pons
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru.
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru.
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Jacquier H, Assao B, Chau F, Guindo O, Condamine B, Magnan M, Bridier-Nahmias A, Sayingoza-Makombe N, Moumouni A, Page AL, Langendorf C, Coldiron ME, Denamur E, de Lastours V. Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger. J Infect 2023; 87:199-209. [PMID: 37369264 DOI: 10.1016/j.jinf.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023]
Abstract
OBJECTIVE Whole genome sequencing (WGS) of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger. METHODS Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads. RESULTS Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome. CONCLUSIONS Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.
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Affiliation(s)
- Hervé Jacquier
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, 94000 Créteil, France.
| | - Bachir Assao
- Epicentre, Médecins Sans Frontières, Maradi, Niger
| | - Françoise Chau
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France
| | | | | | - Mélanie Magnan
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France
| | | | | | | | | | | | | | - Erick Denamur
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Laboratoire de Génétique Moléculaire, Hôpital Universitaire Bichat, 75018 Paris, France
| | - Victoire de Lastours
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Service de Médecine Interne, Hôpital Universitaire Beaujon, 92110 Clichy, France
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8
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Bujňáková D, Kocúreková T, Karahutová L. Distribution of virulence-associated genes, antibiotic resistance and phylogenetic groups in Escherichia coli isolated from domestic and racing pigeons. Vet Res Commun 2023; 47:1697-1705. [PMID: 37076749 DOI: 10.1007/s11259-023-10126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
Despite a lot of information about virulence and resistance of Escherichia coli (E. coli) in poultry, very limited data are currently available on its occurrence in pigeon isolates, although this poses a threat to human and animal health. Therefore, this study was conducted to explore the phylogenetic classification, antibiotic sensitivity, and virulence factors in E. coli isolated from cloacal swabs of domestic pigeons bred for meat (n = 47) and racing pigeons (n = 44). The most frequent phylogroup in racing pigeons was E (36, 82.00%), unlike domestic pigeons (B2- 19, 40.00%). The most abundant iron uptake system in both groups of bird was feoB (racing = 40, 90.90%; domestic = 44, 93.61%). The presence of ibeA (52, 57.10%) and kpsMTII (46, 50.50%) genes was detected in more than half of all strains belonging exclusively to phylogroups B2, D, E, F, clade I. Antibiotic resistance was higher in racing pigeons. All racing pigeon isolates were resistant to tetracycline and trimethoprim + sulphonamide. Resistance to ciprofloxacin was determined in three isolates (6.38%) of domestic and 33 isolates (75%) of racing pigeons. Aminoglycosides and β-lactamases resistance were also recorded. One of the important detected phenotypic mechanisms of resistance occurring in isolates from racing pigeons was AGL AAC(6´)I. Our study confirms that healthy pigeons are a reservoir of antibiotic-resistant E. coli containing an arsenal of virulence factors, thus capable of potentially causing infection. Pigeons with the option to fly to multiple places can transfer virulent and resistant bacteria. Direct contact with pigeons and their faeces and the contamination of water and food pose a threat of infection to humans and other animal species.
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Affiliation(s)
- Dobroslava Bujňáková
- Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, 040 01, Košice, Slovakia
| | - Tímea Kocúreková
- Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, 040 01, Košice, Slovakia
- University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 040 01, Košice, Slovakia
| | - Lívia Karahutová
- Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, 040 01, Košice, Slovakia.
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Abdelraheem WM, Mahdi WKM, Abuelela IS, Hassuna NA. High incidence of fosfomycin-resistant uropathogenic E. coli among children. BMC Infect Dis 2023; 23:475. [PMID: 37460976 DOI: 10.1186/s12879-023-08449-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND There are few epidemiological or molecular data on Escherichia coli (E. coli) strains resistant to fosfomycin. In this study, we described the occurrence and characterization of fosfomycin-resistant uropathogenic E. coli (UPEC) isolated from children. MATERIALS AND METHODS This study was carried out on 96 E. coli isolates obtained from children with urinary tract infections. Two methods were performed to detect fosfomycin resistance: The agar dilution method and the rapid fosfomycin test. The disc diffusion method was done to detect the antimicrobial susceptibility pattern of all isolates. The phylogenetic grouping of all isolates was done according to the modified Clermont method. Conventional PCR was performed to detect plasmid-mediated fosfomycin-resistant genes (fos genes) and the blaCTX-M gene. RESULTS Analyses of data were performed by SPSS software. A high percentage of fosfomycin resistance (37/96; 38.5%) was reported among UPEC isolates. The fosfomycin-resistant strains showed a higher resistance rate than fosfomycin-susceptible isolates to different antibiotics. E group (62.2%) was the most predominant phylogenetic group among the fosfomycin-resistant UPEC isolates, followed by Group B2 (21.6%) and group D (13.5%). The fos genes were detected in 21 isolates with the fosA3 gene as the most frequent, which was detected in 11 isolates followed by fosA (8), fosC2 (4), fosA4(1), and fosA5(1) genes. CONCLUSION This is the first report of a high prevalence of plasmid-mediated fosfomycin-resistant UPEC in Egypt. All of these isolates were multidrug-resistant to the tested antibiotics. Close monitoring of such strains is mandatory to prevent widespread dissemination of the genes code for antibiotic resistance.
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Affiliation(s)
- Wedad M Abdelraheem
- Medical Microbiology and Immunology Department, Faculty of Medicine, Minia University, Minia, Egypt.
| | - W K M Mahdi
- Medical Microbiology and Immunology Department, Faculty of Medicine, Minia University, Minia, Egypt
| | - Ibtehal S Abuelela
- Pediatric Department, Faculty of Medicine, Minia University, Minia, Egypt
| | - Noha Anwar Hassuna
- Medical Microbiology and Immunology Department, Faculty of Medicine, Minia University, Minia, Egypt
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Morales G, Abelson B, Reasoner S, Miller J, Earl AM, Hadjifrangiskou M, Schmitz J. The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria. Microbiol Spectr 2023; 11:e0471022. [PMID: 37195213 PMCID: PMC10269530 DOI: 10.1128/spectrum.04710-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is extremely diverse genotypically and phenotypically. Individual strains can variably carry diverse virulence factors, making it challenging to define a molecular signature for this pathotype. For many bacterial pathogens, mobile genetic elements (MGEs) constitute a major mechanism of virulence factor acquisition. For urinary E. coli, the total distribution of MGEs and their role in the acquisition of virulence factors is not well defined, including in the context of symptomatic infection versus asymptomatic bacteriuria (ASB). In this work, we characterized 151 isolates of E. coli, derived from patients with either urinary tract infection (UTI) or ASB. For both sets of E. coli, we catalogued the presence of plasmids, prophage, and transposons. We analyzed MGE sequences for the presence of virulence factors and antimicrobial resistance genes. These MGEs were associated with only ~4% of total virulence associated genes, while plasmids contributed to ~15% of antimicrobial resistance genes under consideration. Our analyses suggests that, across strains of E. coli, MGEs are not a prominent driver of urinary tract pathogenesis and symptomatic infection. IMPORTANCE Escherichia coli is the most common etiological agent of urinary tract infections (UTIs), with UTI-associated strains designated "uropathogenic" E. coli or UPEC. Across urinary strains of E. coli, the global landscape of MGEs and its relationship to virulence factor carriage and clinical symptomatology require greater clarity. Here, we demonstrate that many of the putative virulence factors of UPEC are not associated with acquisition due to MGEs. The current work enhances our understanding of the strain-to-strain variability and pathogenic potential of urine-associated E. coli and points toward more subtle genomic differences distinguishing ASB from UTI isolates.
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Affiliation(s)
- Grace Morales
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Benjamin Abelson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth Reasoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jordan Miller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
| | - Jonathan Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
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Vitt AR, Sørensen MCH, Bortolaia V, Brøndsted L. A Representative Collection of Commensal Extended-Spectrum- and AmpC-β-Lactamase-Producing Escherichia coli of Animal Origin for Phage Sensitivity Studies. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:35-45. [PMID: 37214655 PMCID: PMC10196081 DOI: 10.1089/phage.2023.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Introduction Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing Escherichia coli from livestock and meat represent a zoonotic risk and biocontrol solutions are needed to prevent transmission to humans. Methods In this study, we established a representative collection of animal-origin ESBL/AmpC E. coli as target to test the antimicrobial potential of bacteriophages. Results Bioinformatic analysis of whole-genome sequence data of 198 ESBL/AmpC E. coli from pigs, broilers, and broiler meat identified strains belonging to all known E. coli phylogroups and 65 multilocus sequence types. Various ESBL/AmpC genes and plasmid types were detected with expected source-specific patterns. Plaque assay using 15 phages previously isolated using the E. coli reference collection demonstrated that Warwickvirus phages showed the broadest host range, killing up to 26 strains. Conclusions 154/198 strains were resistant to infection by all phages tested, suggesting a need for isolating phages specific for ESBL/AmpC E. coli. The strain collection described in this study is a useful resource fulfilling such need.
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Affiliation(s)
- Amira R. Vitt
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Valeria Bortolaia
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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12
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Calvo PA, Mateo-Cáceres V, Díaz-Arco S, Redrejo-Rodríguez M, de Vega M. The enterohemorrhagic Escherichia coli insertion sequence-excision enhancer protein is a DNA polymerase with microhomology-mediated end-joining activity. Nucleic Acids Res 2023; 51:1189-1207. [PMID: 36715333 PMCID: PMC9943667 DOI: 10.1093/nar/gkad017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/31/2023] Open
Abstract
Bacterial genomes contain an abundance of transposable insertion sequence (IS) elements that are essential for genome evolution and fitness. Among them, IS629 is present in most strains of enterohemorrhagic Escherichia coli O157 and accounts for many polymorphisms associated with gene inactivation and/or genomic deletions. The excision of IS629 from the genome is promoted by IS-excision enhancer (IEE) protein. Despite IEE has been identified in the most pathogenic serotypes of E. coli, its biochemical features that could explain its role in IS excision are not yet understood. We show that IEE is present in >30% of all available E. coli genome assemblies, and is highly conserved and very abundant within enterohemorrhagic, enteropathogenic and enterotoxigenic genomes. In vitro analysis of the recombinant protein from E. coli O157:H7 revealed the presence of a Mn2+-dependent error-prone DNA polymerase activity in its N-terminal archaeo-eukaryotic primase (AEP) domain able to promote dislocations of the primer and template strands. Importantly, IEE could efficiently perform in vitro an end-joining reaction of 3'-single-strand DNA overhangs with ≥4 bp of homology requiring both the N-terminal AEP and C-terminal helicase domains. The proposed role for IEE in the novel IS excision mechanism is discussed.
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Affiliation(s)
- Patricia A Calvo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Víctor Mateo-Cáceres
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols (Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Silvia Díaz-Arco
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Nicolás Cabrera 1, Madrid 28049, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas Alberto Sols (Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Miguel de Vega
- To whom correspondence should be addressed. Tel: +34 911964717; Fax: +34 911964420;
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Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microb Genom 2022; 8:mgen000903. [PMID: 36748558 PMCID: PMC9836092 DOI: 10.1099/mgen.0.000903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.
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Affiliation(s)
- Elizabeth A. Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chris Connor
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK,Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - James O. McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK,*Correspondence: Alan McNally,
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Shiga Toxin Subtypes, Serogroups, Phylogroups, RAPD Genotypic Diversity, and Select Virulence Markers of Shiga-Toxigenic Escherichia coli Strains from Goats in Mid-Atlantic US. Microorganisms 2022; 10:microorganisms10091842. [PMID: 36144444 PMCID: PMC9505625 DOI: 10.3390/microorganisms10091842] [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: 05/23/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 12/03/2022] Open
Abstract
Understanding Shiga toxin subtypes in E. coli from reservoir hosts may give insight into their significance as human pathogens. The data also serve as an epidemiological tool for source tracking. We characterized Shiga toxin subtypes in 491 goat E. coli isolates (STEC) from the mid-Atlantic US region (stx1 = 278, stx2 = 213, and stx1/stx2 = 95). Their serogroups, phylogroups, M13RAPD genotypes, eae (intimin), and hly (hemolysin) genes were also evaluated. STEC-positive for stx1 harbored Stx1c (79%), stx1a (21%), and stx a/c (4%). Those positive for Stx2 harbored stx2a (55%) and Stx2b (32%), while stx2a/stx2d and stx2a/stx2b were each 2%. Among the 343 STEC that were serogrouped, 46% (n = 158) belonged to O8, 20% (n = 67) to 076, 12% (n = 42) to O91, 5% (n = 17) to O5, and 5% (n = 18) to O26. Less than 5% belonged to O78, O87, O146, and O103. The hly and eae genes were detected in 48% and 14% of STEC, respectively. Most belonged to phylogroup B1 (73%), followed by D (10%), E (8%), A (4%), B2 (4%), and F (1%). M13RAPD genotyping revealed clonality of 091, O5, O87, O103, and O78 but higher diversity in the O8, O76, and O26 serogroups. These results indicate goat STEC belonged to important non-O157 STEC serogroups, were genomically diverse, and harbored Shiga toxin subtypes associated with severe human disease.
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Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru. Antibiotics (Basel) 2022; 11:antibiotics11050692. [DOI: 10.3390/antibiotics11050692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.
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