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Ncir S, Haenni M, Châtre P, Drapeau A, François P, Chaouch C, Souguir M, Azaiez S, Madec JY, Mansour W. Occurrence and persistence of multidrug-resistant Enterobacterales isolated from urban, industrial and surface water in Monastir, Tunisia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171562. [PMID: 38460700 DOI: 10.1016/j.scitotenv.2024.171562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
The One Health approach of antimicrobial resistance highlighted the role of the aquatic environment as a reservoir and dissemination source of resistance genes and resistant bacteria, especially due to anthropogenic activities. Resistance to extended-spectrum cephalosporins (ESC) conferred by extended-spectrum beta-lactamases (ESBLs) in E. coli has been proposed as the major marker of the AMR burden in cross-sectoral approaches. In this study, we investigated wastewater, surface water and seawater that are subjected to official water quality monitoring in Monastir, Tunisia. While all but one sample were declared compliant according to the official tests, ESC-resistant bacteria were detected in 31 (19.1 %) samples. Thirty-nine isolates, coming from urban, industrial and surface water in Monastir, were collected and characterized using antibiograms and whole-genome sequencing. These isolates were identified as 27 Escherichia coli (69.3 %) belonging to 13 STs, 10 Klebsiella pneumoniae (25.6 %) belonging to six STs, and two Citrobacter freundii (5.1 %). We observed the persistence and dissemination of clones over time and in different sampling sites, and no typically human-associated pathogens could be identified apart from one ST131. All isolates presented a blaCTX-M gene - blaCTX-M-15 (n = 22) and blaCTX-M-55 (n = 8) being the most frequent variants - which were identified on plasmids (n = 20) or on the chromosome (n = 19). In conclusion, we observed ESC resistance in rather ubiquitous bacteria that are capable of surviving in the water environment. This suggests that including the total coliform count and the ESBL count as determined by bacterial growth on selective plates in the official monitoring would greatly improve water quality control in Tunisia.
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Affiliation(s)
- Sana Ncir
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie; ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pierre Châtre
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Antoine Drapeau
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pauline François
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Cherifa Chaouch
- Laboratory of Transmissible Diseases and Biologically Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriem Souguir
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie; ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Sana Azaiez
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Wejdene Mansour
- Université de Sousse, Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, LR12ES02, Tunisie.
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Wolde D, Eguale T, Alemayehu H, Medhin G, Haile AF, Pirs M, Strašek Smrdel K, Avberšek J, Kušar D, Cerar Kišek T, Janko T, Steyer A, Starčič Erjavec M. Antimicrobial Susceptibility and Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia. Antibiotics (Basel) 2024; 13:93. [PMID: 38247652 PMCID: PMC10812509 DOI: 10.3390/antibiotics13010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Antimicrobial resistance of Escherichia coli is a growing problem in both developed and developing countries. This study aimed to investigate the phenotypic antimicrobial resistance of E. coli isolates (n = 260) isolated from the stool specimen of patients attending public health facilities in Addis Ababa and Hossana. This study also aimed to characterize phenotypically confirmed extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates (n = 22) using whole-genome sequencing. Resistance to 18 different antimicrobials was assessed using the disc diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The highest resistance rate among the E. coli isolates was found for ampicillin (52.7%), followed by trimethoprim-sulfamethoxazole (29.6%). Of all isolates, 50 (19.2%) were multidrug-resistant and 22 (8.5%) were ESBL producers. ESBL genes were detected in 94.7% of the sequenced E. coli isolates, and multiple β-lactamase genes were detected in 57.9% of the isolates. The predominant ESBL gene identified was blaCTX-M-15 (78.9%). The blaTEM-1B gene was detected in combination with other ESBL genes in 57.9% of the isolates, while only one of the sequenced isolates contained the blaTEM-1B gene alone. The blaCTX-M-3 gene was detected in three isolates. The genes blaCTX-M-15 and blaTEM-1B as well as blaCTX-M-15 and blaTEM-169 were confirmed to coexist in 52.6% and 10.5% of the sequenced E. coli isolates, respectively. In addition, blaOXA-1 was identified together with blaCTX-M-15 and blaTEM-1B in one isolate, and in one isolate, blaTEM-169 together with blaCTX-M-15 and blaTEM-1B was found. The results obtained show that measures need to be taken to reduce the spread of drug resistance and ensure the long-term use of available antimicrobials.
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Affiliation(s)
- Deneke Wolde
- Department of Medical Laboratory Science, College of Medicine and Health Sciences, Wachemo University, Hossana P.O. Box 667, Ethiopia;
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.E.); (H.A.); (G.M.); (A.F.H.)
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.E.); (H.A.); (G.M.); (A.F.H.)
| | - Haile Alemayehu
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.E.); (H.A.); (G.M.); (A.F.H.)
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.E.); (H.A.); (G.M.); (A.F.H.)
| | - Aklilu Feleke Haile
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.E.); (H.A.); (G.M.); (A.F.H.)
| | - Mateja Pirs
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.P.); (K.S.S.)
| | - Katja Strašek Smrdel
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.P.); (K.S.S.)
| | - Jana Avberšek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (J.A.); (D.K.)
| | - Darja Kušar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (J.A.); (D.K.)
| | - Tjaša Cerar Kišek
- National Laboratory of Health, Environment and Food, 2000 Maribor, Slovenia; (T.C.K.); (T.J.); (A.S.)
| | - Tea Janko
- National Laboratory of Health, Environment and Food, 2000 Maribor, Slovenia; (T.C.K.); (T.J.); (A.S.)
| | - Andrej Steyer
- National Laboratory of Health, Environment and Food, 2000 Maribor, Slovenia; (T.C.K.); (T.J.); (A.S.)
| | - Marjanca Starčič Erjavec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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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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4
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Walas N, Slown S, Amato HK, Lloyd T, Bender M, Varghese V, Pandori M, Graham JP. The role of plasmids in carbapenem resistant E. coli in Alameda County, California. BMC Microbiol 2023; 23:147. [PMID: 37217873 DOI: 10.1186/s12866-023-02900-2] [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: 02/10/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids). RESULTS Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n = 17) followed closely by ST405 (n = 12). blaCTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne blaCTX-M-15 gene and an isolate with a plasmid-borne blaCTX-M-15 gene. CONCLUSIONS This study provides insights into the dominant clonal groups driving carbapenem resistant E. coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance. The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups, potentially complicating clinical and public health intervention.
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Affiliation(s)
- Nikolina Walas
- School of Public Health, University of California, Berkeley, CA, USA.
| | - Samuel Slown
- School of Public Health, University of California, Berkeley, CA, USA
| | - Heather K Amato
- School of Public Health, University of California, Berkeley, CA, USA
| | - Tyler Lloyd
- Alameda County Public Health Laboratory, Oakland, CA, USA
| | - Monica Bender
- Alameda County Public Health Laboratory, Oakland, CA, USA
| | - Vici Varghese
- Alameda County Public Health Laboratory, Oakland, CA, USA
| | - Mark Pandori
- Alameda County Public Health Laboratory, Oakland, CA, USA
- Nevada State Public Health Laboratory, Reno, NV, USA
| | - Jay P Graham
- School of Public Health, University of California, Berkeley, CA, USA
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Narendrakumar L, Chakraborty M, Kumari S, Paul D, Das B. β-Lactam potentiators to re-sensitize resistant pathogens: Discovery, development, clinical use and the way forward. Front Microbiol 2023; 13:1092556. [PMID: 36970185 PMCID: PMC10036598 DOI: 10.3389/fmicb.2022.1092556] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 03/12/2023] Open
Abstract
β-lactam antibiotics are one of the most widely used and diverse classes of antimicrobial agents for treating both Gram-negative and Gram-positive bacterial infections. The β-lactam antibiotics, which include penicillins, cephalosporins, monobactams and carbapenems, exert their antibacterial activity by inhibiting the bacterial cell wall synthesis and have a global positive impact in treating serious bacterial infections. Today, β-lactam antibiotics are the most frequently prescribed antimicrobial across the globe. However, due to the widespread use and misapplication of β-lactam antibiotics in fields such as human medicine and animal agriculture, resistance to this superlative drug class has emerged in the majority of clinically important bacterial pathogens. This heightened antibiotic resistance prompted researchers to explore novel strategies to restore the activity of β-lactam antibiotics, which led to the discovery of β-lactamase inhibitors (BLIs) and other β-lactam potentiators. Although there are several successful β-lactam-β-lactamase inhibitor combinations in use, the emergence of novel resistance mechanisms and variants of β-lactamases have put the quest of new β-lactam potentiators beyond precedence. This review summarizes the success stories of β-lactamase inhibitors in use, prospective β-lactam potentiators in various phases of clinical trials and the different strategies used to identify novel β-lactam potentiators. Furthermore, this review discusses the various challenges in taking these β-lactam potentiators from bench to bedside and expounds other mechanisms that could be investigated to reduce the global antimicrobial resistance (AMR) burden.
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Affiliation(s)
- Lekshmi Narendrakumar
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
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Higgins O, Chueiri A, O'Connor L, Lahiff S, Burke L, Morris D, Pfeifer NM, Santamarina BG, Berens C, Menge C, Caniça M, Manageiro V, Kisand V, Hassan MM, Gardner B, van Vliet AHM, La Ragione RM, Gonzalez-Zorn B, Smith TJ. Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification. Microbiol Spectr 2023; 11:e0331622. [PMID: 36511696 PMCID: PMC9927312 DOI: 10.1128/spectrum.03316-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Sinéad Lahiff
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Liam Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Dearbhaile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Nicola Maria Pfeifer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Belén González Santamarina
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marwa M. Hassan
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brian Gardner
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Arnoud H. M. van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit, Veterinary School and VISAVET, Complutense University of Madrid, Spain
| | - Terry J. Smith
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
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7
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Merhi G, Amayri S, Bitar I, Araj GF, Tokajian S. Whole Genome-Based Characterization of Multidrug Resistant Enterobacter and Klebsiella aerogenes Isolates from Lebanon. Microbiol Spectr 2023; 11:e0291722. [PMID: 36651778 PMCID: PMC9927356 DOI: 10.1128/spectrum.02917-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Enterobacter spp. and Klebsiella aerogenes are rod-shaped Gram-negative opportunistic pathogens. This study aimed at the molecular and genomic characterization of multidrug resistant Enterobacter spp. and K. aerogenes isolates recovered from hospitalized patients in a tertiary care hospital in Lebanon. A total of 59 Enterobacter spp. clinical isolates consisting of 41 carbapenem-resistant and 18 susceptible by Etest were included in this study. Genotypic identification through whole-genome sequencing (WGS) was performed and confirmed in silico. Resistance and plasmid profiles were studied using ResFinder4.0 and Plasmid-Finder2.1. Multilocus sequence typing (MLST) was used to determine the isolates' clonality. Using the average nucleotide identity (ANI) we identified and confirmed that 47 (80%) isolates were E. hormaechei, 11 (18%) were Klebsiella aerogenes and 1 (2%) was an E. cloacae. Carbapenem-resistance was detected among 41 isolates all showing an MIC90 of ≥ 32 μg/mL for ertapenem, imipenem, and meropenem. blaNDM-1 (58.5%), blaACT-16 (54%), and blaOXA-1 (54%) were the most common detected β-lactamases, while blaCTX-M-15 (68%) was the main detected extended-spectrum β-lactamase (ESBL) encoding gene. Chromosomal ampC, carbapenemase encoding genes, and porin modifications were among the detected carbapenem resistance determinants. The carbapenemase encoding genes were linked to three well-defined plasmid Inc groups, IncFII/IncFIB, IncX3, and IncL. MLST typing revealed the diversity within the studied isolates, with ST114 being the most common among the studied E. hormaechei.: The spread of carbapenem-resistant isolates in clinical settings in Lebanon is a serious challenge. Screening and continuous monitoring through WGS analysis could effectively limit the dissemination of drug-resistant isolates in hospitalized patients. IMPORTANCE Drug resistance is an increasing global public health threat that involves most disease-causing organisms and antimicrobial drugs. Drug-resistant organisms spread in health care settings, and resistance to multiple drugs is common. Our study demonstrated the mechanisms leading to resistance against the last resort antimicrobial agents among members of the Enterobacteriaceae family. The spread of carbapenem-resistant bacteria in clinical settings is a serious challenge. Screening and continuous monitoring could effectively limit the dissemination of drug-resistant isolates in hospitalized patients.
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Affiliation(s)
- Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
| | - Sara Amayri
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - George F. Araj
- Department of Pathology & Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
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Martínez-Vázquez AV, Mandujano A, Cruz-Gonzalez E, Guerrero A, Vazquez J, Cruz-Pulido WL, Rivera G, Bocanegra-García V. Evaluation of Retail Meat as a Source of ESBL Escherichia coli in Tamaulipas, Mexico. Antibiotics (Basel) 2022; 11:antibiotics11121795. [PMID: 36551452 PMCID: PMC9774973 DOI: 10.3390/antibiotics11121795] [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: 10/31/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
In recent decades, the appearance of a group of strains resistant to most β-lactam antibiotics, called extended-spectrum β-lactamases (ESBLs), has greatly impacted the public health sector. The present work aimed to identify the prevalence of ESBL-producing Escherichia coli strains in retail meat from northeast Tamaulipas. A total of 228 meat samples were obtained from 76 different stores. A prevalence of E. coli ESBL of 6.5% (15/228) was detected. All (15/15) of the ESBL strains were multiresistant. Altogether, 40% (6/15) of the strains showed the presence of class 1 integrons. The isolates identified with blaCTX-M (20%) also showed co-resistance with the tet (A and B), str (A and B), and sul (2 and 3) genes. A total of 20% of the strains belonged to the B2 and D phylogroups, which are considered pathogenic groups. None of the ESBL-positive strains contained any of the virulence gene factors tested. The presence of ESBL-producing E. coli strains in meat indicates a potential risk to the consumer. Although most of these strains were classified as commensals, they were found to serve as reservoirs of multiresistance to antimicrobials and, therefore, are potential routes of dispersion of this resistance to other bacteria.
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Affiliation(s)
- Ana Verónica Martínez-Vázquez
- Centro de Biotecnología Genómica of Instituto Politécnico Nacional, Reynosa 88710, Mexico
- Correspondence: (A.V.M.-V.); (V.B.-G.); Tel.: +52-8999243627 (ext. 87753) (V.B.-G.)
| | - Antonio Mandujano
- Centro de Biotecnología Genómica of Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Eduardo Cruz-Gonzalez
- Centro de Biotecnología Genómica of Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Abraham Guerrero
- CONACyT Research, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico
| | - Jose Vazquez
- Facultad de Medicina Veterinaria, Universidad Autónoma de Tamaulipas, Cd Victoria 87274, Mexico
| | | | - Gildardo Rivera
- Centro de Biotecnología Genómica of Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Virgilio Bocanegra-García
- Centro de Biotecnología Genómica of Instituto Politécnico Nacional, Reynosa 88710, Mexico
- Correspondence: (A.V.M.-V.); (V.B.-G.); Tel.: +52-8999243627 (ext. 87753) (V.B.-G.)
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Voor in ’t holt AF, van der Schoor AS, Mourik K, Strepis N, Klaassen CHW, Vos MC, Severin JA. Pre-COVID-19 international travel and admission to hospital when back home: travel behavior, carriage of highly resistant microorganisms, and risk perception of patients admitted to a large tertiary care hospital. Antimicrob Resist Infect Control 2022; 11:78. [PMID: 35655236 PMCID: PMC9161189 DOI: 10.1186/s13756-022-01106-x] [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: 10/20/2021] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
Background When people who recently travelled abroad are admitted to a hospital back home, there is a risk of introducing highly resistant microorganisms (HRMO) into the hospital. To minimize this risk, a feasible infection prevention strategy should be developed. In this study, we investigated patients’ travel history and behavior during travel and analyzed whether this was correlated to HRMO carriage at admission. Methods From May 2018 until August 2019, adult patients admitted to a large tertiary care center in the Netherlands were asked upon hospital admission to participate in the study. Included patients received a questionnaire about risk perception, travel history in the last year, and behavior during travel, and were screened for HRMO carriage at admission using a perianal swab. Results Six hundred and eight questionnaires were handed out, of which 247 were returned (40.6%). One hundred and thirty (52.6%) patients did not travel abroad in the last year, of whom eight (6.2%) were HRMO carrier at admission. One hundred seventeen (47.4%) patients travelled in the preceding year, of whom seven patients (6.0%) were HRMO carrier at admission. Thirty patients (12%) travelled outside of Europe; in this group HRMO prevalence was 13.3% (4 out of 30). The majority of patients (71.3%) were aware that international travel could lead to carriage of HRMO, and an even larger majority (89.5%) would support a screening strategy upon hospital admission in case of a travel history, to minimize the risk of introducing HRMO. Conclusions We identified that half of admitted patients to a large tertiary care hospital travelled abroad in the last year, with only a small percentage outside Europe. We discuss several screening strategies and propose a strategy of screening and preemptive isolation of patients who travelled to Asia or Africa in the 2 months before their hospital admission; a strategy that patients would support. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01106-x.
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Mechesso AF, Na SH, Moon DC, Kim SJ, Choi JH, Song HJ, Yoon SS, Lim SK. Antibiotic Resistance Profiles and Molecular Characteristics of blaCTX-M-15-Carrying Salmonella enterica Serovar Enteritidis Isolates from Healthy and Diseased Chickens in Korea. Foodborne Pathog Dis 2022; 19:663-674. [PMID: 36125409 DOI: 10.1089/fpd.2022.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica serovar Enteritidis has emerged as a public health concern. The main objectives of this study were therefore to determine the antimicrobial susceptibility profiles of Salmonella Enteritidis and to investigate the molecular characteristics of identified ESBL-producing isolates. In the study, 237 Salmonella Enteritidis isolates (232 isolates from chickens, 4 from cattle, and 1 from a pig) were recovered from carcasses and fecal samples of healthy and diseased food animals between 2010 and 2017. Ceftiofur resistance was noted only in chicken isolates (43%, 102/237), with the highest in healthy chickens and their carcasses (48.3%, 83/172) compared with that in diseased chickens (31.7%, 19/60). All of the ceftiofur-resistant isolates exhibited resistance to multiple antimicrobials. Indeed, a relatively higher percentage of ceftiofur-resistant isolates demonstrated resistance to the tested aminoglycosides and tetracycline compared with the ceftiofur-susceptible strains. In this study, blaCTX-M-15 was the only ESBL gene detected in all of the ceftiofur-resistant isolates. The blaCTX-M-15-carrying isolates belonged to 11 different pulsotypes. The blaCTX-M-15 gene was transferred from 20.6% (21/102) of the blaCTX-M-15-harboring isolates to a recipient Escherichia coli J53. The coexistence of IncHI2/ST2 and IncFIIs/ST1 plasmids was noted in the majority (81.8%, 18/22) of the transconjugants. E. coli J53 transconjugants carrying blaCTX-M-15 gene showed distinct genetic environments, predominantly ISEcp1-blaCTX-M-15-orf477 (15/21, 71.4%). This study demonstrated that healthy chickens and their carcasses act as reservoirs of blaCTX-M-15-carrying Salmonella Enteritidis that can potentially be transmitted to humans.
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Affiliation(s)
- Abraham Fikru Mechesso
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea.,Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Seok-Hyeon Na
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong Chan Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Su-Jeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Ji-Hyun Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hyun-Ju Song
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
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Distribution of ESBL/AmpC-Escherichia coli on a Dairy Farm. Antibiotics (Basel) 2022; 11:antibiotics11070940. [PMID: 35884193 PMCID: PMC9311582 DOI: 10.3390/antibiotics11070940] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
The aim of the study was to determine the prevalence of ESBL/AmpC-producing Escherichia (E.) coli and to investigate their on-farm distribution on an exemplary dairy farm. For this purpose, sample sizes were calculated, and fecal samples were collected from cattle of all ages and analyzed for the presence of ESBL/AmpC-E. coli using selective media supplemented with cefotaxime. These antibiotic-resistant bacteria were detected in 22.5% of the samples tested. The prevalence was highest in the calf age group, in which 100% of the collected fecal samples were positive. With increasing age, the prevalence decreased in the other sample groups. While ESBL/AmpC E. coli could still be detected in young stock (15%) and breeding heifers (5%), no resistant pathogens could be detected in adult animals. Whole-genome sequencing of the ESBL/AmpC-E. coli isolates revealed, first, that all isolates were ESBL producers (CTX-M-1 and CTX-M-15) and, second, that ST362, which is known as a biofilm producer, was dominant in the calves (85%, n = 17). Based on these results and the evaluation of a questionnaire, possible causes for the occurrence of ESBL/AmpC-E. coli were discussed and recommendations for the reduction in transmission were formulated. Unlike most German dairy farms, no waste milk feeding was apparent; therefore, factors reducing ESBL/AmpC-E. coli are primarily related to an improvement in hygiene management to prevent biofilms, e.g., in nipple buckets, but also to question the use of antibiotics, e.g., in the treatment of diarrheic calves.
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Yoon EJ, Choi YJ, Kim D, Won D, Choi JR, Jeong SH. Amplification of the Chromosomal blaCTX-M-14 Gene in Escherichia coli Expanding the Spectrum of Resistance under Antimicrobial Pressure. Microbiol Spectr 2022; 10:e0031922. [PMID: 35467393 PMCID: PMC9241692 DOI: 10.1128/spectrum.00319-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
Various forms of adaptive evolution occur in clinical isolates in response to the presence of antimicrobial drugs. Among a total of 171 CTX-M-9 group/family extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli blood isolates recovered between 2016 and 2017 in six general hospitals, 50.3% of the isolates possessed the blaCTX-M-14-like gene in their chromosome rather than in a plasmid. Focusing on this unprecedented way of the blaCTX-M ESBL gene possession, molecular epidemiology of the isolates was assessed and the chromosomal location of the acquired cephalosporinase gene was dissected in an evolutionary point of view. Taking advantage of a complete collection of E. coli blood isolates from a limited period, clonal relatedness of the E. coli isolates carrying the blaCTX-M-14-like gene was clarified and the dominant clone, ST131 H30R, was identified. To control the level of resistance and the resistance spectrum to oxyimino-cephalosporin drugs, transcription level of the blaCTX-M-14-like gene was tuned finely through positioning the gene near the chromosomal initiation dnaA gene and amplifying numbers of the gene in a chromosome using either the copy-and-paste or the tandem amplification methods. Inconspicuous fitness cost by chromosomal location of the gene and free adjustment of the oxyimino-cephalosporin resistance would urge the dominancy of E. coli clinical isolates harboring the blaCTX-M ESBL gene in their chromosome. IMPORTANCE Increasing prevalence of E. coli producing CTX-M ESBL is a major concern in clinical settings because it significantly limits treatment options. Thus, it is important to keep watching current molecular mechanisms of resistance and the scheme for dissemination. Recently, chromosomal locations of the blaCTX-M genes are often documented in clinical settings and the bacterial strategies were needed to be dissected in an evolutionary point of view. Both main mechanisms of fine tuning the chromosomal gene expression, bacterial gene amplification either by copy-and-paste or by tandem amplification and positioning the gene near the chromosomal initiation dnaA gene, were demonstrated in the study, and the fitness cost by the chromosomal location was evaluated.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
- Division of Antimicrobial Resistance Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - You Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Ribeiro-Almeida M, Mourão J, Novais Â, Pereira S, Freitas-Silva J, Ribeiro S, Martins da Costa P, Peixe L, Antunes P. High diversity of pathogenic Escherichia coli clones carrying mcr-1 among gulls underlines the need for strategies at the environment-livestock-human interface. Environ Microbiol 2022; 24:4702-4713. [PMID: 35726894 DOI: 10.1111/1462-2920.16111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/30/2022]
Abstract
The expansion of mcr-carrying bacteria is a well-recognized public health problem. Measures to contain mcr spread have mainly been focused on the food-animal production sector. Nevertheless, the spread of MCR-producers at the environmental interface particularly driven by the increasing population of gulls in coastal cities has been less explored. Occurrence of mcr-carrying Escherichia coli in gull's colonies faeces on a Portuguese beach was screened over 7-months. Cultural, molecular, and genomic approaches were used to characterize their diversity, mcr plasmids and adaptive features. Multidrug-resistant mcr-1-carrying E. coli were detected for three consecutive months. Over time, multiple strains were recovered, including zoonotic-related pathogenic E. coli clones (e.g., B2-ST131-H22, A-ST10, and B1-ST162). Diverse mcr-1.1 genetic environments were mainly associated with ST2/ST4-HI2 (ST10, ST131, ST162, ST354 and ST4204) but also IncI2 (ST12990) plasmids or in the chromosome (ST656). Whole-genome sequencing revealed enrichment of these strains on antibiotic resistance, virulence, and metal tolerance genes. Our results underscore gulls as important spreaders of high priority bacteria and genes that may affect the environment, food-animals and/or humans, potentially undermining One-Health strategies to reduce colistin resistance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marisa Ribeiro-Almeida
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal.,School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Joana Mourão
- Faculty of Sciences and Technology, University of Algarve, Gambelas Campus, Faro, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Sofia Pereira
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Joana Freitas-Silva
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Sofia Ribeiro
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Paulo Martins da Costa
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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Aldea I, Gibello A, Hernández M, Leekitcharoenphon P, Bortolaia V, Moreno MA. Clonal and plasmid-mediated flow of ESBL/AmpC genes in Escherichia coli in a commercial laying hen farm. Vet Microbiol 2022; 270:109453. [DOI: 10.1016/j.vetmic.2022.109453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
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15
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Gomi R, Yamamoto M, Tanaka M, Matsumura Y. Chromosomal integration of blaCTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100144. [PMID: 35909619 PMCID: PMC9325909 DOI: 10.1016/j.crmicr.2022.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ryota Gomi
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540, Kyoto, Japan
- Corresponding author
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, 606-8507, Kyoto, Japan
| | - Michio Tanaka
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, 606-8507, Kyoto, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, 606-8507, Kyoto, Japan
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16
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Zheng Z, Lei Y, Wang Y, Lin C, Lin J. Occurrence of mcr Positive Strains and Molecular Characteristics of Two mcr-1 Positive Salmonella typhimurium and Escherichia coli from a Chinese Women's and Children's Hospital. Infect Drug Resist 2021; 14:2925-2932. [PMID: 34349527 PMCID: PMC8327187 DOI: 10.2147/idr.s322686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/22/2021] [Indexed: 12/18/2022] Open
Abstract
Background The purpose of this study was to evaluate the prevalence of mobile colistin resistance genes (mcr) in Gram-negative bacteria and to analyze the molecular characteristics of mcr-1 positive Salmonella typhimurium strain 75 and Escherichia coli strain 107 from the Quanzhou Women’s and Children’s Hospital in China. Methods The genes mcr-1 through mcr-9 were screened via multiplex PCR. Antibiotic susceptibility was detected using a GN11 card with the VITEK-2 compact automated system. Whole genomes were sequenced using PacBio’s single molecule real-time (SMRT) technology. Results In this study, mcr-1 was detected in only four strains, with a positivity rate of 0.65% (4/616). All the four strains were resistant to more than three different kinds of antibiotics. The mcr-1 positive S. typhimurium strain 75 harbored IncHI2 plasmid, which carried mcr-1 gene, while the mcr-1 positive E. coli strain 107 contained four plasmids including one mcr-1 harboring IncHI2 plasmid, one IncFII plasmid and two IncI1-I (Alpha) plasmids. Mobile elements carrying mcr-1 in the 75_plasmid and 107_plasmid-1 were located in the IS1086(ISApl1)-IS30A(ISApl1)-mcr-1-hp and IS1086(ISApl1)-mcr-1-hp regions, respectively. Tn6010 carrying drug efflux pump genes was found in 75_plasmid, while cn_31611_IS26 carrying multi-drug resistance (MDR) genes were found in 107_plasmid-1. Conclusion This study found that mcr-1 was prevalent at a low frequency in the Quanzhou Women’s and Children’s Hospital. A similar genetic pattern of mcr-1 transmission was found in both E. coli and S. typhimurium.
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Affiliation(s)
- Zhenzhu Zheng
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Ying Lei
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Yinna Wang
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Chunli Lin
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Jiansheng Lin
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
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17
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Moor J, Aebi S, Rickli S, Mostacci N, Overesch G, Oppliger A, Hilty M. Dynamics of extended-spectrum cephalosporin-resistant Escherichia coli in pig farms: A longitudinal study. Int J Antimicrob Agents 2021; 58:106382. [PMID: 34157404 DOI: 10.1016/j.ijantimicag.2021.106382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/31/2021] [Accepted: 06/12/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Point prevalence estimates of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. A longitudinal study was therefore performed by sampling individual pigs, pig farmers and the environment. METHODS On average, 30 (range 10-46) piglets of 31 Swiss farms were sampled during the suckling, weaning and fattening stages (n= 2437 samples). In addition, stool from pig farmers and environmental samples were obtained and metadata collected by questionnaires. ESC-R-Ec was identified by routine culture, and clonal relationships and resistance genes were derived from whole genome sequencing data. RESULTS Working on pig farms was not associated with an increased prevalence of ESC-R-Ec in humans. ESC-R-Ec prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively (P < 0.001). Within the 57 ESC-R-positive suckling piglets, persisting carriage was detected in 25 animals at two consecutive time points and one animal at three consecutive time points. Clonal spread (n=7 farms, 22.6%) and horizontal gene transfer (n=1 farm, 3%) within pigs but not between humans and animals was detected. Liquid manure (n=10 samples, 16.7%) was identified as the major environmental reservoir of ESC-R-Ec in the pig farm environment. CONCLUSIONS Pig farming practices like all-in-all-out systems, but not antimicrobial usage, were associated with reduced risk of ESC-R-Ec at the farm level. As carriage duration is normally short within the individual pigs, the risk of recolonisation and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies.
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Affiliation(s)
- Julia Moor
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Susanne Rickli
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Nadezda Mostacci
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Gudrun Overesch
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Anne Oppliger
- Unisante, Department of Occupational and Environmental Health, University of Lausanne, Lausanne, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
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18
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Makhlouf J, Merhi G, Salloum T, Abboud E, Tokajian S. Molecular characterization of a carbapenem-resistant Enterobacter hormaechei ssp. xiangfangensis co-harbouring bla NDM-1 and a chromosomally encoded phage-linked bla CTX-M-15 genes. INFECTION GENETICS AND EVOLUTION 2021; 93:104924. [PMID: 34004359 DOI: 10.1016/j.meegid.2021.104924] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/22/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Enterobacter cloacae complex (ECC) members are rapidly emerging as successful nosocomial pathogens, especially, with the emergence of carbapenem-resistant clones. In this study, we performed a comprehensive molecular characterization of a carbapenem-resistant E. hormaechei ssp. xiangfangensis LAU_ENC1. hsp60 and average nucleotide identity (ANI) were used for its identification. The repertoire of resistance genes and phage content were analyzed. Plasmid sequences were extracted and compared to closest references. The isolate LAU_ENC1 was identified as an E. hormaechei ssp. xiangfangensis and belonged to ST-114A sub-cluster. blaNDM-1, blaCTX-M-15, blaOXA-1, and blaACT-16 genes were detected as β-lactam resistance determinants. A chromosomal hybrid intact phage, Enterobacter phage LAU1, with blaCTX-M-15 integrated in its direct vicinity within an ISEcp1 - blaCTX-M-15 - wbuC - ∆Tn2 rare cassette was detected. blaNDM-1 was integrated within a novel IncFII conjugative plasmid, pLAU_ENC1, through an IS3000- ΔISAba125-blaNDM-1-bleMBL-//-Tn5403 cassette. To our knowledge, this is the first report of a multi-drug resistant (MDR) E. hormaechei ssp. xiangfangensis carrying a blaCTX-M-15 integrated within the proximity of a provirus chromosomal region. Treatment options for MDR ECC members are becoming scarce, thus warranting an increased monitoring of the dissemination of these pathogens in clinical settings.
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Affiliation(s)
- Jana Makhlouf
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Lebanon
| | - Edmond Abboud
- Laboratory Department, Middle East Institute of Health University Hospital, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Lebanon.
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19
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Shawa M, Furuta Y, Mulenga G, Mubanga M, Mulenga E, Zorigt T, Kaile C, Simbotwe M, Paudel A, Hang'ombe B, Higashi H. Novel chromosomal insertions of ISEcp1-bla CTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli. Antimicrob Resist Infect Control 2021; 10:79. [PMID: 33971966 PMCID: PMC8111917 DOI: 10.1186/s13756-021-00941-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Background The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. blaCTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that blaCTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated blaCTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements. Methods A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, blaCTX-M genes were categorized as either chromosomal or plasmid-borne. Results WGS-based genotyping identified 58 AMR genes, including four blaCTX-M alleles (i.e., blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of blaCTX-M genes. Out of 45 blaCTX-M gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal blaCTX-M-15 was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles. Conclusion Our study revealed the co-occurrence of ISEcp1-blaCTX-M-15 and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00941-8.
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Affiliation(s)
- Misheck Shawa
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Gillan Mulenga
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Maron Mubanga
- Department of Para-Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Evans Mulenga
- Department of Para-Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Tuvshinzaya Zorigt
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Christone Kaile
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Manyando Simbotwe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Atmika Paudel
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Bernard Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Hideaki Higashi
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
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20
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Hassen B, Abbassi MS, Ruiz-Ripa L, Mama OM, Ibrahim C, Benlabidi S, Hassen A, Torres C, Hammami S. Genetic characterization of extended-spectrum β-lactamase-producing Enterobacteriaceae from a biological industrial wastewater treatment plant in Tunisia with detection of the colistin-resistance mcr-1 gene. FEMS Microbiol Ecol 2021; 97:5986610. [PMID: 33202005 DOI: 10.1093/femsec/fiaa231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022] Open
Abstract
This study evaluated the occurrence of extended-spectrum β-lactamases (ESBL) and associated resistance genes, integrons, and plasmid types, as well as the genetic relatedness of enterobacterial isolates in the wastewater treatment plant (WWTP) of La Charguia, Tunis City (Tunisia). A total of 100 water samples were collected at different points of the sewage treatment process during 2017-2019. Antimicrobial susceptibility was conducted by the disc-diffusion method. blaCTX-M, blaTEM and blaSHV genes as well as those encoding non-β-lactam resistance, the plasmid types, occurrence of class1 integrons and phylogenetic groups of Escherichia coli isolates were determined by PCR/sequencing. Genomic relatedness was determined by multi-locus sequence typing (MLST) for selected isolates. In total, 57 ESBL-producer isolates were recovered (47 E. coli, eight Klebsiella pneumoniae, 1 of the Citrobacter freundii complex and 1 of the Enterobacter cloacae complex). The CTX-M-15 enzyme was the most frequently detected ESBL, followed by CTX-M-27, CTX-M-55 and SHV-12. One E. coli isolate harboured the mcr-1 gene. The following phylogroups/sequence types (STs) were identified among ESBL-producing E. coli isolates: B2/ST131 (subclade-C1), A/ST3221, A/ST8900, D/ST69, D/ST2142, D/ST38, B1/ST2460 and B1/ST6448. High numbers of isolates harboured the class 1 integrons with various gene cassette arrays as well as IncP-1 and IncFIB plasmids. Our findings confirm the importance of WWTPs as hotspot collectors of ESBL-producing Enterobacteriaceae with a high likelihood of spread to human and natural environments.
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Affiliation(s)
- Bilel Hassen
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia.,Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de résistance aux antibiotiques LR99ES09, Tunisia
| | - Laura Ruiz-Ripa
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Olouwafemi M Mama
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Chourouk Ibrahim
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Saloua Benlabidi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Carmen Torres
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Salah Hammami
- Université de la Manouba, IRESA, École Nationale de Médecine Vétérinaire de Sidi Thabet, Sidi Thabet 2020, Sidi Thabet, Ariana, Tunisia
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21
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Findlay J, Gould VC, North P, Bowker KE, Williams MO, MacGowan AP, Avison MB. Characterization of cefotaxime-resistant urinary Escherichia coli from primary care in South-West England 2017-18. J Antimicrob Chemother 2021; 75:65-71. [PMID: 31538190 DOI: 10.1093/jac/dkz397] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Third-generation cephalosporin-resistant Escherichia coli from community-acquired urinary tract infections are increasingly reported worldwide. We sought to determine and characterize the mechanisms of cefotaxime resistance employed by urinary E. coli obtained from primary care, over 12 months, in Bristol and surrounding counties in South-West England. METHODS Cefalexin-resistant E. coli isolates were identified from GP-referred urine samples using disc susceptibility testing. Cefotaxime resistance was determined by subsequent plating onto MIC breakpoint plates. β-Lactamase genes were detected by PCR. WGS was performed on 225 isolates and analyses were performed using the Center for Genomic Epidemiology platform. Patient information provided by the referring general practices was reviewed. RESULTS Cefalexin-resistant E. coli (n=900) isolates were obtained from urines from 146 general practices. Following deduplication by patient approximately 69% (576/836) of isolates were cefotaxime resistant. WGS of 225 isolates identified that the most common cefotaxime-resistance mechanism was blaCTX-M carriage (185/225), followed by plasmid-mediated AmpCs (pAmpCs) (17/225), AmpC hyperproduction (13/225), ESBL blaSHV variants (6/225) or a combination of both blaCTX-M and pAmpC (4/225). Forty-four STs were identified, with ST131 representing 101/225 isolates, within which clade C2 was dominant (54/101). Ciprofloxacin resistance was observed in 128/225 (56.9%) of sequenced isolates, predominantly associated with fluoroquinolone-resistant clones ST131 and ST1193. CONCLUSIONS Most cefalexin-resistant E. coli isolates were cefotaxime resistant, predominantly caused by blaCTX-M carriage. The correlation between cefotaxime resistance and ciprofloxacin resistance was largely attributable to the high-risk pandemic clones ST131 and ST1193. Localized epidemiological data provide greater resolution than regional data and can be valuable for informing treatment choices in the primary care setting.
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Affiliation(s)
- Jacqueline Findlay
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Virginia C Gould
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Paul North
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Karen E Bowker
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Martin O Williams
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Alasdair P MacGowan
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Matthew B Avison
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
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22
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Skarżyńska M, Zaja C M, Bomba A, Bocian Ł, Kozdruń W, Polak M, Wia Cek J, Wasyl D. Antimicrobial Resistance Glides in the Sky-Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic Potential. Front Microbiol 2021; 12:656223. [PMID: 33897669 PMCID: PMC8062882 DOI: 10.3389/fmicb.2021.656223] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global health concerns; therefore, the identification of AMR reservoirs and vectors is essential. Attention should be paid to the recognition of potential hazards associated with wildlife as this field still seems to be incompletely explored. In this context, the role of free-living birds as AMR carriers is noteworthy. Therefore, we applied methods used in AMR monitoring, supplemented by colistin resistance screening, to investigate the AMR status of Escherichia coli from free-living birds coming from natural habitats and rescue centers. Whole-genome sequencing (WGS) of strains enabled to determine resistance mechanisms and investigate their epidemiological relationships and virulence potential. As far as we know, this study is one of the few that applied WGS of that number (n = 71) of strains coming from a wild avian reservoir. The primary concerns arising from our study relate to resistance and its determinants toward antimicrobial classes of the highest priority for the treatment of critical infections in people, e.g., cephalosporins, quinolones, polymyxins, and aminoglycosides, as well as fosfomycin. Among the numerous determinants, bla CTX-M-15, bla CMY-2, bla SHV-12, bla TEM-1B, qnrS1, qnrB19, mcr-1, fosA7, aac(3)-IIa, ant(3")-Ia, and aph(6)-Id and chromosomal gyrA, parC, and parE mutations were identified. Fifty-two sequence types (STs) noted among 71 E. coli included the global lineages ST131, ST10, and ST224 as well as the three novel STs 11104, 11105, and 11194. Numerous virulence factors were noted with the prevailing terC, gad, ompT, iss, traT, lpfA, and sitA. Single E. coli was Shiga toxin-producing. Our study shows that the clonal spread of E. coli lineages of public and animal health relevance is a serious avian-associated hazard.
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Affiliation(s)
- Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Magdalena Zaja C
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Arkadiusz Bomba
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Łukasz Bocian
- Department of Epidemiology and Risk Assessment, National Veterinary Research Institute, Puławy, Poland
| | - Wojciech Kozdruń
- Department of Poultry Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Marcin Polak
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jarosław Wia Cek
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.,Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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23
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Pet and Stray Dogs as Reservoirs of Antimicrobial-Resistant Escherichia coli. Int J Microbiol 2021; 2021:6664557. [PMID: 33564312 PMCID: PMC7850822 DOI: 10.1155/2021/6664557] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/28/2020] [Accepted: 01/14/2021] [Indexed: 11/17/2022] Open
Abstract
The close contact between dogs and humans creates the best bridge for interspecies transmission of antimicrobial-resistant bacteria. The surveillance of its resistance including the detection of extended-spectrum beta-lactamases (ESBLs) in Escherichia coli as indicator bacteria is an important tool to control the use of antimicrobials. The aim of this research was to evaluate the E. coli resistance in strains by phenotypic methods, isolated from pet and stray dogs of La Plata city, Argentina. Faecal samples were collected using rectal swabs from 50 dogs with owners (home dogs = HD) and 50 homeless dogs (stray dogs = SD). They were cultured in 3 MacConkey agar plates, with and without antibiotics (ciprofloxacin and cefotaxime). 197 strains were isolated, of which only 95 strains were biochemically identified as E. coli, 46 strains were from HD, and 49 were from SD. Antimicrobial susceptibility was evaluated by the Kirby-Bauer disk diffusion method. The most prevalent resistance was for tetracycline, streptomycin, and ampicillin. In both groups, the level of resistance to 3rd generation cephalosporins was high, and there were multiresistant strains. There was a higher level of antimicrobial resistance in strains from SD compared to HD. There were 8% of strains suspected of being ESBLs among samples of HD and 36% of SD. One (2%) of the strains isolated from HD and 11 (22%) from SD were phenotypically confirmed as ESBL. Pets and stray dogs are a potential source of E. coli antibiotic resistance in Argentina; therefore, its surveillance must be guaranteed.
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24
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Park J, Shin E, Park AK, Kim S, Jeong HJ, Kim JS, Jin YH, Park NJ, Chun JH, Hwang K, Lee KJ, Kim J. Co-infection With Chromosomally-Located bla CTX-M-14 and Plasmid-Encoding bla CTX-M-15 in Pathogenic Escherichia coli in the Republic of Korea. Front Microbiol 2020; 11:545591. [PMID: 33262742 PMCID: PMC7686028 DOI: 10.3389/fmicb.2020.545591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
The emergence of third-generation cephalosporin resistance in Escherichia coli is increasing at an alarming rate in many countries. Thus, the aim of this study was to analyze co-infecting bla CTX-M-producing pathogenic E. coli isolates linked to three school outbreaks. Among 66 E. coli isolates, 44 were identified as ETEC O25, an ETEC isolate serotype was O2, and the other 21 were confirmed as EAEC O44. Interestingly, six patients were co-infected with EAEC O44 and ETEC O25. For these isolates, molecular analysis [antibiotic susceptibility testing, identification of the β-lactamase gene, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE)] was performed for further characterization. In addition, the transmission capacity of bla CTX-M genes was examined by conjugation experiments. Whole-genome sequencing (WGS) was performed on representative EAEC O44 and ETEC O25 isolates associated with co-infection and single-infection. All isolates were resistant to cefotaxime and ceftriaxone. All EAEC isolates carried the bla CTX-M-14 gene and all ETEC isolates the bla CTX-M-15 gene, as detected by multiplex PCR and sequencing analysis. Sequence type and PFGE results indicated three different patterns depending on the O serotype. WGS results of representative isolates revealed that the ETEC O25 strains harbored bla CTX-M-15 located on IncK plasmids associated with the Δbla TEM-bla CTX-M-15-orf477 transposon. The representative EAEC O44 isolates carried bla CTX-M-14 on the chromosome, which was surrounded by the ISEcp1-bla CTX-M-14-IS903 transposon. To the best of our knowledge, this is the first report of co-infection with chromosomally located bla CTX-M-14 and plasmid-encoding bla CTX-M-15 in pathogenic E. coli. Our findings indicate that resistance genes in clinical isolates can spread through concurrent combinations of chromosomes and plasmids.
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Affiliation(s)
- Jungsun Park
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Eunkyung Shin
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Ae Kyung Park
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Soojin Kim
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Hyun Ju Jeong
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Jin Seok Kim
- Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Seoul, South Korea
| | - Young-Hee Jin
- Infectious Diseases Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Seoul, South Korea
| | - Nan Joo Park
- Microbiology Team, Gyeonggi-do Institute of Health and Environment, Suwon, South Korea
| | - Jeong-Hoon Chun
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Kyujam Hwang
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
| | - Kwang Jun Lee
- Division of Antimicrobial Resistance, National Institute of Health, Center for Infectious Diseases Research, Centers for Disease Control and Prevention, Chungcheongbuk-do, South Korea
| | - Junyoung Kim
- Division of Bacterial Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Chungju, South Korea
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25
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Perez-Lopez A, Sundararaju S, Al-Mana H, Tsui KM, Hasan MR, Suleiman M, Janahi M, Al Maslamani E, Tang P. Molecular Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Among the Pediatric Population in Qatar. Front Microbiol 2020; 11:581711. [PMID: 33262745 PMCID: PMC7686840 DOI: 10.3389/fmicb.2020.581711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Although extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. AIM To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. METHODS Whole-genome sequencing was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. RESULTS A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-β-lactam antibiotics for both species were 18.1 and 30.1% for gentamicin, 0.8 and 4.1% for amikacin, 41.3 and 41.1% for ciprofloxacin, and 65.8 and 76.1% for cotrimoxazole. The most common sequence types (STs) were ST131 (16.9%), ST38 and ST10 (8.2% each) in E. coli and ST307 (9.7%), and ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBLs were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other β-lactamases, TEM-1B and OXA-1 were coproduced in 41 and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes cocarried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only two of 57 isolates harboring aac(6')-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae. CONCLUSION Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited, given the frequent coproduction of OXA-1 and TEM-1B enzymes and coresistance to antibiotic classes other than β-lactams.
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Affiliation(s)
- Andres Perez-Lopez
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | | | - Hassan Al-Mana
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Kin Ming Tsui
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mohammad Rubayet Hasan
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Mohammed Suleiman
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Mohammed Janahi
- Weill Cornell Medical College in Qatar, Doha, Qatar
- Division of Pediatric Infectious Diseases, Sidra Medicine, Doha, Qatar
| | - Eman Al Maslamani
- Weill Cornell Medical College in Qatar, Doha, Qatar
- Division of Pediatric Infectious Diseases, Sidra Medicine, Doha, Qatar
| | - Patrick Tang
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
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Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States. mSphere 2020; 5:5/5/e00990-20. [PMID: 33115839 PMCID: PMC8534314 DOI: 10.1128/msphere.00990-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). blaCMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), blaCTX-M (carried by IncF, IncHI2, and IncN plasmids), and blaSHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb′-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health. IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli. Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.
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27
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Jama-Kmiecik A, Sarowska J, Frej-Mądrzak M, Choroszy-Król I. Extraintestinal pathogenic E. coli infections: The spread of antibiotic resistance through the food products. POSTEP HIG MED DOSW 2020. [DOI: 10.5604/01.3001.0014.4137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
With the increasing demand for poultry meat and poultry products and the growing poultry industry around the world, food safety is an important challenge for public health. To assess the dissemination of extraintestinal pathogenic E. coli (ExPEC) strains, one should examine the level of genetic similarity between isolates from different hosts. In the proposed review paper, multiple levels of genotyping are proposed, in which typing of strains, plasmids, and genes are compared in order to obtain the more complete picture of this complex issue. The ExPEC group includes uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), and sepsis-associated E. coli (SEPEC). ExPEC presents an elaborated phylogenetic structure, a wide range of virulence factors (VF), and considerable plasticity of the genome. These strains cause not only uncomplicated UTIs, but also other dangerous illnesses such as bacteremia or sepsis. Mechanisms underlying ExPEC transmission dynamics and the selection of resistant to drugs clones are still poorly understood and require further investigations. Overuse and inappropriate use of antibiotics and chemotherapeutics has led to a global threat, which is the emergence and spread of microbial resistance. Food, depending on certain products and processing technology, provides an excellent substrate for the growth of microorganisms. Intensive trade and wide use of antibiotics in contemporary food production favor the emergence and spread of resistant bacteria. Currently, antibiotic use in vegetable and animal food production is significantly higher compared to the number of antibiotics used in medicine to treat infections, which is a huge threat. We need new strategies to prevent, quickly diagnose, and treat ExPEC infections, especially in the context of the recently observed clonal expansion of strains with increased antibiotic resistance.
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Affiliation(s)
| | - Jolanta Sarowska
- Department of Basic Sciences, Wroclaw Medical University, Wrocław, Poland
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Nagaoka H, Hirai S, Morinushi H, Mizumoto S, Suzuki K, Shigemura H, Takahashi N, Suzuki F, Mochizuki M, Asanuma M, Maehata T, Ogawa A, Ohkoshi K, Sekizuka T, Ishioka T, Suzuki S, Kimura H, Kuroda M, Suzuki M, Murakami K, Kanda T. Coinfection with Human Norovirus and Escherichia coli O25:H4 Harboring Two Chromosomal blaCTX-M-14 Genes in a Foodborne Norovirus Outbreak in Shizuoka Prefecture, Japan. J Food Prot 2020; 83:1584-1591. [PMID: 32866241 DOI: 10.4315/jfp-20-042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/06/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Hospital-acquired infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a global problem. Healthy people can carry ESBL-producing E. coli in the intestines; thus, E. coli from healthy people can potentially cause hospital-acquired infections. Therefore, the transmission routes of ESBL-producing E. coli from healthy persons should be determined. A foodborne outbreak of human norovirus (HuNoV) GII occurred at a restaurant in Shizuoka, Japan, in 2018. E. coli O25:H4 was isolated from some of the HuNoV-infected customers. Pulsed-field gel electrophoresis showed that these E. coli O25:H4 strains originated from one clone. Because the only epidemiological link among the customers was eating food from this restaurant, the customers were concurrently infected with E. coli O25:H4 and HuNoV GII via the restaurant food. Whole genome analysis revealed that the E. coli O25:H4 strains possessed genes for regulating intracellular iron and expressing the flagellum and flagella. Extraintestinal pathogenic E. coli often express these genes on the chromosome. Additionally, the E. coli O25:H4 strains had plasmids harboring nine antimicrobial resistance genes. These strains harbored ESBL-encoding blaCTX-M-14 genes on two loci of the chromosome and had higher ESBL activity. Multilocus sequence typing and fimH subtyping revealed that the E. coli O25:H4 strains from the outbreak belonged to the subclonal group, ST131-fimH30R, which has been driving ESBL epidemics in Japan. Because the E. coli O25:H4 strains isolated in the outbreak belonged to a subclonal group spreading in Japan, foods contaminated with ESBL-producing E. coli might contribute to spreading these strains among healthy persons. The isolated E. coli O25:H4 strains produced ESBL and contained plasmids with multiple antimicrobial resistance genes, which may make it difficult to select antimicrobials for treating extraintestinal infections caused by these strains. HIGHLIGHTS
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Affiliation(s)
- Hiromi Nagaoka
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
| | - Shinichiro Hirai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan (ORCID: https://orcid.org/0000-0001-5597-2518 [S.H.])
| | - Hirotaka Morinushi
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
| | - Shiro Mizumoto
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
| | - Kana Suzuki
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
| | - Hiroaki Shigemura
- Division of Pathology and Bacteriology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan
| | - Naoto Takahashi
- Department of Microbiology, Shizuoka City Institute of Environmental Sciences and Public Health, 1-4-7 Oguro, Suruga-ku, Shizuoka, Shizuoka 422-8072, Japan
| | - Fumie Suzuki
- Department of Microbiology, Shizuoka City Institute of Environmental Sciences and Public Health, 1-4-7 Oguro, Suruga-ku, Shizuoka, Shizuoka 422-8072, Japan
| | - Mizuha Mochizuki
- Department of Microbiology, Shizuoka City Institute of Environmental Sciences and Public Health, 1-4-7 Oguro, Suruga-ku, Shizuoka, Shizuoka 422-8072, Japan
| | - Michiko Asanuma
- Department of Microbiology, Shizuoka City Institute of Environmental Sciences and Public Health, 1-4-7 Oguro, Suruga-ku, Shizuoka, Shizuoka 422-8072, Japan
| | - Takaharu Maehata
- Department of Microbiology, Shizuoka City Institute of Environmental Sciences and Public Health, 1-4-7 Oguro, Suruga-ku, Shizuoka, Shizuoka 422-8072, Japan
| | - Aya Ogawa
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
| | - Kai Ohkoshi
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo 162-8640, Japan
| | - Taisei Ishioka
- Environmental Health Division, Takasaki City Health Center, 5-28, Takamatsu, Takasaki, Gunma 370-0829, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aobachou, Higashimurayama, Tokyo 189-0002, Japan
| | - Hirokazu Kimura
- School of Medical Technology, Faculty of Health Science, Gunma Paz University, 1-7-1 Tonyamachi, Takasaki, Gunma 370-0006, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo 162-8640, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan (ORCID: https://orcid.org/0000-0001-5597-2518 [S.H.])
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan (ORCID: https://orcid.org/0000-0001-5597-2518 [S.H.])
| | - Takashi Kanda
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, 4-27-2 Kitaando, Aoi-ku, Shizuoka, Shizuoka 420-8637, Japan
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Finton MD, Meisal R, Porcellato D, Brandal LT, Lindstedt BA. Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond. Front Microbiol 2020; 11:1273. [PMID: 32625184 PMCID: PMC7311804 DOI: 10.3389/fmicb.2020.01273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
The presence of extended-spectrum β-lactamase (ESBL)-producing bacteria in environmental sources has been reported worldwide and constitutes a serious risk of community-acquired infections with limited treatment options. The current study aimed to explore the presence of these worrisome bacteria in a pond located at the Norwegian University of Life Sciences in Ås, Norway. A total of 98 bacterial isolates survived growth on selective chromogenic media and were identified by 16S rRNA Sanger sequencing. All strains were evaluated for the presence of the most commonly found β-lactamases and ESBLs in clinical settings (blaCTX–M groups 1, 2, and 9, blaCMY, blaSHV, and blaTEM) and carbapenemases (blaIMP, blaKPC, blaNDM, blaOXA, blaSFC1, blaVIM) through multiplex PCR. A total of eight strains were determined to contain one or more genes of interest. Phenotypic resistance to 18 antimicrobial agents was assessed and isolates were subjected to whole genome sequencing through a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq. Results revealed the presence of β-lactamase and ESBL-producing Escherichia coli, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and a Paraburkholderia spp. Identified β-lactamases and ESBLs include blaCTX–M, blaTEM, blaCMY, blaSHV and a possible blaKPC-like gene, with both documented and novel sequences established. In addition, two inducible β-lactamases were found, a class A β-lactamase (L1) and a cephalosporinase (L2). All strains were determined to be multidrug resistant and numerous resistance genes to non-β-lactams were observed. In conclusion, this study demonstrates that environmental sources are a potential reservoir of clinically relevant ESBL-producing bacteria that may pose a health risk to humans upon exposure.
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Affiliation(s)
- Misti D Finton
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Roger Meisal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lin T Brandal
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| | - Bjørn-Arne Lindstedt
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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30
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Shigemura H, Sakatsume E, Sekizuka T, Yokoyama H, Hamada K, Etoh Y, Carle Y, Mizumoto S, Hirai S, Matsui M, Kimura H, Suzuki M, Onozuka D, Kuroda M, Inoshima Y, Murakami K. Food Workers as a Reservoir of Extended-Spectrum-Cephalosporin-Resistant Salmonella Strains in Japan. Appl Environ Microbiol 2020; 86:e00072-20. [PMID: 32276982 PMCID: PMC7301857 DOI: 10.1128/aem.00072-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/07/2020] [Indexed: 11/20/2022] Open
Abstract
Dissemination of extended-spectrum-cephalosporin (ESC)-resistant Salmonella, especially extended-spectrum-β-lactamase (ESBL)-producing Salmonella, is a concern worldwide. Here, we assessed Salmonella carriage by food workers in Japan to clarify the prevalence of ESC-resistant Salmonella harboring blaCTX-M We then characterized the genetic features, such as transposable elements, of blaCTX-M-harboring plasmids using whole-genome sequencing. A total of 145,220 stool samples were collected from food workers, including cooks and servers from several restaurants, as well as food factory workers, from January to October 2017. Isolated salmonellae were subjected to antimicrobial susceptibility testing (disk diffusion method), and whole-genome sequencing was performed for Salmonella strains harboring blaCTX-M Overall, 164 Salmonella isolates (0.113%) were recovered from 164 samples, from which we estimated that at least 0.113% (95% confidence interval [CI]: 0.096 to 0.132%) of food workers may carry Salmonella Based on this estimation, 3,473 (95% CI = 2,962 to 4,047) individuals among the 3,075,330 Japanese food workers are likely to carry Salmonella Of the 158 culturable isolates, seven showed resistance to ESCs: three isolates harbored blaCMY-2 and produced AmpC β-lactamase, while four ESBL-producing isolates harbored blaCTX-M-14 (n = 1, Salmonella enterica serovar Senftenberg) or blaCTX-M-15 (n = 3, S. enterica serovar Haardt). blaCTX-M-15 was chromosomally located in the S Haardt isolates, which also contained ISEcp1, while the S Senftenberg isolate contained an IncFIA(HI1)/IncHI1A/IncHI1B(R27) hybrid plasmid carrying blaCTX-M-14 along with ISEcp1 This study indicates that food workers may be a reservoir of ESBL-producing Salmonella and associated genes. Thus, these workers may contribute to the spread of blaCTX-M via plasmids or mobile genetic elements such as ISEcp1IMPORTANCE Antimicrobial-resistant Salmonella bacteria arise in farm environments through imprudent use of antimicrobials. Subsequently, these antimicrobial-resistant strains, such as extended-spectrum-β-lactamase (ESBL)-producing Salmonella, may be transmitted to humans via food animal-derived products. Here, we examined Salmonella carriage among food handlers in Japan. Overall, 164 of 145,220 fecal samples (0.113%) were positive for Salmonella Among the 158 tested isolates, four were identified as ESBL-producing isolates carrying ESBL determinants blaCTX-M-15 or blaCTX-M-14 In all cases, the genes coexisted with ISEcp1, regardless of whether they were located on the chromosome or on a plasmid. Our findings suggest that food workers may be a reservoir of ESBL-producing strains and could contribute to the spread of resistance genes from farm-derived Salmonella to other bacterial species present in the human gut.
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Affiliation(s)
- Hiroaki Shigemura
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Eri Sakatsume
- Kotobiken Medical Laboratories, Inc., Fukushima, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | | | - Yoshiki Etoh
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Yuki Carle
- Division of Pathology and Microbiology, Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Shiro Mizumoto
- Department of Microbiology, Shizuoka Institute of Environment and Hygiene, Shizuoka, Japan
| | - Shinichiro Hirai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- School of Medical Technology, Faculty of Health Science, Gunma Paz University, Gunma, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Onozuka
- Department of Preventive Medicine and Epidemiology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasuo Inoshima
- Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Koichi Murakami
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
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Grevskott DH, Salvà-Serra F, Moore ERB, Marathe NP. Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway. BMC Microbiol 2020; 20:134. [PMID: 32450819 PMCID: PMC7249450 DOI: 10.1186/s12866-020-01821-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health. This study applied a combination of long-read Oxford Nanopore MinION and short-read Illumina MiSeq-based sequencing to obtain closed complete genome sequences of two CTX-M-producing multidrug-resistant Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway, in order to understand the potential for mobility of the detected antibiotic resistance genes (ARGs). RESULTS The complete genome sequence of strain 631 (E. coli sequence type 38) was assembled into a circular chromosome of 5.19 Mb and five plasmids (between 98 kb and 5 kb). The majority of ARGs cluster in close proximity to each other on the chromosome within two separate multidrug-resistance determining regions (MDRs), each flanked by IS26 transposases. MDR-1 carries blaTEM-1, tmrB, aac(3)-IId, aadA5, mph(A), mrx, sul1, qacEΔ1 and dfrA17; while MDR-2 harbors aph(3″)-Ib, aph(6)-Id, blaTEM-1, catA1, tet(D) and sul2. Four identical chromosomal copies of blaCTX-M-14 are located outside these regions, flanked by ISEc9 transposases. Strain 1500 (E. coli sequence type 191) exhibited a circular chromosome of 4.73 Mb and two plasmids (91 kb and 4 kb). The 91 kb conjugative plasmid belonging to IncI1 group carries blaCTX-M-15 and blaTEM-1 genes. CONCLUSION This study confirms the efficacy of combining Nanopore long-read and Illumina short-read sequencing for determining complete bacterial genome sequences, enabling detection and characterization of clinically important ARGs in the marine environment in Norway, with potential for further dissemination. It also highlights the need for environmental surveillance of antibiotic resistance in low prevalence settings like Norway.
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Affiliation(s)
- Didrik H Grevskott
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Edward R B Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Nachiket P Marathe
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway.
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant
Salmonella
successful clones is associated with diverse
ars
operons and genetic contexts. Environ Microbiol 2020; 22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Center for Innovative Biomedicine and BiotechnologyUniversity of Coimbra Coimbra Portugal
- Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
- Institute for Interdisciplinary Research, University of Coimbra Coimbra Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Scientific Area of Environmental HealthSchool of Health, Polytechnic Institute of Porto Porto Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Carla Novais
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Faculty of Nutrition and Food SciencesUniversity of Porto Porto Portugal
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Environmental Presence and Genetic Characteristics of Carbapenemase-Producing Enterobacteriaceae from Hospital Sewage and River Water in the Philippines. Appl Environ Microbiol 2020; 86:AEM.01906-19. [PMID: 31704681 PMCID: PMC6952235 DOI: 10.1128/aem.01906-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) cause severe health care-associated infections, and their increasing prevalence is a serious concern. Recently, natural ecosystems have been recognized as important reservoirs of antibiotic resistance genes. We investigated the prevalence and genetic characteristics of CPE isolated from the environment (hospital sewage and river water) in the Philippines and found several CPE, including Escherichia coli and other species, with different carbapenemases. The most prevalent carbapenemase gene type was NDM, which is endemic in clinical settings. This study revealed that isolates belonging to carbapenemase-producing E. coli CC10 and K. pneumoniae sequence type 147 (ST147), which are often detected in clinical settings, were dominant in the natural environment. Our work here provides a report on the presence and characteristics of CPE in the environment in the Philippines and demonstrates that both hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups. This study aimed to evaluate the prevalence and genetic characteristics of carbapenemase-producing Enterobacteriaceae (CPE) in hospital sewage and river water in the Philippines, which has a typical tropical maritime climate. We collected 83 water samples from 7 hospital sewage and 10 river water sites. CPE were identified using CHROMagar mSuperCARBA, and Gram-negative strains were identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA gene sequencing. Resistance genes in Enterobacteriaceae strains were identified using PCR and DNA sequencing, and transferability of carbapenemase genes from the CPE was investigated with conjugation experiments. Genotyping was performed using multilocus sequence typing (MLST) for Escherichia coli and Klebsiella pneumoniae. Out of 124 Enterobacteriaceae isolates, we identified 51 strains as CPE and divided these into 7 species, 11 E. coli, 14 Klebsiella spp., 15 Enterobacter spp., and 11 others, including 4 additional species. Conjugation experiments via broth mating and using E. coli J53 revealed that 24 isolates can transfer carbapenemase-encoding plasmids. MLST analysis showed that 6 of 11 E. coli isolates belonged to clonal complex 10 (CC10). Of 11 K. pneumoniae strains, 9 unique sequence types (STs) were identified, including ST147. Five types of carbapenemase genes were identified, with the most prevalent being NDM (n = 39), which is epidemic in clinical settings in the Philippines. E. coli CC10 and K. pneumoniae ST147, which are often detected in clinical settings, were the dominant strains. In summary, our results indicate that hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups. IMPORTANCE Carbapenemase-producing Enterobacteriaceae (CPE) cause severe health care-associated infections, and their increasing prevalence is a serious concern. Recently, natural ecosystems have been recognized as important reservoirs of antibiotic resistance genes. We investigated the prevalence and genetic characteristics of CPE isolated from the environment (hospital sewage and river water) in the Philippines and found several CPE, including Escherichia coli and other species, with different carbapenemases. The most prevalent carbapenemase gene type was NDM, which is endemic in clinical settings. This study revealed that isolates belonging to carbapenemase-producing E. coli CC10 and K. pneumoniae sequence type 147 (ST147), which are often detected in clinical settings, were dominant in the natural environment. Our work here provides a report on the presence and characteristics of CPE in the environment in the Philippines and demonstrates that both hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups.
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Sepp E, Andreson R, Balode A, Bilozor A, Brauer A, Egorova S, Huik K, Ivanova M, Kaftyreva L, Kõljalg S, Kõressaar T, Makarova M, Miciuleviciene J, Pai K, Remm M, Rööp T, Naaber P. Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe. Front Microbiol 2019; 10:2465. [PMID: 31824436 PMCID: PMC6882919 DOI: 10.3389/fmicb.2019.02465] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022] Open
Abstract
Extended-spectrum beta-lactamases (ESBL) and AmpC producing-Escherichia coli have spread worldwide, but data about ESBL-producing-E. coli in the Northern and Eastern regions of Europe is scant. The aim of this study has been to describe the phenotypical and molecular epidemiology of different ESBL/AmpC/Carbapenemases genes in E. coli strains isolated from the Baltic States (Estonia, Latvia, and Lithuania), Norway and St. Petersburg (Russia), and to determine the predominant multilocus sequence type and single nucleotide polymorphisms diversity of E. coli isolates deduced by whole genome sequencing (WGS). A total of 10,780 clinical E. coli strains were screened for reduced sensitivity to third-generation cephalosporins. They were collected from 21 hospitals located in Estonia, Latvia, Lithuania, Norway and St. Petersburg during a 5 month period in 2012. The overall prevalence of ESBL/AmpC strains was 4.7% by phenotypical test and 3.9% by sequencing. We found more strains with the ESBL/AmpC phenotype and genotype in St. Petersburg and Latvia than other countries. Of phenotypic E. coli strains, 85% contained confirmed ESBL genes (including blaCTX–M, blaTEM–29, blaTEM–71), AmpC genes (blaCMY–59, blaACT–12/–15/–20, blaESC–6, blaFEC–1, blaDHA–1), or carbapenemase genes (blaNDM–1). blaCTX–M–1, blaCTX–M–14 and blaCTX–M–15 were found in all countries, but blaCTX–M–15 prevalence was higher in Latvia than in St. Petersburg (Russia), Estonia, Norway and Lithuania. The dominating AmpC genes were blaCMY–59 in the Baltic States and Norway, and blaDHA–1 in St. Petersburg. E. coli strains belonged to 83 different sequence types, of which the most prevalent was ST131 (40%). In conclusion, we generally found low ESBL/AmpC/Carbapenemase prevalence in E. coli strains isolated in Northern/Eastern Europe. However, several inter-country differences in distribution of particular genes and multilocus sequence types were found.
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Affiliation(s)
- Epp Sepp
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Reidar Andreson
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Arta Balode
- Department of Biology and Microbiology, Rīga Stradiņš University, Riga, Latvia
| | - Anastasia Bilozor
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Department of Microbiology, Central Laboratory, East-Tallinn Central Hospital, Tallinn, Estonia
| | - Age Brauer
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Svetlana Egorova
- Department of Enteric Infections, St. Petersburg Pasteur Institute, Saint Petersburg, Russia
| | - Kristi Huik
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Marina Ivanova
- Department of Microbiology, Central Laboratory, East-Tallinn Central Hospital, Tallinn, Estonia
| | - Lidia Kaftyreva
- Department of Enteric Infections, St. Petersburg Pasteur Institute, Saint Petersburg, Russia
| | - Siiri Kõljalg
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Triinu Kõressaar
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maria Makarova
- Department of Enteric Infections, St. Petersburg Pasteur Institute, Saint Petersburg, Russia
| | | | - Kristiine Pai
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tiiu Rööp
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Paul Naaber
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,SYNLAB Eesti, Tallinn, Estonia
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The Washing Machine as a Reservoir for Transmission of Extended-Spectrum-Beta-Lactamase (CTX-M-15)-Producing Klebsiella oxytoca ST201 to Newborns. Appl Environ Microbiol 2019; 85:AEM.01435-19. [PMID: 31562168 PMCID: PMC6821978 DOI: 10.1128/aem.01435-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Washing machines should be further investigated as possible sites for horizontal gene transfer (ESBL genes) and cross-contamination with clinically important Gram-negative strains. Particularly in the health care sector, the knowledge of possible (re-)contamination of laundry (patients’ clothes and staff uniforms) with multidrug-resistant Gram-negative bacteria could help to prevent and to control nosocomial infections. This report describes an outbreak with a single strain of a multidrug-resistant bacterium (Klebsiella oxytoca sequence type 201) in a neonatal intensive care unit that was terminated only when the washing machine was removed. In addition, the study implies that changes in washing machine design and processing are required to prevent accumulation of residual water where microbial growth can occur and contaminate clothes. During the period from April 2012 to May 2013, 13 newborns (1 to 4 weeks of age) and 1 child in a pediatric hospital ward in Germany were colonized with Klebsiella oxytoca producing an extended-spectrum beta-lactamase (ESBL) (CTX-M-15). A microbiological source-tracking analysis with human and environmental samples was carried out to identify the source and transmission pathways of the K. oxytoca clone. In addition, different hygienic intervention methods were evaluated. K. oxytoca isolates were detected in the detergent drawer and on the rubber door seal of a domestic washer-extractor machine that was used in the same ward to wash laundry for the newborns, as well as in two sinks. These strains were typed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. The environmental findings were compared with those for the human strains and the isolates detected on clothing. The results from both techniques showed that the strains were identical (sequence type 201 and PFGE type 00531, a clone specific to this hospital and not previously isolated in Germany), emphasizing the washing machine as a reservoir and fomite for the transmission of these multidrug-resistant bacteria. After the washing machine was taken out of use, no further colonizations were detected during the subsequent 4-year period. IMPORTANCE Washing machines should be further investigated as possible sites for horizontal gene transfer (ESBL genes) and cross-contamination with clinically important Gram-negative strains. Particularly in the health care sector, the knowledge of possible (re-)contamination of laundry (patients’ clothes and staff uniforms) with multidrug-resistant Gram-negative bacteria could help to prevent and to control nosocomial infections. This report describes an outbreak with a single strain of a multidrug-resistant bacterium (Klebsiella oxytoca sequence type 201) in a neonatal intensive care unit that was terminated only when the washing machine was removed. In addition, the study implies that changes in washing machine design and processing are required to prevent accumulation of residual water where microbial growth can occur and contaminate clothes.
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Distribution and molecular characterization of beta-lactamases in Gram-negative bacteria in Colombia, 2001-2016. ACTA ACUST UNITED AC 2019; 39:199-220. [PMID: 31529860 DOI: 10.7705/biomedica.v39i3.4351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 12/18/2022]
Abstract
Beta-lactamases are enzymes with hydrolytic activity over beta-lactam antibiotics and they are the main resistance mechanism in Gram-negative bacteria. Extended-spectrum beta-lactamases (ESBL), AmpC, and carbapenemases have the greatest clinical and epidemiological impact in hospital settings. The increasing frequency and worldwide spread of these enzymes have limited the therapeutic options in hospital-acquired infections and those originating in the community.
In Colombia, surveillance networks and research groups began studying them in the late 90s. Different variants of these enzymes have been molecularly characterized and their high prevalence and dissemination in medium and high complexity hospitals, along with a high clinical impact, have been reported. Furthermore, many studies in Colombia have evidenced high endemicity for some of these beta-lactamases, which requires an urgent implementation of antimicrobial stewardship programs in order to preserve the few therapeutic options and infection control strategies to prevent and limit their dissemination.
In this publication, we carried out a review of the different enzyme variants, geographic distribution, and molecular characterization of these beta-lactamases in Colombia. Additionally, we describe the available information in the literature regarding studies conducted between the late 1990s and 2016, which provide an overview of the beta-lactamases circulating in different regions of Colombia, their increase over time, and their clinical implications.
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Laurens C, Jean-Pierre H, Licznar-Fajardo P, Hantova S, Godreuil S, Martinez O, Jumas-Bilak E. Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human. J Glob Antimicrob Resist 2018; 15:88-92. [DOI: 10.1016/j.jgar.2018.06.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 06/17/2018] [Accepted: 06/29/2018] [Indexed: 11/16/2022] Open
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Hamamoto K, Hirai I. Characterisation of chromosomally-located bla CTX-M and its surrounding sequence in CTX-M-type extended-spectrum β-lactamase-producing Escherichia coli isolates. J Glob Antimicrob Resist 2018; 17:53-57. [PMID: 30445208 DOI: 10.1016/j.jgar.2018.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Although it has been regarded that the CTX-M-type extended-spectrum β-lactamase (ESBL) gene blaCTX-M is mainly carried by antimicrobial resistance plasmids, Escherichia coli possessing chromosomally-located blaCTX-M has been reported in previous studies. This study aimed to characterise the genetic structure of the chromosomally-located blaCTX-M transposition unit and its surrounding sequence in ESBL-producing E. coli isolated in a Japanese hospital. METHODS A total of 81 ESBL-producing E. coli isolates were studied. The existence of chromosomally-located blaCTX-M was confirmed by S1 nuclease-digested pulsed-field gel electrophoresis (PFGE) and Southern blot hybridisation and by sequencing analysis of the PCR-amplified DNA fragments. RESULTS Chromosomally-located blaCTX-M was confirmed in 22 (27.2%) of the 81 E. coli isolates examined; five and four location types of chromosomally-located blaCTX-M-14 and blaCTX-M-15 were determined, respectively. Among the 22 E. coli isolates, 15 (68.2%) possessed single chromosomally-located blaCTX-M gene, probably due to single transposition of a plasmidic blaCTX-M to the chromosome. In isolate N0057, the blaCTX-M-15 transposition unit was transferred from a plasmid into two different chromosomal regions. In addition, 'recurrent' transposition of already existing chromosomally-located blaCTX-M-14 to another chromosomal region was observed in isolates N0211, N0214, N01127, N1682 and N1753; consequently, these isolates possessed two copies of chromosomally-located blaCTX-M-14. CONCLUSION Considering that isolates N0211, N0214, N01127, N1682 and N1753 in which the 'recurrent' transposition event occurred were genetically related according to PFGE, these data suggest the possibility of accumulation of blaCTX-M on the chromosome in CTX-M-type ESBL-producing E. coli.
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Affiliation(s)
- Kouta Hamamoto
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan; Japan Society for the Promotion of Science (JSPS), Japan
| | - Itaru Hirai
- Laboratory of Microbiology, School of Health Sciences, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan; Japan Agency for Medical Research and Development (AMED)/Japan International Cooperation Agency (JICA), Science and Technology Research Partnership for Sustainable Development (SATREPS), Japan.
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Bubpamala J, Khuntayaporn P, Thirapanmethee K, Montakantikul P, Santanirand P, Chomnawang MT. Phenotypic and genotypic characterizations of extended-spectrum beta-lactamase-producing Escherichia coli in Thailand. Infect Drug Resist 2018; 11:2151-2157. [PMID: 30464558 PMCID: PMC6223337 DOI: 10.2147/idr.s174506] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose Extended-spectrum β-lactamases (ESBLs) have become an issue in community worldwide due to an increase in antibiotic resistance over the past decade. This study was aimed to investigate the phenotypic and genotypic characteristics of ESBL-producing Escherichia coli in Thailand. Materials and methods In this study, all clinical isolates collected from tertiary hospitals in Thailand were identified as E. coli by biochemical tests and MALDI-TOF mass spectrometry. ESBL-producing E. coli was preliminary screened with disk diffusion method by cephalosporin disks and confirmed by the method of combination disk diffusion. Antimicrobial susceptibility test was used to determine MIC values of all ESBL-producing E. coli. For genotypic detection, a variety of ESBL genes were determined by PCR. Moreover, multilocus sequence typing (MLST) analysis was performed on internal portions of seven housekeeping genes for the diversity and phylogenetic relatedness of E. coli clonal group. Results Of the 285 ESBL-producing E. coli, most were susceptible to carbapenems. These strains showed a high resistance rate to ciprofloxacin (85.26%). The most frequently detected gene was blaCTX-M1 group at about 71.23% followed by blaCTX-M9 group (38.95%). The blaTEM, blaPER, blaGES, blaVEB, and blaSHV genes were identified in 31.93%, 5.96%, 4.56%, 3.51%, and 0.70% of ESBL-producing isolates, respectively. The bla OXA-10 gene was detected in only one strain. ESBL-producing E. coli isolates with high antimicrobial resistance were further investigated. Among those, E. coli sequence type ST38 was mostly found, followed by ST405, ST410, and ST131. It is noteworthy that the blaCTX-M gene was mainly detected in all four ST-type E. coli clones (ST38, ST405, ST410, and ST131). Conclusion This study provided a recent evidence of the genetic diversity of ESBL-producing E. coli in Thailand. In addition, the profile related to antimicrobial resistance pattern in this region was also demonstrated.
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Affiliation(s)
- Jiranun Bubpamala
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
| | | | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Mullika T Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand,
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Guiral E, Pons MJ, Vubil D, Marí-Almirall M, Sigaúque B, Soto SM, Alonso PL, Ruiz J, Vila J, Mandomando I. Epidemiology and molecular characterization of multidrug-resistant Escherichia coli isolates harboring blaCTX-M group 1 extended-spectrum β-lactamases causing bacteremia and urinary tract infection in Manhiça, Mozambique. Infect Drug Resist 2018; 11:927-936. [PMID: 30013375 PMCID: PMC6037150 DOI: 10.2147/idr.s153601] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The emergence and spread of extended-spectrum β-lactamases (ESBLs), especially CTX-M, is an important public health problem with serious implications for low-income countries where second-line treatment is often unavailable. Knowledge of the local prevalence of ESBL is critical to define appropriate empirical therapeutic strategies for multidrug-resistant (MDR) organisms. This study aimed to assess and characterize the presence of ESBL and especially CTX-M-producing Escherichia coli MDR isolates from patients with urinary tract infections (UTIs) and bacteremia in a rural hospital in Mozambique. Materials and methods One hundred and fifty-one E. coli isolates from bacteremia and UTI in children were screened for CTX-M, TEM, SHV and OXA β-lactamases by polymerase chain reaction and sequencing. Isolates carrying CTX-M group 1 β-lactamases were further studied. The resistance to other antibiotic families was determined by phenotypic and genotypic methods, the location of the blaCTX-M gene and the epidemiology of the isolates were studied, and extensive plasmid characterization was performed. Results Approximately 11% (17/151) of E. coli isolates causing bacteremia and UTI were ESBL producers. CTX-M-15 was the most frequently detected ESBL, accounting for 75% of the total isolates characterized. The blaCTX-M gene is located in different plasmids belonging to different incompatibility groups and can be found in non-epidemiologically related isolates, indicating the high capacity of this resistance determinant to spread widely. Conclusion Our data suggest the presence of a co-selection of third-generation cephalosporin-resistant determinants in the study area despite limited access to these antibiotics. This highlights the importance of continuous surveillance of antimicrobial resistance of both genetic elements of resistance and resistant isolates in order to monitor the emergence and trends of ESBL-producing isolates to promote adequate therapeutic strategies for the management of MDR bacterial infections.
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Affiliation(s)
- Elisabet Guiral
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Maria Jesús Pons
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique,
| | - Marta Marí-Almirall
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Betuel Sigaúque
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique, .,Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique,
| | - Sara Maria Soto
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Pedro Luís Alonso
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique,
| | - Joaquim Ruiz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.,Microbiology Department, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique, .,Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique,
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ESBL-plasmid carriage in E. coli enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost. Gut Pathog 2018; 10:24. [PMID: 29983750 PMCID: PMC6003029 DOI: 10.1186/s13099-018-0243-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/13/2018] [Indexed: 12/26/2022] Open
Abstract
Background Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic Escherichia coli infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carriage of plasmids has been suggested to result in a fitness burden, but recently it was shown that ESBL-plasmids enhanced virulence in pandemic ST131 and ST648 lineages without affecting their fitness. Herein, we investigated the influence of ESBL-plasmids on bacterial competition and serum resistance, both of which are essential characteristics of ExPEC during infections. Methods Triplets of ESBL-plasmid-carrying wildtype (WT), plasmid-cured variant (PCV) and transformant (T) of five ExPEC strains of ST131 and ST648 were used for bacterial competition experiments with colicin-producing commensal E. coli, competitive adhesion experiments and serum survival. In addition, resilience after SDS, acid, osmotic challenges and RNA sequence data were analyzed. Results In all five strains tested, ESBL-plasmid carriage did not negatively influence E. coli fitness in direct bacterial competition with commensal E. coli in vitro. That is, WTs did not show any disadvantages when compared to their isogenic plasmid-free PCV. For one strain we even found the opposite as PCV17433 was out-competed by a commensal strain, which suggests an even protective role of the ESBL-plasmid carried by the WT17433. Similarly, in the serum-resistance experiments, the PCVs of two strains (PCV17433 and PCV17887) were more sensitive to serum, unlike WTs and Ts. The observed inter-strain differences could be explained by the different genetic content of plasmids carried in those strains. Conclusions Overall, we found no compelling evidence for an increased burden resulting from the carriage of ESBL-plasmids in the absence of antimicrobial selection pressure in the strains of pandemic ST131 and ST648; rather, the possession of certain ESBL-plasmids was beneficial for some strains in regarding competition fitness and serum survival. Electronic supplementary material The online version of this article (10.1186/s13099-018-0243-z) contains supplementary material, which is available to authorized users.
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Melo LC, Oresco C, Leigue L, Netto HM, Melville PA, Benites NR, Saras E, Haenni M, Lincopan N, Madec JY. Prevalence and molecular features of ESBL/pAmpC-producing Enterobacteriaceae in healthy and diseased companion animals in Brazil. Vet Microbiol 2018; 221:59-66. [PMID: 29981709 DOI: 10.1016/j.vetmic.2018.05.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/13/2018] [Accepted: 05/29/2018] [Indexed: 01/08/2023]
Abstract
Extended-spectrum beta-lactamase (ESBL)- and plasmid-mediated AmpC (pAmpC)-carrying Enterobacteriaceae have widely disseminated in human, animal and environmental reservoirs. Pets have been recognized as a source of ESBL/pAmpC worldwide, and are possibly also a source of human contamination. The aim of this study was to document to what extent cats and dogs may act as a driving force in the spread of ESBLs and pAmpCs in Brazil. A total of 113 healthy stray cats and dogs and 74 sick pets were sampled, and extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESC-R) were detected in 28/113 (24.8%) and 8/74 (10.8%) tested animals, respectively. Different Enterobacteriaceae isolates (mostly E. coli), a large number of E. coli clones (with ST90, ST457, ST973 and ST2541 being predominant), and several ESBL/pAmpC genes and plasmids were characterized, highlighting the ability of stray and pet cats and dogs to further spread a wide range of ESC-resistance determinants. The ESBL phenotype was due to the blaCTX-M-2 and blaCTX-M-8 genes, as found in human epidemiology in Brazil, but blaCTX-M-9 and blaCTX-M-15 were also identified. The pAmpC phenotype was systematically due to the presence of the blaCMY-2 gene, mostly carried by IncI1 ST12 plasmids. Our results showed that pets can be considered a significant reservoir of multidrug-resistant bacteria in Brazil. This is especially true for healthy stray dogs that displayed the highest prevalence (24.8%) of ESBLs/pAmpC resistance determinants, which can then be further spread both to the environment and to other animals or humans by contact.
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Affiliation(s)
- Luana C Melo
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil; Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Cíntia Oresco
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Lucianne Leigue
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | | | - Priscilla A Melville
- Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine, Universidade de São Paulo, São Paulo, Brazil
| | - Nilson R Benites
- Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine, Universidade de São Paulo, São Paulo, Brazil
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon - Université Claude Bernard Lyon 1, Lyon, France.
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon - Université Claude Bernard Lyon 1, Lyon, France
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Kawamura K, Hayashi K, Matsuo N, Kitaoka K, Kimura K, Wachino JI, Kondo T, Iinuma Y, Murakami N, Fujimoto S, Arakawa Y. Prevalence of CTX-M-Type Extended-Spectrum β-Lactamase-Producing Escherichia coli B2-O25-ST131 H30R Among Residents in Nonacute Care Facilities in Japan. Microb Drug Resist 2018; 24:1513-1520. [PMID: 29791251 DOI: 10.1089/mdr.2018.0068] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the prevalence and characteristics of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli among 258 residents of long-term care facilities (LTCFs) in Japan. Out of 258 fecal samples collected from nine LTCFs between November 2015 and March 2017, we recovered 59 ESBL-producing E. coli isolates. All isolates carried blaCTX-M genes, mainly blaCTX-M-27 (42.4%), blaCTX-M-14 (23.7%), and blaCTX-M-15 (18.6%). The isolates showed 7 serotypes (STs), including ST131 (n = 49, 83.1%) and ST38 (n = 4, 6.8%), and 47 (79.7%) out of 49 isolates belonging to ST131 were identified as H30R. The 59 ESBL producers were divided into four groups, B2 (86.4%), D (8.5%), A (3.4%), and C (1.7%); 44 (74.6%) were epidemic clone B2-O25-ST131 H30R, of which 21, 11, and 6 harbored blaCTX-M-27, blaCTX-M-15, and blaCTX-M-14, respectively. Most plasmids were of IncF replicon types (n = 33), and 22 blaCTX-M-27-carrying plasmids showed multiple replicon types, including IncFII, FIA, and FIB. The ESBL producers were susceptible to imipenem, amikacin, and fosfomycin, but resistant to ceftazidime (49.2%), and ciprofloxacin (88.1%); in particular, the isolates harboring the blaCTX-M-15 gene showed significantly high resistance rate to ceftazidime (p < 0.01). Our findings indicate that a considerable proportion of the examined LTCF residents carried ESBL-producing E. coli isolates in feces and had high prevalence of epidemic clone B2-O25-ST131. Furthermore, continuous investigations would be very necessary to monitor actual carriage states of ESBL-producers among the LTCF residents from the viewpoint of both public health and healthcare viewpoints.
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Affiliation(s)
- Kumiko Kawamura
- 1Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kengo Hayashi
- 1Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Nao Matsuo
- 1Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kazuki Kitaoka
- 2Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kouji Kimura
- 2Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Jun-Ichi Wachino
- 2Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Takaaki Kondo
- 1Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Yoshitsugu Iinuma
- 3Department of Infectious Diseases, Kanazawa Medical University, Ishikawa, Japan
| | - Nobuo Murakami
- 4Center for Nutrition Support and Infection Control, Gifu University Hospital, Gifu, Japan
| | - Shuhei Fujimoto
- 5Department of Bacteriology and Bacterial Infection Division of Host Defence Mechanism, Tokai University School of Medicine, Kanagawa, Japan
| | - Yoshichika Arakawa
- 2Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
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Gay N, Leclaire A, Laval M, Miltgen G, Jégo M, Stéphane R, Jaubert J, Belmonte O, Cardinale E. Risk Factors of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Occurrence in Farms in Reunion, Madagascar and Mayotte Islands, 2016-2017. Vet Sci 2018; 5:vetsci5010022. [PMID: 29473906 PMCID: PMC5876575 DOI: 10.3390/vetsci5010022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/11/2022] Open
Abstract
In South Western Indian ocean (IO), Extended-Spectrum β-Lactamase producing Enterobacteriaceae (ESBL-E) are a main public health issue. In livestock, ESBL-E burden was unknown. The aim of this study was estimating the prevalence of ESBL-E on commercial farms in Reunion, Mayotte and Madagascar and genes involved. Secondly, risk factors of ESBL-E occurrence in broiler, beef cattle and pig farms were explored. In 2016-2017, commercial farms were sampled using boot swabs and samples stored at 4 °C before microbiological analysis for phenotypical ESBL-E and gene characterization. A dichotomous questionnaire was performed. Prevalences observed in all production types and territories were high, except for beef cattle in Reunion, which differed significantly. The most common ESBL gene was blaCTX-M-1. Generalized linear models explaining ESBL-E occurrence varied between livestock production sectors and allowed identifying main protective (e.g., water quality control and detergent use for cleaning) and risk factors (e.g., recent antibiotic use, other farmers visiting the exploitation, pet presence). This study is the first to explore tools for antibiotic resistance management in IO farms. It provides interesting hypothesis to explore about antibiotic use in IO territories and ESBL-E transmission between pig, beef cattle and humans in Madagascar.
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Affiliation(s)
- Noellie Gay
- Animals, Health, Territories, Risks and Ecosystems, Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Alexandre Leclaire
- Bacteriology laboratory, Félix Guyon Hospital, Saint-Denis, 97400 Reunion, France.
| | - Morgane Laval
- Animals, Health, Territories, Risks and Ecosystems, Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Guillaume Miltgen
- Bacteriology laboratory, Félix Guyon Hospital, Saint-Denis, 97400 Reunion, France.
- UMR PIMIT, CNRS 9192, INSERM U1187, IRD 249, F-97418 Sainte-Clotilde, La Réunion, France.
| | - Maël Jégo
- Animals, Health, Territories, Risks and Ecosystems, Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Ramin Stéphane
- Animals, Health, Territories, Risks and Ecosystems, Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
| | - Julien Jaubert
- Bacteriology laboratory, Félix Guyon Hospital, Saint-Denis, 97400 Reunion, France.
| | - Olivier Belmonte
- Bacteriology laboratory, Félix Guyon Hospital, Saint-Denis, 97400 Reunion, France.
| | - Eric Cardinale
- Animals, Health, Territories, Risks and Ecosystems, Avenue Agropolis, 34398 Montpellier CEDEX 5, France.
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45
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Liakopoulos A, van den Bunt G, Geurts Y, Bootsma MCJ, Toleman M, Ceccarelli D, van Pelt W, Mevius DJ. High Prevalence of Intra-Familial Co-colonization by Extended-Spectrum Cephalosporin Resistant Enterobacteriaceae in Preschool Children and Their Parents in Dutch Households. Front Microbiol 2018. [PMID: 29515562 PMCID: PMC5826366 DOI: 10.3389/fmicb.2018.00293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Extended-spectrum cephalosporin-resistant (ESCR) Enterobacteriaceae pose a serious infection control challenge for public health. The emergence of the ESCR phenotype is mostly facilitated by plasmid-mediated horizontal extended-spectrum β-lactamases (ESBLs) and AmpC gene transfer within Enterobacteriaceae. Current data regarding the plasmid contribution to this emergence within the Dutch human population is limited. Hence, the aim of this study was to gain insight into the role of plasmids in the dissemination of ESBL/AmpC genes inside Dutch households with preschool children and precisely delineate co-colonization. In 87 ESCREnterobacteriaceae from fecal samples of parents and preschool children within 66 Dutch households, genomic localization, plasmid type and insertion sequences linked to ESBL/AmpC genes were determined. Chromosomal location of ESBL/AmpC genes was confirmed when needed. An epidemiologically relevant subset of the isolates based on household co-carriage was assessed by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis for genetic relatedness. The narrow-host range I1α and F plasmids were the major facilitators of ESBL/AmpC-gene dissemination. Interestingly, we documented a relatively high occurrence of chromosomal integration of typically plasmid-encoded ESBL/AmpC-genes. A high diversity of non-epidemic Escherichia coli sequence types (STs) was revealed; the predominant STs belonged to the pandemic lineages of extraintestinal pathogenic E. coli ST131 and ST69. Intra-familiar co-carriage by identical ESCREnterobacteriaceae was documented in 7 households compared to 14 based on sole gene typing, as previously reported. Co-carriage was more frequent than expected based on pure chance, suggesting clonal transmission between children and parents within the household.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Gerrita van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Yvon Geurts
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Martin C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Mathematics, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Mark Toleman
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Dik J Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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46
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Complete Genome Sequence of a blaCTX-M-1-Harboring Escherichia coli Isolate Recovered from Cattle in Germany. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01476-17. [PMID: 29371351 PMCID: PMC5786677 DOI: 10.1128/genomea.01476-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We describe here the whole-genome sequence and basic characteristics of Escherichia coli isolate 15-AB01393, recovered from German beef within a national monitoring program in 2015. This isolate was identified as an extended-spectrum-β-lactamase-producing E. coli strain of multilocus sequence type (MLST) ST58 harboring the antimicrobial resistance genes blaCTX-M-1, mph(A), sul2, dfrA5, strA, and strB.
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47
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Touzain F, Le Devendec L, de Boisséson C, Baron S, Jouy E, Perrin-Guyomard A, Blanchard Y, Kempf I. Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers. PLoS One 2018; 13:e0188768. [PMID: 29360838 PMCID: PMC5779644 DOI: 10.1371/journal.pone.0188768] [Citation(s) in RCA: 26] [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: 07/05/2017] [Accepted: 11/13/2017] [Indexed: 12/24/2022] Open
Abstract
Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20 of them carrying the sul2 or tet(A) genes respectively. Despite their diverse origins, several plasmids showed very high percentages of identity. None of the blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of them were detected in the parental strains. Three plasmids had the blaCMY-2 gene, but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3 plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT, etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid. In conclusion, our results show the dominance and high similarity of blaCTX-M-1 IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a blaCMY-2 plasmid.
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Affiliation(s)
- Fabrice Touzain
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Laetitia Le Devendec
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Claire de Boisséson
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Sandrine Baron
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Eric Jouy
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Agnès Perrin-Guyomard
- Université Bretagne Loire, Rennes, France
- ANSES, Fougères Laboratory, Fougères, France
| | - Yannick Blanchard
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Isabelle Kempf
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
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48
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Guenther S, Semmler T, Stubbe A, Stubbe M, Wieler LH, Schaufler K. Chromosomally encoded ESBL genes in Escherichia coli of ST38 from Mongolian wild birds. J Antimicrob Chemother 2018; 72:1310-1313. [PMID: 28158613 DOI: 10.1093/jac/dkx006] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/04/2017] [Indexed: 01/16/2023] Open
Abstract
Objectives ESBL genes in Escherichia coli are mainly plasmid encoded, although recent studies have also shown chromosomal integration, e.g. in clinical E. coli isolates of ST38. As ESBL-producing E. coli are also found in non-clinical settings, we were interested in determining whether chromosomally integrated ESBL genes occur in ST38 isolates from non-clinical habitats, e.g. wildlife. Methods Four ESBL-producing E. coli isolates of ST38 originating from Mongolian birds of prey sampled in 2015 were subjected to a detailed analysis in terms of phenotypic resistance, plasmid profiling and WGS, followed by the determination of genotypic resistance factors including the chromosomal integration of ESBL and carbapenemase genes. Results Results based on phenotypic and genotypic plasmid profiling, contiguous sequence (contig) sizes and PCR analysis of flanking insertion site regions showed that three of four ST38 isolates harboured chromosomally encoded bla CTX-M genes of three different types ( bla CTX-M-14 , bla CTX-M-15 and bla CTX-M-24 ) that were inserted into three different chromosomal locations. A comparison of WGS data with ST38 isolates from a clinical outbreak in the UK indicated only low numbers of core-genome SNPs detected among one Mongolian wild bird isolate and eight clinical isolates from the UK. Conclusions The chromosomal integration of bla CTX-M genes in E. coli isolates of ST38 appears to be common and is likely independent of antimicrobial selective pressure in clinical environments. Our data corroborate the zoonotic potential of environmental isolates of ESBL-producing E. coli , which harbour stably integrated, chromosomally encoded resistance factors.
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Affiliation(s)
- Sebastian Guenther
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | | | - Annegret Stubbe
- Department of Zoology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
| | - Michael Stubbe
- Department of Zoology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
| | | | - Katharina Schaufler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
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49
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Paitan Y. Current Trends in Antimicrobial Resistance of Escherichia coli. Curr Top Microbiol Immunol 2018; 416:181-211. [PMID: 30088148 DOI: 10.1007/82_2018_110] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Escherichia coli is the most common Gram-negative bacterial pathogen, presenting both a clinical and an epidemiological challenge. In the last decade, several successful multidrug-resistant high-risk strains, such as strain E. coli ST131 have evolved, mainly due to the growing selective pressure of antimicrobial use. These strains present enhanced fitness and pathogenicity, effective transmission and colonization abilities, global distribution due to efficient dissemination, and resistance to various antimicrobial resistances. Here, we describe the emerging trends and epidemiology of resistant E. coli, including carbapenemase-producing E. coli, E. coli ST131 and colistin resistant E. coli.
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Affiliation(s)
- Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44282, Kfar Saba, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 39978, Tel Aviv, Israel.
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50
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Mohsin M, Raza S, Schaufler K, Roschanski N, Sarwar F, Semmler T, Schierack P, Guenther S. High Prevalence of CTX-M-15-Type ESBL-Producing E. coli from Migratory Avian Species in Pakistan. Front Microbiol 2017; 8:2476. [PMID: 29312186 PMCID: PMC5733096 DOI: 10.3389/fmicb.2017.02476] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/29/2017] [Indexed: 12/21/2022] Open
Abstract
The increased presence of clinically relevant multidrug resistant bacteria in natural environments is an emerging challenge for global health care. Little is known regarding the occurrence of extended-spectrum beta-lactamase producing Escherichia coli (ESBL-E. coli) from environmental sentinels in Pakistan. The goal of the current study was to gain insights into the prevalence and phylogenetic relationships of ESBL-E. coli recovered from wild birds in Pakistan during winter migration. After initial screening of fecal samples on selective chromogenic agar, ESBL-E.coli were analyzed phenotypically using the Vitek-2 automated system. Genotypic characterization was performed using whole genome sequencing (WGS) followed by an in-depth in silico analysis. Of 150 birds screened, 26 (17.3%) were fecal carriers of ESBL-E. coli. Of these, 88.4% isolates exhibited multidrug resistance (MDR) phenotypes. Resistance to cefotaxime, ceftazidime, ampicillin, doxycycline, tetracycline and sulfamethoxazole/trimethoprim (CTX-CAZ-AM-DC-TE-SXT) represented the most common pattern of MDR (76.9%). WGS data analysis found blaCTX-M-15 as the predominant ESBL genotype (92.3%). Other genes encoding resistance to sulfonamides (sul1/sul2/sul3), aminoglycosides (strA, strB, aadA1, aadA2, aadA5, aac(3)-IId-like, aac(3)-IVa-like and aph(4)-Ia), trimethoprim (dfrA14 or dfrA17), tetracyclines [tet(A)/tet(B)], and fluoroquinolones (qnrS1) were detected commonly, often encoded on IncF-type plasmids (76.9%). ESBL-E. coli were assigned to 17 different sequence types (STs) of which ST10 and ST7097 (4 isolates each) were the most abundant followed by ST4720, ST93, and ST1139 (2 isolates each). Core-genome phylogeny of the isolates found low numbers (0-29) of single nucleotide polymorphisms (SNPs) in isolates belonged to ST7097 originated from two different locations (Chashma barrage and Rasul barrage). Similar trends were found among isolates belong to ST1139. In addition, WGS-based plasmid typing and S1-digestion found plasmids of the same pMLST type (IncF[F-:A-:B53]) and similar sizes in different bacterial and avian hosts suggesting horizontal gene transfer as another possibility for the spread of ESBL-E. coli in avian wildlife in Pakistan.
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Affiliation(s)
- Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Shahbaz Raza
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Katharina Schaufler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Nicole Roschanski
- Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Fatima Sarwar
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Torsten Semmler
- NG 1-Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Peter Schierack
- Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Sebastian Guenther
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
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