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Zhao QY, Cai RM, Cai P, Zhang L, Jiang HX, Zeng ZL. Characterization of Salmonella Phage P1-CTX and the Potential Mechanism Underlying the Acquisition of the blaCTX-M-27 Gene. Antibiotics (Basel) 2024; 13:446. [PMID: 38786174 PMCID: PMC11117986 DOI: 10.3390/antibiotics13050446] [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: 04/08/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The P1 phage has garnered attention as a carrier of antibiotic resistance genes (ARGs) in Enterobacteriaceae. However, the transferability of ARGs by P1-like phages carrying ARGs, in addition to the mechanism underlying ARG acquisition, remain largely unknown. In this study, we elucidated the biological characteristics, the induction and transmission abilities, and the acquisition mechanism of the blaCTX-M-27 gene in the P1 phage. The P1-CTX phage exhibited distinct lytic plaques and possessed a complete head and tail structure. Additionally, the P1-CTX phage was induced successfully under various conditions, including UV exposure, heat treatment at 42 °C, and subinhibitory concentrations (sub-MICs) of antibiotics. Moreover, the P1-CTX phage could mobilize the blaCTX-M-27 gene into three strains of Escherichia coli (E. coli) and the following seven different serotypes of Salmonella: Rissen, Derby, Kentucky, Typhimurium, Cerro, Senftenberg, and Muenster. The mechanism underlying ARG acquisition by the P1-CTX phage involved Tn1721 transposition-mediated movement of blaCTX-M-27 into the ref and mat genes within its genome. To our knowledge, this is the first report documenting the dynamic processes of ARG acquisition by a phage. Furthermore, this study enriches the research on the mechanism underlying the phage acquisition of drug resistance genes and provides a basis for determining the risk of drug resistance during phage transmission.
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Affiliation(s)
- Qiu-Yun Zhao
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China
| | - Run-Mao Cai
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Ping Cai
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Lin Zhang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Zhen-Ling Zeng
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
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2
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Banerjee J, Batabyal S, Biswas S, Bhattacharyya D, Habib M, Das AK, Nanda PK, Samanta I, Dandapat P, Bandyopadhyay S. Stray Dogs (Mongrels) Are Potent Reservoir of Drug-Resistant Pathogens: A Study in Peri-Urban Areas of Kolkata, India. Microb Drug Resist 2024. [PMID: 38656133 DOI: 10.1089/mdr.2023.0249] [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: 04/26/2024] Open
Abstract
This study depicts the drug-resistance and phylogenomic characteristics of 365 Escherichia coli (EC) and 76 Klebsiella pneumoniae (KP) isolated from stray dogs (293) in and around Kolkata, India. Initial screening found 59 isolates, including 48 E. coli and 11 KP multidrug resistant, which included 33 extended-spectrum β-lactamase, 41 AmpC β-lactamase and 18 metallo-β-lactamase producers carrying blaNDM-1 (11) and blaNDM-5 (7) genes. Majority of them had the resistant genes such as blaCTX-M (33), blaTEM (18), blaSHV (4), blaOXA (17), blaFOX (2), blaDHA (2), blaCITM (15), blaCMY-2 (13), blaGES (2) and blaVEB (2), qnrS (15), qnrB (3), aac-6'-Ib-cr (14), tetA (26), tetB (14), sul-1 (25), armA (2) and rmtB (6), in addition to adherence genes such as csgA (33), fimA (27), fliC (13), sdiA (33), rcsA (38), and rpoS (39). They also carried plasmid of diverse replicon types of which IncFIA and FIB were the most frequent. Phylogrouping categorized most of the MDR E. coli in phylogroup A (20), B1 (14), and B2 (6). Enterobacteriaceae repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) showed genetic diversity of multidrug resistant isolates irrespective of their origin, resistance, and virulence types, differentiating the EC in five clades (A-E) and KP in four clades (A-D). As these stray dogs, which had no history or scope of previous antimicrobial therapy, were found to have contracted potential antimicrobial resistance pathogens, the role of environment in spread of such pathogens and further possibility of human infections cannot be ruled out.
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Affiliation(s)
- Jaydeep Banerjee
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Subhasis Batabyal
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Suman Biswas
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | | | - Md Habib
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Arun K Das
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Pramod K Nanda
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
| | - Indranil Samanta
- West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Premanshu Dandapat
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, India
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3
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El Chaar M, Khoury Y, Douglas GM, El Kazzi S, Jisr T, Soussi S, Merhi G, Moghnieh RA, Shapiro BJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients. Microbiol Spectr 2024; 12:e0312823. [PMID: 38171007 PMCID: PMC10846182 DOI: 10.1128/spectrum.03128-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.
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Affiliation(s)
- Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Yaralynn Khoury
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Gavin M. Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Samir El Kazzi
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima Jisr
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Shatha Soussi
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Georgi Merhi
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Rima A. Moghnieh
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center, Beirut, Lebanon
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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4
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Zurita J, Sevillano G, Paz Y Miño A, Haro N, Larrea-Álvarez M, Alcocer I, Ortega-Paredes D. Dominance of ST131, B2, blaCTX-M-15, and papA-papC-kpsMII-uitA among ESBL Escherichia coli isolated from bloodstream infections in Quito, Ecuador: a 10-year surveillance study (2009-2019). J Appl Microbiol 2023; 134:lxad269. [PMID: 37974051 DOI: 10.1093/jambio/lxad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/21/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
AIMS This study aimed to examine antibiotic resistance and the epidemiology of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli associated with bloodstream infections over a period of 10 years. METHODS AND RESULTS Isolates were collected from January 2009 to December 2019 and those testing for E. coli were included. Antibiotic susceptibility was tested using the VITEK® system. Selected isolates were further characterized by amplification of marker genes (virulence traits, phylogroups, and sequence types). A total of 166 ESBL-producing E. coli were recovered. The blaCTX-M-15 allele was the most abundant. Most of the isolates were resistant to ceftriaxone, cefepime, ceftazidime, ampicillin/sulbactam, piperacillin/tazobactam, and ciprofloxacin. No resistance to carbapenems was registered. More than 80% of bacteria were classified as extraintestinal pathogenic E. coli (ExPEC), and the combination of virulence traits:papA-papC-kpsMII-uitA was the most common. Phylogroup B2 was the most prevalent, and bacteria predominantly belonged to ST131. CONCLUSIONS There was an increase in the ExPEC ESBL-E coli in bloodstream infections and the relationship between the isolates found in these infections during these 10 years.
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Affiliation(s)
- Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
- Servicio de Microbiología y Tuberculosis, Hospital Vozandes, Quito 170521, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Ariane Paz Y Miño
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Nathalí Haro
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Marco Larrea-Álvarez
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Km 2.5 vía a Samborondón 0901952, Ecuador
| | - Iliana Alcocer
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
| | - David Ortega-Paredes
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Km 2.5 vía a Samborondón 0901952, Ecuador
- Unidad de Investigación en Enfermedades Transmitidas por Alimentos y Resistencia a los, Antimicrobianos (UNIETAR), Facultad de Veterinaria, Universidad Central del Ecuador, Quito 170129, Ecuador
- Laboratorio de Referencia de E. coli, Department of Microbiology and Parasitology, Veterinary Faculty, University of Santiago de Compostela, Lugo 15782, Spain
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5
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Mills EG, Martin MJ, Luo TL, Ong AC, Maybank R, Corey BW, Harless C, Preston LN, Rosado-Mendez JA, Preston SB, Kwak YI, Backlund MG, Bennett JW, Mc Gann PT, Lebreton F. A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network. Genome Med 2022; 14:147. [PMID: 36585742 PMCID: PMC9801656 DOI: 10.1186/s13073-022-01150-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Extra-intestinal pathogenic Escherichia coli (ExPEC) are a leading cause of bloodstream and urinary tract infections worldwide. Over the last two decades, increased rates of antibiotic resistance in E. coli have been reported, further complicating treatment. Worryingly, specific lineages expressing extended-spectrum β-lactamases (ESBLs) and fluoroquinolone resistance have proliferated and are now considered a serious threat. Obtaining contemporary information on the epidemiology and prevalence of these circulating lineages is critical for containing their spread globally and within the clinic. METHODS Whole-genome sequencing (WGS), phylogenetic analysis, and antibiotic susceptibility testing were performed for a complete set of 2075 E. coli clinical isolates collected from 1776 patients at a large tertiary healthcare network in the USA between October 2019 and September 2020. RESULTS The isolates represented two main phylogenetic groups, B2 and D, with six lineages accounting for 53% of strains: ST-69, ST-73, ST-95, ST-131, ST-127, and ST-1193. Twenty-seven percent of the primary isolates were multidrug resistant (MDR) and 5% carried an ESBL gene. Importantly, 74% of the ESBL-E.coli were co-resistant to fluoroquinolones and mostly belonged to pandemic ST-131 and emerging ST-1193. SNP-based detection of possible outbreaks identified 95 potential transmission clusters totaling 258 isolates (12% of the whole population) from ≥ 2 patients. While the proportion of MDR isolates was enriched in the set of putative transmission isolates compared to sporadic infections (35 vs 27%, p = 0.007), a large fraction (61%) of the predicted outbreaks (including the largest cluster grouping isolates from 12 patients) were caused by the transmission of non-MDR clones. CONCLUSION By coupling in-depth genomic characterization with a complete sampling of clinical isolates for a full year, this study provides a rare and contemporary survey on the epidemiology and spread of E. coli in a large US healthcare network. While surveillance and infection control efforts often focus on ESBL and MDR lineages, our findings reveal that non-MDR isolates represent a large burden of infections, including those of predicted nosocomial origins. This increased awareness is key for implementing effective WGS-based surveillance as a routine technology for infection control.
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Affiliation(s)
- Emma G. Mills
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Melissa J. Martin
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ting L. Luo
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ana C. Ong
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Rosslyn Maybank
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Brendan W. Corey
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Casey Harless
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Lan N. Preston
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Joshua A. Rosado-Mendez
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Scott B. Preston
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Yoon I. Kwak
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Michael G. Backlund
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Jason W. Bennett
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Patrick T. Mc Gann
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Francois Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
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6
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Neffe L, Forde TL, Oravcova K, Köhler U, Bautsch W, Tomasch J, Häussler S. Genomic epidemiology of clinical ESBL-producing Enterobacteriaceae in a German hospital suggests infections are primarily community- and regionally-acquired. Microb Genom 2022; 8:mgen000901. [PMID: 36748515 PMCID: PMC9837565 DOI: 10.1099/mgen.0.000901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Clinical Enterobacteriaceae isolates that produce extended-spectrum β-lactamases (ESBLs) have been increasingly reported at a global scale. However, comprehensive data on the molecular epidemiology of ESBL-producing strains are limited and few studies have been conducted in non-outbreak situations.We used whole-genome sequencing to describe the population structure of 294 ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates that were recovered from a German community hospital throughout a 1 year sampling period in a non-outbreak situation.We found a high proportion of E. coli isolates (61.5 %) belonged to the globally disseminated extraintestinal pathogenic ST131, whereas a wider diversity of STs was observed among K. pneumoniae isolates. The E. coli ST131 population in this study was shaped by multiple introductions of strains as demonstrated by contextual genomic analysis including ST131 strains from other geographical sources. While no recent common ancestor of the isolates of the current study and other international isolates was found, our clinical isolates clustered with those previously recovered in the region. Furthermore, we found that the isolation of ESBL-producing clinical strains in hospitalized patients could only rarely be associated with likely patient-to-patient transmission, indicating primarily a community and regional acquisition of strains.Further genomic analyses of clinical, carriage and environmental isolates is needed to uncover hidden transmissions and thus discover the most common sources of ESBL-producing pathogen infections in our hospitals.
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Affiliation(s)
- Lisa Neffe
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ute Köhler
- Städtisches Klinikum Braunschweig gGmbH, Germany
| | | | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany,Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany,*Correspondence: Susanne Häussler,
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7
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Zamudio R, Boerlin P, Beyrouthy R, Madec JY, Schwarz S, Mulvey MR, Zhanel GG, Cormier A, Chalmers G, Bonnet R, Haenni M, Eichhorn I, Kaspar H, Garcia-Fierro R, Wood JLN, Mather AE. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America. Nat Commun 2022; 13:7490. [PMID: 36509735 PMCID: PMC9744880 DOI: 10.1038/s41467-022-34970-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.
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Affiliation(s)
- Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Racha Beyrouthy
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand, 63001, France.,Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, 63000, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Ashley Cormier
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Richard Bonnet
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand, 63001, France.,Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, 63000, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Heike Kaspar
- Department Method Standardisation, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin, 12277, Germany
| | - Raquel Garcia-Fierro
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK. .,University of East Anglia, Norwich, NR4 7TJ, UK.
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8
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Neffe L, Abendroth L, Bautsch W, Häussler S, Tomasch J. High plasmidome diversity of extended-spectrum beta-lactam-resistant Escherichia coli isolates collected during one year in one community hospital. Genomics 2022; 114:110368. [PMID: 35447310 DOI: 10.1016/j.ygeno.2022.110368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 04/09/2022] [Indexed: 01/14/2023]
Abstract
Plasmid-encoded antibiotic resistance encompasses many classes of currently used antibiotics. In globally distributed Escherichia coli lineages plasmids, which spread via horizontal gene transfer, are responsible for the dissemination of genes encoding extended-spectrum β-lactamases (ESBL). In this study, we combined 2nd and 3rd generation sequencing techniques to reconstruct the plasmidome of overall 97 clinical ESBL-E. coli isolates. Our results highlight the enormous plasmid diversity in respect to size, replicon-type and genetic content. Furthermore, we emphasize the diverse plasmid distribution patterns among the clinical isolates and the high intra- and extracellular mobility potential of resistance conferring genes. While the majority of resistance conferring genes were located on large plasmids of known replicon type, small cryptic plasmids seem to be underestimated resistance gene vectors. Our results contribute to a better understanding of the dissemination of resistance-conferring genes through horizontal gene transfer as well as clonal spread.
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Affiliation(s)
- Lisa Neffe
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa Abendroth
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, Hannover, Germany; Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, 2100 Copenhagen, Denmark; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30265 Hannover, Germany.
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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9
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Belas A, Marques C, Menezes J, da Gama LT, Cavaco-Silva P, Pomba C. ESBL/ pAmpC-Producing Escherichia coli Causing Urinary Tract Infections in Non-Related Companion Animals and Humans. Antibiotics (Basel) 2022; 11:antibiotics11050559. [PMID: 35625203 PMCID: PMC9137695 DOI: 10.3390/antibiotics11050559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI) caused by Escherichia coli are frequently diagnosed in humans and companion animals. Extended-spectrum beta-lactamase (ESBL)- and cephalosporinase (pAmpC)-producing Escherichia coli are worldwide-disseminated and frequently multidrug-resistant, hence leading to treatment failure and public health concerns. This study aimed to characterize and compare ESBL/pAmpC-producing E. coli strains causing community-acquired UTI in companion animals and non-related humans. Third-generation cephalosporin (3GC)-resistant E. coli (companion animals n = 35; humans n = 85) isolated from patients with UTI were tested against 14 antimicrobials following CLSI guidelines. PCR-based assays were used to detect the major E. coli phylogenetic groups, pathogenicity associated-islands (PAIs), virulence genes, and ESBLs/pAmpC resistance genes. ESBL/pAmpC-producing E. coli isolates were typed by multi-locus sequence typing (MLST) and PCR. E. coli strains from companion animals and humans shared two MDR high-risk clonal lineages: ST131 and ST648. To the best of our knowledge, this study reports the first description of E. coli ST131 clade C1-M27 and the clonal lineage ST131 clade A in humans with community-acquired UTI in Portugal. Considering that companion animals with UTI are generally treated at home by the owners, measures should be implemented to avoid the spread of multidrug-resistant high-risk clones to humans and their household environment.
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Affiliation(s)
- Adriana Belas
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Cátia Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Juliana Menezes
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Luís Telo da Gama
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Patrícia Cavaco-Silva
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Caparica, Portugal;
- Technophage, 1649-028 Lisboa, Portugal
| | - Constança Pomba
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Correspondence:
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10
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Osińska M, Nowakiewicz A, Zięba P, Gnat S, Łagowski D, Trościańczyk A. A rich mosaic of resistance in extended-spectrum β-lactamase-producing Escherichia coli isolated from red foxes (Vulpes vulpes) in Poland as a potential effect of increasing synanthropization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151834. [PMID: 34808162 DOI: 10.1016/j.scitotenv.2021.151834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
In our research, we analyzed the resistance of cephalosporin-resistant E. coli strains to antimicrobial agents. The strains were collected during five years from wild animal species commonly inhabiting Poland. We have identified the type of β-lactamases produced and the multidrug-resistance profile. Most strains (73.8%) had genes encoding ESBL enzymes, mainly CTX-M-1 and TEM. Almost all AmpC-β-lactamase-producing isolates had the blaCMY-2 gene. Almost 70% of the strains tested showed a multi-drug resistance profile. The dominant phenotype was resistance to tetracycline (69.05%), and/or sulfamethoxazole (57.1%). We also found high resistance to quinolones: ciprofloxacin 35.7% and nalidixic acid 52.4%. The phenotypic resistance of the strains was in most cases confirmed by the presence of corresponding genes. Among strains, 26.2% were carriers of plasmid-mediated quinolone resistance genes (PMQR). MLST analysis revealed a large clonal variation of the strains, which was reflected in 28 different sequence types. More than half of the strains (54.7%) were classified into the following sequence complexes: 10, 23, 69, 101, 155, 156, 168, 354, 398, 446, and 648. Only one strain in the studied group was assigned to the ExPEC pathotype and represented sequence type 117. The results of our research have confirmed that isolates obtained from wild animals possess many resistance determinants and sequence types, which are also found in food-producing animals and humans. This reflects the doctrine of "One health", which clearly indicates that human health is inextricably linked with animal health as well as degree of environmental contamination. We conclude that the resistance and virulence profiles of strains isolated from wildlife animals may be a resultant of various sources encountered by animals, creating a rich and varied mosaic of genes, which is very often unpredictable and not reflected in the correlation between the sequence type and the gene profile of resistance or virulence observed in epidemic clones.
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Affiliation(s)
- Marcelina Osińska
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Aneta Nowakiewicz
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Przemysław Zięba
- State Veterinary Laboratory, Droga Męczenników Majdanka 50, 20-325 Lublin, Poland
| | - Sebastian Gnat
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Dominik Łagowski
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Aleksandra Trościańczyk
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
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11
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Zhu Y, Huang WE, Yang Q. Clinical Perspective of Antimicrobial Resistance in Bacteria. Infect Drug Resist 2022; 15:735-746. [PMID: 35264857 PMCID: PMC8899096 DOI: 10.2147/idr.s345574] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/18/2022] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial resistance (AMR) has become a global clinical problem in recent years. With the discovery of antibiotics, infections were not a deadly problem for clinicians as they used to be. However, worldwide AMR comes with the overuse/misuse of antibiotics and the spread of resistance is deteriorated by a multitude of mobile genetic elements and relevant resistant genes. This review provides an overview of the current situation, mechanism, epidemiology, detection methods and clinical treatment for antimicrobial resistant genes in clinical important bacteria including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), penicillin-resistant Streptococcus pneumoniae (PRSP), extended-spectrum β-lactamase-producing Enterobacteriaceae, acquired AmpC β-lactamase-producing Enterobacteriaceae, carbapenemase-producing Enterobacteriaceae (CPE), multidrug-resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa.
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Affiliation(s)
- Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
- Correspondence: Qiwen Yang; Wei E Huang, Email ;
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12
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Kurittu P, Khakipoor B, Jalava J, Karhukorpi J, Heikinheimo A. Whole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli From Human Infections in Finland Revealed Isolates Belonging to Internationally Successful ST131-C1-M27 Subclade but Distinct From Non-human Sources. Front Microbiol 2022; 12:789280. [PMID: 35058905 PMCID: PMC8764355 DOI: 10.3389/fmicb.2021.789280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL-producing Escherichia coli clinical samples from Finland to the genomic level and investigation of possible zoonotic transmission routes are scarce. This study characterizes ESBL-producing E. coli from clinical samples in Finland using whole genome sequencing (WGS). Comparison is made between animal, food, and environmental sources in Finland to gain insight into potential zoonotic transmission routes and to recognize successful AMR genes, bacterial sequence types (STs), and plasmids. ESBL-producing E. coli isolates (n = 30) obtained from the Eastern Finland healthcare district between 2018 and 2020 underwent WGS and were compared to sequences from non-human and healthy human sources (n = 67) isolated in Finland between 2012 and 2018. A majority of the clinical isolates belonged to ST131 (n = 21; 70%), of which 19 represented O25:H4 and fimH30 allele, and 2 O16:H5 and fimH41 allele. Multidrug resistance was common, and the most common bla gene identified was bla CTX-M-27 (n = 14; 47%) followed by bla CTX-M-15 (n = 10; 33%). bla CTX-M-27 was identified in 13 out of 21 isolates representing ST131, with 12 isolates belonging to a recently discovered international E. coli ST131 C1-M27 subclade. Isolates were found to be genetically distinct from non-human sources with core genome multilocus sequence typing based analysis. Most isolates (n = 26; 87%) possessed multiple replicons, with IncF family plasmids appearing in 27 (90%) and IncI1 in 5 (17%) isolates. IncF[F1:A2:B20] replicon was identified in 11, and IncF[F-:A2:B20] in 4 isolates. The results indicate the ST131-C1-M27 clade gaining prevalence in Europe and provide further evidence of the concerning spread of this globally successful pathogenic clonal group. This study is the first to describe ESBL-producing E. coli in human infections with WGS in Finland and provides important information on global level of the spread of ESBL-producing E. coli belonging to the C1-M27 subclade. The results will help guide public health actions and guide future research.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Jalava
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jari Karhukorpi
- Eastern Finland Laboratory Centre Joint Authority Enterprise (ISLAB), Joensuu, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinäjoki, Finland
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13
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Suminda GGD, Bhandari S, Won Y, Goutam U, Kanth Pulicherla K, Son YO, Ghosh M. High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance. Comput Struct Biotechnol J 2022; 20:5378-5392. [PMID: 36212529 PMCID: PMC9526013 DOI: 10.1016/j.csbj.2022.09.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.
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14
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Li D, Wyrsch ER, Elankumaran P, Dolejska M, Marenda MS, Browning GF, Bushell RN, McKinnon J, Chowdhury PR, Hitchick N, Miller N, Donner E, Drigo B, Baker D, Charles IG, Kudinha T, Jarocki VM, Djordjevic SP. Genomic comparisons of Escherichia coli ST131 from Australia. Microb Genom 2021; 7:000721. [PMID: 34910614 PMCID: PMC8767332 DOI: 10.1099/mgen.0.000721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically blaCTX-M-15 and blaCTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.
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Affiliation(s)
- Dmitriy Li
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ethan R. Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic,Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic,Biomedical Center, Charles University, Czech Republic,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
| | - Marc S. Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Glenn F. Browning
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Rhys N. Bushell
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Jessica McKinnon
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Nola Hitchick
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Natalie Miller
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | | | | | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Veronica M. Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Veronica M. Jarocki,
| | - Steven Philip Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Steven Philip Djordjevic,
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15
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Vaiyapuri M, Sebastian AS, George I, Variem SS, Vasudevan RN, George JC, Badireddy MR, Sivam V, Peeralil S, Sanjeev D, Thandapani M, Moses SA, Nagarajarao RC, Mothadaka MP. Predominance of genetically diverse ESBL Escherichia coli identified in resistance mapping of Vembanad Lake, the largest fresh-cum-brackishwater lake of India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:66206-66222. [PMID: 34328620 DOI: 10.1007/s11356-021-15110-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance (AMR) burden in Escherichia coli along the 90 km stretch of Vembanad Lake, Kerala, India, was assessed. Seventy-seven percent of water samples drawn from 35 different stations of the lake harbored E. coli. Antibiotic susceptibility test performed on 116 E. coli isolates revealed resistance to ≥ one antibiotic with 39 AMR profiles in 81%, multidrug resistance in 30%, and extended spectrum β-lactamase (ESBL) producers in 32%. Of all the 15 antibiotics tested, the probability of isolating cefotaxime-resistant E. coli was the highest (P ≤ 0.05) in the lake. Genetically diverse ESBL types, namely blaTEM-116, blaCTX-M -152, blaCTX-M -27, blaCTX-M -55, blaCTX-M-205, and blaSHV-27, were identified in the lake. This is probably the first report in India for the presence of blaCTX-M-205 (blaCTX-M-group 2) in the Vembanad Lake. ST11439 and single and double loci variants of ST443 and ST4533 were identified in multilocus sequence typing (MLST). Inc plasmids (B/O, F, W, I1, FIIA, HI1, P-1α, K/B, and N) identified in the lake evidences the resistance transmission potential of the E. coli isolated from the lake. Molecular typing (ERIC-PCR, MLST, and PBRT) delineated diverse E. coli, both between and within the sampling stations. Low multiple antibiotic resistance index (average MAR< 0.2) indicates a lower risk of the lake to the human population, but the occurrence of genetically diverse ESBL E. coli in the Vembanad Lake signals health hazards and necessitates pragmatic control measures.
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Affiliation(s)
- Murugadas Vaiyapuri
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India.
| | - Anna SherinPulithara Sebastian
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
| | - Iris George
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
- Biological Oceanography Division, CSIR - National Institute of Oceanography, Dona Paula, 403 004, Goa, India
| | - Sandhya Soolamkandath Variem
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
- Agharkar Research Institute, Gopal Ganesh, Agarkar Rd, Shivajinagar, Pune, Maharashtra, 411004, India
| | - Radhakrishnan Nair Vasudevan
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
| | | | | | - Visnuvinayagam Sivam
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
| | - Shaheer Peeralil
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
| | - Devi Sanjeev
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
| | - Muthulakshmi Thandapani
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
| | | | | | - Mukteswar Prasad Mothadaka
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology (ICAR-CIFT), Cochin, 682029, Kerala, India
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16
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Hapuarachchi IU, Hannaway RF, Roman T, Biswas A, Dyet K, Morgan X, Ussher JE. Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand. JAC Antimicrob Resist 2021; 3:dlab147. [PMID: 34778763 PMCID: PMC8578626 DOI: 10.1093/jacamr/dlab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES The incidence of infections with ESBL-producing Escherichia coli (ESBL-Ec) in New Zealand is increasing. ESBL-Ec most commonly cause urinary tract infections and are seen in both community and hospitalized patients. The reason for the increasing incidence of ESBL-Ec infections is unknown. METHODS In this study, 65 urinary ESBL-Ec isolates from the Otago region in 2015 were fully genetically characterized to understand the mechanisms of transmission. The ESBL gene, E. coli STs, plasmid types and genetic context (e.g. insertion sequences) of ESBL genes were determined by a combination of whole genome and plasmid sequencing. The phylogenetic relationships of the isolates were compared with ESBL-Ec isolates sequenced as part of the 2016 nationwide survey. RESULTS Significant diversity of E. coli strains, plasmids, and the genetic context of ESBL genes was seen. However, there was evidence of common mobile genetic elements in unrelated ESBL-Ec. CONCLUSIONS Multiple introductions of ESBL resistance genes or resistant bacterial strains with limited horizontal transmission of mobile genetic elements accounts for the increased incidence of ESBL-Ec in this low prevalence area. Future studies should investigate modes of transmission of ESBL-Ec in the Otago region.
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Affiliation(s)
- Isuri U Hapuarachchi
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rachel F Hannaway
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Tabatha Roman
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- AgResearch, Palmerston North, New Zealand
| | | | - Xochitl Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Southern Community Laboratories, Dunedin, New Zealand
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17
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López-Cerero L, Salamanca E, Delgado-Valverde M, Rodríguez-Martínez JM, Rodríguez-Baño J, Pascual Á. Higher prevalence of CTX-M-27-producing Escherichia coli belonging to ST131 clade C1 among residents of two long-term care facilities in Southern Spain. Eur J Clin Microbiol Infect Dis 2021; 41:335-338. [PMID: 34787750 DOI: 10.1007/s10096-021-04380-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
Abstract
Recently, the emergence of an international lineage of the CTX-M-27-producing clade C1 of Escherichia coli ST131 is being observed. The aim is to see if this strain has also been introduced in our area. Twenty-eight (33%) out of 86 individuals from two LTCFs in Seville were found to be colonized with fluoroquinolone-resistant E. coli ST131 and 46% isolates were ESBL/pAmpC producers. C1 isolates were more common than C2 and more frequently produced blaESBL/pAmpC genes (53% vs 33%). Strain sharing was observed in 6 groups of 2-5 cases (61%). A differentiated cluster of 5 C1-CTX-M-27 isolates was found which lacked the M27PP1 region.
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Affiliation(s)
- Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain. .,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain.
| | - Elena Salamanca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain
| | - Mercedes Delgado-Valverde
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain
| | | | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain.,Departamento de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario, Virgen Macarena, Sevilla, Spain.,Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
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18
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Castanheira M, Simner PJ, Bradford PA. Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection. JAC Antimicrob Resist 2021; 3:dlab092. [PMID: 34286272 PMCID: PMC8284625 DOI: 10.1093/jacamr/dlab092] [Citation(s) in RCA: 218] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.
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19
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Rohde AM, Zweigner J, Wiese-Posselt M, Schwab F, Behnke M, Kola A, Schröder W, Peter S, Tacconelli E, Wille T, Feihl S, Querbach C, Gebhardt F, Gölz H, Schneider C, Mischnik A, Vehreschild MJGT, Seifert H, Kern WV, Gastmeier P, Hamprecht A. Prevalence of third-generation cephalosporin-resistant Enterobacterales colonization on hospital admission and ESBL genotype-specific risk factors: a cross-sectional study in six German university hospitals. J Antimicrob Chemother 2021; 75:1631-1638. [PMID: 32173738 DOI: 10.1093/jac/dkaa052] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES To assess the admission prevalence of third-generation cephalosporin-resistant Enterobacterales (3GCREB) and to assess whether risk factors vary by β-lactamase genotype. METHODS Adult patients were recruited within 72 h of admission to general wards of six university hospitals in 2014 and 2015. Rectal swabs were screened for 3GCREB and isolates were analysed phenotypically and genotypically. Patients were questioned on potential risk factors. Multivariable analyses were performed to identify risk factors for 3GCREB colonization and for specific β-lactamases. RESULTS Of 8753 patients screened, 828 were 3GCREB positive (9.5%). Eight hundred and thirteen isolates were available for genotyping. CTX-M-15 was the most common ESBL (38.0%), followed by CTX-M-1 (22.5%), CTX-M-14 (8.7%), CTX-M-27 (7.5%) and SHV-ESBL (4.4%). AmpC was found in 11.9%. Interestingly, 18 Escherichia coli isolates were AmpC positive, 12 of which (67%) contained AmpC on a gene of plasmid origin [CMY (n = 10), DHA (n = 2)]. Risk factors for 3GCREB colonization varied by genotype. Recent antibiotic exposure and prior colonization by antibiotic-resistant bacteria were risk factors for all β-lactamases except CTX-M-14 and CTX-M-27. Travel outside Europe was a risk factor for CTX-M-15 and CTX-M-27 [adjusted OR (aOR) 3.49, 95% CI 2.88-4.24 and aOR 2.73, 95% CI 1.68-4.43]. A previous stay in a long-term care facility was associated with CTX-M-14 (aOR 3.01, 95% CI 1.98-4.59). A preceding hospital stay in Germany increased the risk of CTX-M-15 (aOR 1.27, 95% CI 1.14-1.41), while a prior hospital stay in other European countries increased the risk of SHV-ESBL colonization (aOR 3.85, 95% CI 1.67-8.92). CONCLUSIONS The detection of different ESBL types is associated with specific risk factor sets that might represent distinct sources of colonization and ESBL-specific dissemination routes.
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Affiliation(s)
- Anna M Rohde
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - Janine Zweigner
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health.,Department of Hospital Hygiene and Infection Control, University Hospital Cologne, Cologne, Germany
| | - Miriam Wiese-Posselt
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - Frank Schwab
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - Michael Behnke
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - Axel Kola
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - Wiebke Schröder
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Division of Infectious Diseases, Department of Internal Medicine 1, University Hospital Tübingen, Tübingen, Germany
| | - Silke Peter
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Evelina Tacconelli
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Division of Infectious Diseases, Department of Internal Medicine 1, University Hospital Tübingen, Tübingen, Germany
| | - Thorsten Wille
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
| | - Susanne Feihl
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Christiane Querbach
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Friedemann Gebhardt
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Hannah Gölz
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Christian Schneider
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Alexander Mischnik
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Maria J G T Vehreschild
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Department I of Internal Medicine, University Hospital of Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, Goethe University, Frankfurt am Main, Germany
| | - Harald Seifert
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
| | - Winfried V Kern
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Division of Infectious Diseases, Department of Medicine II, Medical Centre and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Petra Gastmeier
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Germany, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
| | - Axel Hamprecht
- German Centre for Infection Research Association (DZIF), Braunschweig Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University Hospital Cologne, Cologne, Germany
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20
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Fernandes MR, Sellera FP, Cunha MPV, Lopes R, Cerdeira L, Lincopan N. Emergence of CTX-M-27-producing Escherichia coli of ST131 and clade C1-M27 in an impacted ecosystem with international maritime traffic in South America. J Antimicrob Chemother 2021; 75:1647-1649. [PMID: 32167559 PMCID: PMC7225873 DOI: 10.1093/jac/dkaa069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Marcos P V Cunha
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Ralf Lopes
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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21
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Kazmierczak KM, de Jonge BLM, Stone GG, Sahm DF. Longitudinal analysis of ESBL and carbapenemase carriage among Enterobacterales and Pseudomonas aeruginosa isolates collected in Europe as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme, 2013-17. J Antimicrob Chemother 2021; 75:1165-1173. [PMID: 32040168 DOI: 10.1093/jac/dkz571] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/21/2019] [Accepted: 12/24/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the spread of ESBLs and carbapenemases in Enterobacterales and Pseudomonas aeruginosa in Europe. METHODS 45 335 Gram-negative bacilli were collected in 18 European countries as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme from 2013 to 2017. Antimicrobial susceptibility was determined using broth microdilution, and 9546 isolates were screened for β-lactamase genes by PCR and sequencing. RESULTS ESBLs were identified in 35.5% of Klebsiella pneumoniae and 18.5% of Escherichia coli. ESBL carriage was lowest among isolates in Northern/Western Europe and highest in Eastern Europe. CTX-M-15 was the dominant ESBL in all countries except Greece, where SHV-type ESBLs were more common. Carbapenemases (KPC, OXA-48-like, GES, NDM and VIM) were found in 3.4% of Enterobacterales and were most common among K. pneumoniae (10.5% of those collected). Carbapenemase carriage was lowest in Northern/Western and highest in Southern Europe. KPC-positive Enterobacterales were most abundant but the percentages of OXA-48-like-, NDM- and VIM-positive isolates increased over time and were correlated with an increase in meropenem non-susceptibility. Carbapenemases (VIM, IMP, NDM and GES) were also identified in 5.1% of P. aeruginosa and were commonly found in Eastern Europe. Carbapenemase carriage and meropenem non-susceptibility among P. aeruginosa fluctuated over the 5 years studied and were not well correlated. CONCLUSIONS ESBL and carbapenemase carriage varied by species and European subregion. Meropenem non-susceptibility in European isolates of Enterobacterales can be attributed to carbapenemase carriage and is increasingly caused by MBLs and OXA-48-like carbapenemases. Carbapenemases or other β-lactamases are not a common cause of meropenem non-susceptibility in P. aeruginosa in Europe.
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Affiliation(s)
| | | | | | - Daniel F Sahm
- International Health Management Associates, Inc., Schaumburg, IL, USA
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22
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Peirano G, Lynch T, Matsumara Y, Nobrega D, Finn TJ, DeVinney R, Pitout JDD. Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-2016 1. Emerg Infect Dis 2021; 26:2907-2915. [PMID: 33219650 PMCID: PMC7706940 DOI: 10.3201/eid2612.201221] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Global expansion of antimicrobial drug–resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E. coli from blood samples (n = 1,784) obtained in Calgary, Alberta, Canada, during 2006, 2012, and 2016 by PCR for ST131 and positive samples (n = 344) underwent whole-genome sequencing. The incidence rate per 100,000 residents increased from 4.91 during 2006 to 12.35 during 2012 and 10.12 during 2016. ST131 belonged to clades A (10%), B (9%), and C (81%). Clades C1-nonM27 and B were common during 2006, and C2 containing blaCTX-M-15, C1-M27 containing blaCTX-M-27, and A were responsible for the increase of ST131 during 2012 and 2016. C2 was the most antimicrobial drug–resistant subclade and increased exponentially over time. Eradicating ST131, more specifically the C2 subclade, will lead to considerable public health benefits for persons in Calgary.
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23
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Homeier-Bachmann T, Heiden SE, Lübcke PK, Bachmann L, Bohnert JA, Zimmermann D, Schaufler K. Antibiotic-Resistant Enterobacteriaceae in Wastewater of Abattoirs. Antibiotics (Basel) 2021; 10:antibiotics10050568. [PMID: 34065908 PMCID: PMC8150771 DOI: 10.3390/antibiotics10050568] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/08/2021] [Accepted: 05/09/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic-resistant Enterobacteriaceae are regularly detected in livestock. As pathogens, they cause difficult-to-treat infections and, as commensals, they may serve as a source of resistance genes for other bacteria. Slaughterhouses produce significant amounts of wastewater containing antimicrobial-resistant bacteria (AMRB), which are released into the environment. We analyzed the wastewater from seven slaughterhouses (pig and poultry) for extended-spectrum β-lactamase (ESBL)-carrying and colistin-resistant Enterobacteriaceae. AMRB were regularly detected in pig and poultry slaughterhouse wastewaters monitored here. All 25 ESBL-producing bacterial strains (19 E. coli and six K. pneumoniae) isolated from poultry slaughterhouses were multidrug-resistant. In pig slaughterhouses 64% (12 of 21 E. coli [57%] and all four detected K. pneumoniae [100%]) were multidrug-resistant. Regarding colistin, resistant Enterobacteriaceae were detected in 54% of poultry and 21% of pig water samples. Carbapenem resistance was not detected. Resistant bacteria were found directly during discharge of wastewaters from abattoirs into water bodies highlighting the role of slaughterhouses for environmental surface water contamination.
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Affiliation(s)
- Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald-Insel Riems, Germany;
- Correspondence: ; Tel.: +49-38351-7-1505
| | - Stefan E. Heiden
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Phillip K. Lübcke
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald-Insel Riems, Germany;
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Lisa Bachmann
- Leibniz-Institut für Nutztierbiologie, Institute of Nutritional Physiology “Oskar Kellner”, 18196 Dummerstorf, Germany;
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany;
| | | | - Katharina Schaufler
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
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24
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Falgenhauer L, Zur Nieden A, Harpel S, Falgenhauer J, Domann E. Clonal CTX-M-15-Producing Escherichia coli ST-949 Are Present in German Surface Water. Front Microbiol 2021; 12:617349. [PMID: 33912141 PMCID: PMC8072356 DOI: 10.3389/fmicb.2021.617349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacterial isolates are emerging within the last years. To understand this emergence, a thorough genome-based analysis of ESBL isolates from different sources (One Health approach) is needed. Among these, analysis of surface water is underrepresented. Therefore, we performed a genome-based analysis of ESBL-producing Escherichia coli isolates from surface water samples. Water samples were collected from eleven different surface water sites (lakes, river). ESBL-producing E. coli were recovered from these samples using filters and chromogenic media. Whole-genome sequencing of ESBL-producing E. coli was performed followed by determination of the multilocus sequence type (ST), ESBL-type, and virulence genes. Phylogenetic analysis was done using single nucleotide analysis. From all water samples taken, nineteen ESBL-producing E. coli were recovered. All of them harbored an ESBL gene. Nine different multilocus STs were determined, among which ST-949 was the ST detected most frequently. Phylogenetic analysis of ST-949 isolates revealed that all those isolates were closely related. In addition, they harbored an identical chromosomal insertion of bla CTX-M-15 , indicating a clonal relationship among these isolates. Genetic comparison with isolates from all over the world revealed that these isolates were closely related to human clinical isolates derived from New Zealand and Sweden. An ESBL-producing E. coli ST-949 clone was detected in German surface waters. Its close relationship to human clinical isolates suggests its ability to colonize or even infect humans. Our findings reveal that water sources indeed may play a hitherto underreported role in spread of ESBL-producing isolates.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Anja Zur Nieden
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Harpel
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Eugen Domann
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
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25
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Yasugi M, Hatoya S, Motooka D, Matsumoto Y, Shimamura S, Tani H, Furuya M, Mie K, Miyake M, Nakamura S, Shimada T. Whole-genome analyses of extended-spectrum or AmpC β-lactamase-producing Escherichia coli isolates from companion dogs in Japan. PLoS One 2021; 16:e0246482. [PMID: 33544781 PMCID: PMC7864471 DOI: 10.1371/journal.pone.0246482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 11/21/2022] Open
Abstract
The emergence and global spread of extended-spectrum or AmpC β-lactamase (ESBL/AmpC)-producing Enterobacteriaceae in companion animals have led to the hypothesis that companion animals might be reservoirs for cross-species transmission because of their close contact with humans. However, current knowledge in this field is limited; therefore, the role of companion animals in cross-species transmission remains to be elucidated. Herein, we studied ESBL/AmpC-producing Enterobacteriaceae, Escherichia coli in particular, isolated from extraintestinal sites and feces of companion dogs. Whole-genome sequencing analysis revealed that (i) extraintestinal E. coli isolates were most closely related to those isolated from feces from the same dog, (ii) chromosomal sequences in the ST131/C1-M27 clade isolated from companion dogs were highly similar to those in the ST131/C1-M27 clade of human origin, (iii) certain plasmids, such as IncFII/pMLST F1:A2:B20/blaCTX-M-27, IncI1/pMLST16/blaCTX-M-15, or IncI1/blaCMY-2 from dog-derived E. coli isolates, shared high homology with those from several human-derived Enterobacteriaceae, (iv) chromosomal blaCTX-M-14 was identified in the ST38 isolate from a companion dog, and (v) eight out of 14 tested ESBL/AmpC-producing E. coli isolates (i.e., ST131, ST68, ST405, and ST998) belonged to the human extraintestinal pathogenic E. coli (ExPEC) group. All of the bla-coding plasmids that were sequenced genome-wide were capable of horizontal transfer. These results suggest that companion dogs can spread ESBL/AmpC-producing ExPEC via their feces. Furthermore, at least some ESBL/AmpC-producing ExPECs and bla-coding plasmids can be transmitted between humans and companion dogs. Thus, companion dogs can act as an important reservoir for ESBL/AmpC-producing E. coli in the community.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institiute, Osaka Prefecture University, Izumisano, Osaka, Japan
- * E-mail:
| | - Shingo Hatoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shunsuke Shimamura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Hiroyuki Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masaru Furuya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Keiichiro Mie
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masami Miyake
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Terumasa Shimada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institiute, Osaka Prefecture University, Izumisano, Osaka, Japan
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26
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Zhao QY, Li W, Cai RM, Lu YW, Zhang Y, Cai P, Webber MA, Jiang HX. Mobilization of Tn1721-like structure harboring bla CTX-M-27 between P1-like bacteriophage in Salmonella and plasmids in Escherichia coli in China. Vet Microbiol 2020; 253:108944. [PMID: 33370618 DOI: 10.1016/j.vetmic.2020.108944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/25/2020] [Indexed: 01/15/2023]
Abstract
The aim of this study was to explore the characteristics of blaCTX-M-27 carriage and mobilization in Salmonella and Escherichia coli isolates from food-producing animals in China. A total of 2280 E. coli and 229 Salmonella isolates collected from food animals from June 2003 to September 2014 were screened for the presence of blaCTX-M-27 gene. The blaCTX-M-27-positive isolates were typed and plasmid DNA sequenced to determine the genetic context of blaCTX-M-27 and plasmid types present. Bacterial fitness was evaluated by growth curve and plasmid stability in vitro. CTX-M-27-positive E. coli (18, 0.79 %) and Salmonella (34, 14.85 %) were detected. PFGE profiles of CTX-M-27-positive strains revealed a wide variety of genotypes and S. Indiana was the most prevalent serotype. Replicon typing, S1-PFGE and hybridization of CTX-M-27-carrying plasmids confirmed that blaCTX-M-27 gene was located on IncFII (12/18), IncN (4/18), and non-typeable (2/18) plasmids in E. coli and on P1-like bacteriophage (21/34), IncP (4/34), IncFIB (4/34), IncN (2/34), IncHI2 (2/34), and IncA/C (1/34) plasmids in Salmonella. Comparison and analysis of gene context of blaCTX-M-27 in P1-like bacteriophage and plasmids revealed they shared the same structure and contained an identical genetic context with the Tn1721-like structure ΔISEcp1B-blaCTX-M-27-IS903D-iroN-Δmap-Tn1721. In addition, plasmid stability tests indicated that the blaCTX-M-27 P1-like bacteriophage were more stable than plasmids in the absence of cefotaxime selective pressure. These results demonstrate that Tn1721-like transposons harboring CTX-M-27 could be mobilized between different plasmids in E. coli and P1-like bacteriophage disseminated among Salmonella.
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Affiliation(s)
- Qiu-Yun Zhao
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Wan Li
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Run-Mao Cai
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yue-Wei Lu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yan Zhang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Ping Cai
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance. Sci Rep 2020; 10:19880. [PMID: 33199763 PMCID: PMC7670430 DOI: 10.1038/s41598-020-76877-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
To tackle the problem of antimicrobial resistance (AMR) surveillance programmes are in place within Europe applying phenotypic methods, but there are plans for implementing whole genome sequencing (WGS). We tested the benefits of WGS using Escherichia coli collected from pig surveillance performed between 2013 to 2017. WGS was performed on 498 E. coli producing ESBL and AmpC enzymes, recovered from pig caeca on MacConkey + cefotaxime (McC + CTX) agar, as recommended by the European Commission, or ESBL agar, used additionally by United Kingdom. Our results indicated WGS was extremely useful for monitoring trends for specific ESBL genes, as well as a plethora of AMR genotypes, helping to establish their prevalence and co-linkage to certain plasmids. Recovery of isolates with multi-drug resistance (MDR) genotypes was lower from McC + CTX than ESBL agar. The most widespread ESBL genes belonged to the blaCTX-M family. blaCTX-M-1 dominated all years, and was common in two highly stable IncI1 MDR plasmids harbouring (blaCTX-M-1,sul2, tetA) or (blaCTX-M-1, aadA5, sul2, dfrA17), in isolates which were phylogenetically dissimilar, suggesting plasmid transmission. Therefore, WGS provided a wealth of data on prevalence of AMR genotypes and plasmid persistence absent from phenotypic data and, also, demonstrated the importance of culture media for detecting ESBL E. coli.
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Ayeni FA, Falgenhauer J, Schmiedel J, Schwengers O, Chakraborty T, Falgenhauer L. Detection of blaCTX-M-27-encoding Escherichia coli ST206 in Nigerian poultry stocks. J Antimicrob Chemother 2020; 75:3070-3072. [PMID: 32688376 DOI: 10.1093/jac/dkaa293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Funmilola A Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Oliver Schwengers
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany.,Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
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29
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Melo LC, Haenni M, Saras E, Duprilot M, Nicolas-Chanoine MH, Madec JY. Emergence of the C1-M27 cluster in ST131 Escherichia coli from companion animals in France. J Antimicrob Chemother 2020; 74:3111-3113. [PMID: 31299071 DOI: 10.1093/jac/dkz304] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Luana C Melo
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES laboratoire de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES laboratoire de Lyon, Lyon, France
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES laboratoire de Lyon, Lyon, France
| | - Marion Duprilot
- INSERM and Université Paris Diderot, IAME, UMR, Paris, France.,Hôpital Beaujon, APHP, Clichy, France
| | | | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES laboratoire de Lyon, Lyon, France
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30
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Characterization of bla CTX-M-27/F1:A2:B20 Plasmids Harbored by Escherichia coli Sequence Type 131 Sublineage C1/ H30R Isolates Spreading among Elderly Japanese in Nonacute-Care Settings. Antimicrob Agents Chemother 2020; 64:AAC.00202-20. [PMID: 32152084 DOI: 10.1128/aac.00202-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/03/2020] [Indexed: 01/02/2023] Open
Abstract
We characterized 29 bla CTX-M-27-harboring plasmids of Escherichia coli sequence type 131 (ST131) sublineage C1/H30R isolates from healthy individuals and long-term-care facility (LTCF) residents. Most (27/29) plasmids were of the FIA, FIB, and FII multireplicon type with the same plasmid multilocus sequence typing (pMLST). Several plasmids (7/23) from LTCF residents harbored only bla CTX-M-27 as the resistance gene; however, their fundamental structures were very similar to those of previously isolated bla CTX-M-27/F1:A2:B20 plasmids, suggesting their prevalence as a newly arising public health concern.
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31
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Comparison of Commensal and Clinical Isolates for Diversity of Plasmids in Escherichia coli and Klebsiella pneumoniae. Antimicrob Agents Chemother 2020; 64:AAC.02064-19. [PMID: 32122890 DOI: 10.1128/aac.02064-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/24/2020] [Indexed: 01/23/2023] Open
Abstract
In this study, the plasmid content of clinical and commensal strains was analyzed and compared. The replicon profile was similar in both populations, except for L, M, A/C, and N (detected only in clinical strains) and HI1 (only in commensal strains). Although I1 and F were the most frequent replicons, only IncI1, sequence type 12 (ST12) was associated with bla CMY-2 in both populations. In contrast, the widespread resistant IncF plasmids were not linked to a single epidemic plasmid.
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32
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Peirano G, Pitout JDD. Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae: Update on Molecular Epidemiology and Treatment Options. Drugs 2020; 79:1529-1541. [PMID: 31407238 DOI: 10.1007/s40265-019-01180-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are a major global public health concern. Presently, Escherichia coli with CTX-Ms are the most common species associated with global ESBLs; CTX-M-15 is the most frequent CTX-M worldwide and is followed by CTX-M-14, which is often found in South-East Asia. Recent surveillance studies showed that CTX-M-27 is emerging in certain parts of the world especially in Japan and Europe. The population structure of ESBL-producing E. coli is dominated globally by an high-risk clone named ST131. Escherichia coli ST131 belongs to three clades (A, B, and C) and three different subclades (C1, C1-M27, and C2). Clade C1-M27 is associated with blaCTX-M-27, and C2 with blaCTX-M-15. Recent whole genome sequencing studies have shown that clade C has evolved from clade B in a stepwise fashion, resulting in one of the most influential global antimicrobial resistance clones that has emerged during the 2000's. Other important E. coli clones that have been detected among ESBL producers include ST405, ST38, ST648, ST410, and ST1193. The INCREMENT project has shown that ertapenem is as effective as other carbapenems for treating serious infections due to ESBL-producing Enterobacteriaceae. The results of the MERINO open-label randomized controlled study has provided clear evidence that piperacillin-tazobactam should be avoided for targeted therapy of blood-stream infections due to ESBL-producing E. coli and K. pneumoniae, regardless of the patient population, source of infection, bacterial species, and susceptibility result of piperacillin-tazobactam. Research is still warranted to define the optimal therapy of less severe infections due to ESBL-producing Enterobactericeae.
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Affiliation(s)
- Gisele Peirano
- Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.,Departments of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Johann D D Pitout
- Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada. .,Departments of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada. .,Microbiology, Immunology and Infectious Diseases, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada. .,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
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33
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Pepin-Puget L, El Garch F, Bertrand X, Valot B, Hocquet D. Genome analysis of enterobacteriaceae with non-wild type susceptibility to third-generation cephalosporins recovered from diseased dogs and cats in Europe. Vet Microbiol 2020; 242:108601. [PMID: 32122604 DOI: 10.1016/j.vetmic.2020.108601] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Extended-spectrum-β-lactamases (ESBL) and plasmid-mediated cephalosporinases (pAmpC)-producing Enterobacteriaceae isolates are now reported worldwide in humans, animals, and in the environment. We identified the determinants of resistance to β-lactams and associated resistance genes as well as phylogenetic diversity of 53 ESBL- or pAmpC-producing Enterobacteriaceae isolated from dogs and cats in Europe. MATERIALS/METHODS Of a collection of 842 Enterobacteriaceae isolates that were recovered in 2013 and 2014 from 842 diseased and untreated dogs and cats, for 242 ampicillin or amoxicillin resistant isolates (MIC ≥ 16 mg/L), cefotaxime (CTX) and ceftazidime (CAZ) MICs were determined. Isolates with CTX and/or CAZ MIC ≥ 1 mg/L (n = 63) were selected, and their genomes were fully sequenced using Illumina Technology. Genomic data were explored to identify the resistance determinants, the plasmid incompatibility groups, and the sequence types (STs). Plasmid location of blaESBL and blaAmpC was evaluated for all isolates based on the co-localization of resistance and plasmid incompatibility group genes on the same contig. Phylogenetic trees were constructed using core-genome MLST. RESULTS Of the 63 sequenced isolates, 53 isolates harbored a blaESBL or blaAmpC gene. Ten CTX and/or CAZ non-wild type isolates had neither blaESBL nor blaAmpC. Among the 63 isolates, 44 (69.8 %) were Escherichia coli, 11 (17.5 %) were Klebsiella pneumoniae, and 8 (12.7 %) were Proteus mirabilis. Fifty-one (80.9 %) isolates originated from dogs and 12 (19.1 %) from cats. Isolates were sampled from urinary tract (n = 36), skin and soft tissue (n = 22) and respiratory tract infections (n = 5). Thirty-two isolates (32/53, 60.4 %) carried blaESBL genes, including blaCTX-M-15 (n = 12), blaCTX-M-14 (n = 6), blaCTX-M-1 (n = 5), blaCTX-M-2 (n = 3), blaCTX-M-27 (n = 3), blaSHV-28 (n = 4), blaSHV-12 (n = 2), and blaVEB-6 (n = 1). Four isolates of K. pneumoniae had both blaCTX-M-15 and blaSHV-28. Twenty-one isolates (21/53, 39.6 %) carried genes encoding pAmpC, including blaCMY-2 (n = 19) and blaDHA-1 (n = 2). Thirteen E. coli isolates harbored both blaESBL or blaAmpC genes and plasmids of incompatibility groups IncIB (9/13), IncI1 (8/13), and IncFII (6/13). In addition to the reduced susceptibility to CTX and/or CAZ, reduced susceptibility or evidence of acquired resistance to at least one other relevant class of antibiotics was observed for all 63 isolates. E. COLI: isolates clustered in 23 STs, including B2 virulent clones from humans such as ST131 (n = 5), K. pneumoniae isolates mostly clustered in 3 STs: ST11 (n = 4), ST307 (n = 3), and ST16 (n = 2). Phylogenetic analysis identified the spread of E. coli ST131 blaCTX-M-27, and of K. pneumoniae ST307 harboring blaCTX-M-15 and blaSHV-28 or ST11 blaCTX-M-15. CONCLUSIONS We report here a 6.3 % prevalence of ESBL/pAmpC producing Enterobacteriaceae in diseased dogs and cats. This EU survey confirms that dogs and cats can be infected with epidemic multidrug resistant clones that may also spread in humans.
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Affiliation(s)
| | - Farid El Garch
- Vétoquinol SA, Scientific division, Lure, France; ComPath Study Group, Bruxelles, Belgium
| | - Xavier Bertrand
- Hygiène Hospitalière, CHU Besançon, France; Université de Bourgogne Franche-Comté, UMR CNRS Chrono-environnement, Besançon, France
| | - Benoit Valot
- Université de Bourgogne Franche-Comté, UMR CNRS Chrono-environnement, Besançon, France; Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Hygiène Hospitalière, CHU Besançon, France; Université de Bourgogne Franche-Comté, UMR CNRS Chrono-environnement, Besançon, France; Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France.
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34
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Broussier M, Gbaguidi-Haoré H, Rachidi-Berjamy F, Bertrand X, Slekovec C. Prevalence, genetic diversity of and factors associated with ESBL-producing Enterobacterales carriage in residents of French nursing homes. J Hosp Infect 2019; 104:469-475. [PMID: 31843559 DOI: 10.1016/j.jhin.2019.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
Abstract
OBJECTIVE To determine the prevalence and genotypic characteristics of extended-spectrum β-lactamase-producing Enterobacterales (ESBLE) and carbapenemase-producing Enterobacterales (CPE) in nursing homes (NHs) in a French region. Risk factors associated with their carriage were also investigated. METHODS A point-prevalence survey was proposed from November 2017 to June 2018 to NHs in the study region. Volunteer residents were screened for ESBLE and CPE carriage. Escherichia coli and Klebsiella pneumoniae isolates were genotyped using multi-locus sequence typing, pulsed-field gel electrophoresis (PFGE) and phylogrouping (for E. coli alone). Collective and individual data were analysed by random-effects logistic regression. RESULTS The study was conducted in 18 NHs and included 262 patients. Fifty-two patients (19.8%) carried at least one ESBLE, corresponding to 56 isolates (42 E. coli, 11 K. pneumoniae and three others), while no CPE was detected. The majority (27/42) of ESBL E. coli belonged to phylogroup B2, and ST131 was over-represented in this subset (21/27). PFGE analysis revealed ST131 cross-transmission within NHs. Regarding ESBL K. pneumoniae, nine of 11 isolates belonged to ST663, and PFGE suggested diffusion of the clone in six NHs. Significant individual risk factors for colonization by ESBLE were: use of a shared bathroom, previous antibiotic use and recent history of hospitalization. Significant collective protective factors were proper compliance with glove use and support of the NH by a healthcare facility. CONCLUSION This study shows that NHs in the study region are an important reservoir of ESBLE, whereas no residents were CPE carriers. The control of ESBLE in NHs should focus on antibiotic stewardship and excreta management policies.
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Affiliation(s)
- M Broussier
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - H Gbaguidi-Haoré
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | - F Rachidi-Berjamy
- CPias Bourgogne-Franche-Comté, Centre Hospitalier Régional Universitaire, Besançon, France
| | - X Bertrand
- Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | - C Slekovec
- UMR 6249 Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France; CPias Bourgogne-Franche-Comté, Centre Hospitalier Régional Universitaire, Besançon, France.
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35
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Zendri F, Maciuca IE, Moon S, Jones PH, Wattret A, Jenkins R, Baxter A, Timofte D. Occurrence of ESBL-Producing Escherichia coli ST131, Including the H30-Rx and C1-M27 Subclones, Among Urban Seagulls from the United Kingdom. Microb Drug Resist 2019; 26:697-708. [PMID: 32519936 DOI: 10.1089/mdr.2019.0351] [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] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial resistance is a public health concern. Understanding any role that urban seagulls may have as a reservoir of resistant bacteria could be important for reducing transmission. This study investigated fecal Escherichia coli isolates from seagulls (herring gulls and lesser black-backed gulls) to determine the prevalence of extended-spectrum cephalosporin-resistant (ESC-R) and fluoroquinolone-resistant E. coli among gull species from two cities (Taunton and Birmingham) in the United Kingdom (UK). We characterized the genetic background and carriage of plasmid-mediated resistance genes in extended-spectrum β-lactamase (ESBL)-producing E. coli obtained from these birds. Sixty ESC-R E. coli isolates were obtained from 39 seagulls (39/78, 50%), of which 28 (28/60, 46.7%) were positive for plasmid-mediated CTX-M and/or AmpC β-lactamase resistance genes. Among these, blaCTX-M-15, blaCTX-M-14, and blaCMY-2 predominated. Three isolates belonging to the B2-ST131 clone were detected, of which two harbored blaCTX-M-15 (typed to C2/H30Rx) and one harbored blaCTX-M-27 and was typed to C1/H30-R (recently described as the C1-M27 sublineage). The plasmid-mediated quinolone resistance (PMQR) gene carriage prevalence (11.7%) consisted of aac(6')-Ib-cr and qnrB genes. No carbapenem or colistin resistance genes were detected. Urban seagulls in the UK are colonized and can spread major antimicrobial-resistant E. coli isolates harboring ESBL and PMQR determinants, including clinically important strains such as the pandemic clone B2-ST131 and the C1-M27 subclade. This is the first report of ST131-C1-M27 subclade in wildlife in the UK and in seagulls worldwide.
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Affiliation(s)
- Flavia Zendri
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Iuliana E Maciuca
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Simon Moon
- Somerset West and Taunton Council, Environmental Health, Taunton, United Kingdom
| | - Philip H Jones
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Andy Wattret
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Richard Jenkins
- School of Allied Health Sciences, De Montfort University, Leicester, United Kingdom
| | - Andy Baxter
- Birdstrike Management Ltd., York, United Kingdom
| | - Dorina Timofte
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
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Chen Y, Liu Z, Zhang Y, Zhang Z, Lei L, Xia Z. Increasing Prevalence of ESBL-Producing Multidrug Resistance Escherichia coli From Diseased Pets in Beijing, China From 2012 to 2017. Front Microbiol 2019; 10:2852. [PMID: 31921034 PMCID: PMC6915038 DOI: 10.3389/fmicb.2019.02852] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022] Open
Abstract
We investigated antimicrobial resistance trends and characteristics of ESBL-producing Escherichia coli isolates from pets and whether this correlates with antibiotic usage in the clinic. Clinical samples containing E. coli from diseased cats and dogs were screened for antibiotic sensitivity and associated genotypic features. We identified 127 E. coli isolates from 1886 samples from dogs (n = 1565) and cats (n = 321) with the majority from urinary tract infections (n = 108, 85%). High rates of resistance were observed for β-lactams and fluoroquinolones and resistance to > 3 antibiotic classes (MDR) increased from 67% in 2012 to 75% in 2017 (P < 0.0001). This was especially true for strains resistant to 6-9 antibiotics that increased from 26.67 to 60.71%. Increased rates in β-lactam use for clinical treatment accompanied these increasing resistance rates. Accordingly, the most frequently encountered subtypes were bla CTX-M (n = 44, 34.65%), bla CTX-M-65 (n = 19) and bla CTX-M-15 (n = 18) and qnrB (n = 119, 93.70%). The bla CTX-M-isolates possessed 36 unique pulsed field electrophoretic types (PFGEs) and 28 different sequence types (STs) in ST405 (7, 15.9%), ST131 (3, 6.8%), ST73, ST101, ST372, and ST827 (2, 4.5% each) were the most prevalent. This data demonstrated a high level of diversity for the bla CTX-M-positive E. coli isolates. Additionally, bla NDM-5 was detected in three isolates (n = 3, 2.36%), comprised of two ST101 and one ST405 isolates, and mcr-1 was also observed in three colistin-resistant E. coli with three different STs (ST6316, ST405, and ST46). Our study demonstrates an increasing trend in MDR and ESBL-producing E. coli and this correlated with β-lactam antibiotic usage for treatment of these animals. This data indicates that there is significant risk for the spread of resistant bacteria from pets to humans and antibiotic use for pets should be more strictly regulated.
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Affiliation(s)
- Yanyun Chen
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhihai Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yaru Zhang
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China.,The New Hope Liuhe Co., Ltd., Qingdao, China
| | - Zhenbiao Zhang
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lei Lei
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
| | - Zhaofei Xia
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
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37
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Independent Host Factors and Bacterial Genetic Determinants of the Emergence and Dominance of Escherichia coli Sequence Type 131 CTX-M-27 in a Community Pediatric Cohort Study. Antimicrob Agents Chemother 2019; 63:AAC.00382-19. [PMID: 31085515 DOI: 10.1128/aac.00382-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/07/2019] [Indexed: 11/20/2022] Open
Abstract
The recent emergence and diffusion in the community of Escherichia coli isolates belonging to the multidrug-resistant and CTX-M-27-producing sequence type 131 (ST131) C1-M27 cluster makes this cluster potentially as epidemic as the worldwide E. coli ST131 subclade C2 composed of multidrug-resistant isolates producing CTX-M-15. Thirty-five extended-spectrum beta-lactamase (ESBL)-producing ST131 isolates were identified in a cohort of 1,885 French children over a 5-year period. They were sequenced to characterize the ST131 E. coli isolates producing CTX-M-27 recently emerging in France. ST131 isolates producing CTX-M-27 (n = 17), and particularly those belonging to the C1-M27 cluster (n = 14), carried many resistance-encoding genes and predominantly an F1:A2:B20 plasmid type. In multivariate analysis, having been hospitalized since birth (odds ratio [OR], 10.9; 95% confidence interval [CI], 2.4 to 48.8; P = 0.002) and being cared for in a day care center (OR, 9.4; 95% CI, 1.5 to 59.0; P = 0.017) were independent risk factors for ST131 CTX-M-27 fecal carriage compared with ESBL-producing non-ST131 isolates. No independent risk factor was found when comparing CTX-M-15 (n = 11)- and CTX-M-1/14 (n = 7)-producing ST131 isolates with ESBL-producing non-ST131 isolates or with non-ESBL-producing isolates. Several factors may contribute to the increase in fecal carriage of CTX-M-27-producing E. coli isolates, namely, resistance to multiple antibiotics, capacity of the CTX-M-27 enzyme to hydrolyze both cefotaxime and ceftazidime, carriage of a peculiar F-type plasmid, and/or capacity to colonize children who have been hospitalized since birth or who attend day care centers.
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38
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Bortolami A, Zendri F, Maciuca EI, Wattret A, Ellis C, Schmidt V, Pinchbeck G, Timofte D. Diversity, Virulence, and Clinical Significance of Extended-Spectrum β-Lactamase- and pAmpC-Producing Escherichia coli From Companion Animals. Front Microbiol 2019; 10:1260. [PMID: 31231344 PMCID: PMC6560200 DOI: 10.3389/fmicb.2019.01260] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/21/2019] [Indexed: 11/26/2022] Open
Abstract
Escherichia coli are opportunistic pathogens with the potential to cause a variety of infections in both humans and animals and in many cases have developed antimicrobial resistance. In this study, we characterized extended-spectrum cephalosporin resistant (ESCR) E. coli isolates from diseased companion animals (dogs, cats, and horses) and related the results to clinical findings. ESCR E. coli clinical isolates obtained over a 6-year period were screened for extended-spectrum β-lactamase (ESBL) and/or plasmid mediated AmpC (pAmpC) and virulence markers likely to be associated with extraintestinal pathogenic E. coli (ExPEC). ESBL and/or pAmpC genetic determinants were identified in 79.9% of the ESCR E. coli isolates with blaCTX-M genes being the most common ESBL genotype of which blaCTX-M-15, blaCTX-M-14, and blaCTX-M-55 were the most prevalent. In addition, blaCMY -2 was the most common genotype identified amongst pAmpC producing isolates. Phylogenetic group typing showed that B2 was the most prevalent phylogroup among the ESCR E. coli isolates, followed by the closely related phylogroups D and F which are also associated with extra-intestinal infections. ESCR was also identified in phylogroups commonly regarded as commensals (B1, A, and C). Virulence factor (VF) scores >2 were mostly present amongst isolates in phylogroup B2. Higher virulence scores were found in isolates lacking ESBL/pAmpC resistance genes compared with those carrying both genes (p < 0.05). Five of phylogroup B2 isolates, were typed to the pandemic virulent O25b-ST131 clone and three ST131 isolates carrying blaCTX-M-15 belonged to the subclade C2/H30Rx whilst one isolate carrying blaCTX-M-27 typed to the recently described sub-clade C1-M27. MLST typing also identified other sequence types commonly associated with infections in humans (ST410, ST10, and ST648). Most ESCR E. coli isolates obtained in pure growth were cultured from normally sterile body sites (mostly from urinary tract infections, UTIs) whilst only a small proportion were obtained from body sites populated with commensal flora (p < 0.0001). Our study has shown that ExPEC ESBL/pAmpC producing E. coli isolates are common amongst companion animal isolates and are associated with colonization and infection. In addition, their isolation from a normally sterile site is likely to be clinically significant and warrants antimicrobial treatment.
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Affiliation(s)
- Alessio Bortolami
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Flavia Zendri
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Elena Iuliana Maciuca
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Andy Wattret
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Christine Ellis
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Vanessa Schmidt
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom.,Department of Small Animal Clinical Science, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Gina Pinchbeck
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Dorina Timofte
- Department of Veterinary Pathology and Public Health, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom.,Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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Khan ER, Aung MS, Paul SK, Ahmed S, Haque N, Ahamed F, Sarkar SR, Roy S, Rahman MM, Mahmud MC, Hossain MA, Urushibara N, Kawaguchiya M, Sumi A, Kobayashi N. Prevalence and Molecular Epidemiology of Clinical Isolates of Escherichia coli and Klebsiella pneumoniae Harboring Extended-Spectrum Beta-Lactamase and Carbapenemase Genes in Bangladesh. Microb Drug Resist 2018; 24:1568-1579. [DOI: 10.1089/mdr.2018.0063] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Emily Rahman Khan
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shyamal Kumar Paul
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Salma Ahmed
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Nazia Haque
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Farid Ahamed
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Santana Rani Sarkar
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Sangjukta Roy
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | | | - Muhammad Chand Mahmud
- Department of Microbiology, President Abdul Hamid Medical College, Kishoreganj, Bangladesh
| | - Muhammad Akram Hossain
- Department of Microbiology and Mycology, National Institute of Preventive and Social Medicine, Dhaka, Bangladesh
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Ayako Sumi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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40
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Interspecies plasmid transfer appears rare in sequential infections with extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. Diagn Microbiol Infect Dis 2018; 93:380-385. [PMID: 30527621 DOI: 10.1016/j.diagmicrobio.2018.10.014] [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] [Received: 07/02/2018] [Revised: 09/29/2018] [Accepted: 10/24/2018] [Indexed: 02/08/2023]
Abstract
From a cohort of 1836 Swedish patients infected with ESBL-producing Enterobacteriaceae (EPE) during 2004-2014, 513 patients with recurrent EPE infection were identified. Only in 14 of the 513 patients was a change of species (ESBL-E. coli to ESBL-K. pneumoniae or vice versa) found between the index and subsequent infection. Eleven sequential urine isolates from 5 of the 14 patients were available for further analysis of possible transfer of ESBL-carrying plasmids. The plasmid content was studied using optical DNA mapping (ODM), PCR-based replicon typing, and ESBL gene sequencing. ODM allowed us to directly compare whole plasmids between isolates and found similar ESBL-carrying plasmids in 3 out of the 5 patients. The ODM results and the rarity in shift of species between ESBL-E. coli and ESBL-K. pneumoniae imply that in recurrent EPE infections interspecies plasmid transfer is uncommon.
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41
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Merino I, Hernández-García M, Turrientes MC, Pérez-Viso B, López-Fresneña N, Diaz-Agero C, Maechler F, Fankhauser-Rodriguez C, Kola A, Schrenzel J, Harbarth S, Bonten M, Gastmeier P, Canton R, Ruiz-Garbajosa P, Desilets M, Dul S, Scherrer-Muller F, Huttner B, Uçkay I, Prendki V, Renzi G. Emergence of ESBL-producing Escherichia coli ST131-C1-M27 clade colonizing patients in Europe. J Antimicrob Chemother 2018; 73:2973-2980. [DOI: 10.1093/jac/dky296] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/26/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Irene Merino
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - María-Carmen Turrientes
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Nieves López-Fresneña
- Servicio de Medicina Preventiva, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cristina Diaz-Agero
- Servicio de Medicina Preventiva, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Friederike Maechler
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | | | - Axel Kola
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | - Jacques Schrenzel
- Infection Control Program and Genomic Research Laboratory, University of Geneva Hospitals, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program and Genomic Research Laboratory, University of Geneva Hospitals, Geneva, Switzerland
| | - Marc Bonten
- Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Petra Gastmeier
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | - R Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - P Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
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Zogg AL, Simmen S, Zurfluh K, Stephan R, Schmitt SN, Nüesch-Inderbinen M. High Prevalence of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Among Clinical Isolates From Cats and Dogs Admitted to a Veterinary Hospital in Switzerland. Front Vet Sci 2018; 5:62. [PMID: 29662886 PMCID: PMC5890143 DOI: 10.3389/fvets.2018.00062] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/12/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives This study aimed to identify and characterize extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae among clinical samples of companion animals. Methods A total of 346 non-duplicate Enterobacteriaceae isolates were collected between 2012 and 2016 from diseased cats (n = 115) and dogs (n = 231). The presence of blaESBL, PMQR genes, and the azithromycin resistance gene mph(A) was confirmed by PCR and sequencing of bla genes. Isolates were further characterized by antimicrobial resistance profiling, multilocus sequence typing, phylogenetic grouping, identification of mutations in the QRDR of gyrA and parC, and screening for virulence-associated genes. Results Among the 346 isolates, 72 (20.8%) were confirmed ESBL producers [58 Escherichia coli (E. coli), 11 Klebsiella pneumoniae (K. pneumoniae), and 3 Enterobacter cloacae]. The strains were cultured from urine (n = 45), skin and skin wounds (n = 8), abscesses (n = 6), surgical sites (n = 6), bile (n = 4), and other sites (n = 3). ESBL genes included blaCTX-M-1, 14, 15, 27, 55, and blaSHV-12, predominantly blaCTX-M-15 (54.8%, 40/73), and blaCTX-M-1 (24.7%, 18/73). Further genes included qnrB (4.2%, 3/72), qnrS (9.7%, 7/72), aac(6')-Ib-cr (47.2%, 34/72), and mph(A) (38.9%, 28/72). Seventeen (23.6%) isolates belonged to the major lineages of human pathogenic K. pneumoniae ST11, ST15, and ST147 and E. coli ST131. The most prevalent ST was E. coli ST410 belonging to phylogenetic group C. Conclusion The high prevalence of ESBL producing clinical Enterobacteriaceae from cats and dogs in Switzerland and the presence of highly virulent human-related K. pneumoniae and E. coli clones raises concern about transmission prevention as well as infection management and prevention in veterinary medicine.
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Affiliation(s)
- Anna Lena Zogg
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Sabrina Simmen
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Katrin Zurfluh
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Roger Stephan
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Sarah N Schmitt
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zürich, Zürich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
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43
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Aung MS, San N, Maw WW, San T, Urushibara N, Kawaguchiya M, Sumi A, Kobayashi N. Prevalence of Extended-Spectrum Beta-Lactamase and Carbapenemase Genes in Clinical Isolates of Escherichia coli in Myanmar: Dominance of bla NDM-5 and Emergence of bla OXA-181. Microb Drug Resist 2018; 24:1333-1344. [PMID: 29565227 DOI: 10.1089/mdr.2017.0387] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The increasing trend of Escherichia coli producing extended-spectrum beta-lactamases (ESBLs) and carbapenemases is a global public health concern. In this study, prevalence and molecular characteristics of E. coli harboring ESBL and carbapenemase genes were investigated for 426 isolates derived from various clinical specimens in a teaching hospital in Yangon, Myanmar, for the 1-year period beginning January 2016. A total of 157 isolates (36.9%) were ESBL producers and harbored CTX-M-1 group genes (146 isolates; blaCTX-M-15, blaCTX-M55) or CTX-M-9 group genes (11 isolates; blaCTX-M-14, blaCTX-M-27). Carbapenem resistance was detected in 35 isolates (8.2%), among which 26 isolates had carbapenemase genes encoding NDM-1 (2 isolates), NDM-4 (6 isolates), NDM-5 (14 isolates), NDM-7 (3 isolates), and OXA-181 (2 isolates). blaNDM-5 was identified in phylogenetic groups A, B1, and D isolates belonging to various genotypes (ST101, ST354, ST405, ST410, ST1196) associated with blaTEM-1, blaCTX-M-15, blaOXA-181, blaCMY-2, blaCMY-6, blaCMY-42, qnrB, qnrS, or aac6'-Ib-cr. While two isolates with blaOXA-181 belonged to phylogenetic group A-ST410, one isolate had also blaNDM-5, as well as blaCTX-M-15 and blaCMY-2, and the other harbored blaCMY-42 and aac6'-Ib-cr, showing different resistance patterns. Phylogenetic group B2 isolates examined were classified into mostly ST131 and had solely blaCTX-M-15 or blaCTX-M-27, harboring more virulence factors than other phylogenetic groups. The present study revealed high prevalence of ESBL genes represented by blaCTX-M-15 and dominance of blaNDM-5 among NDM genes, disseminating to various E. coli clones. Notably, carbapenemase gene encoding OXA-181 was first identified in Myanmar, suggesting its spread together with NDM genes.
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Affiliation(s)
- Meiji Soe Aung
- 1 Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| | - Nilar San
- 2 Department of Microbiology, University of Medicine 2 , Yangon, Yangon, Myanmar
| | - Win Win Maw
- 2 Department of Microbiology, University of Medicine 2 , Yangon, Yangon, Myanmar
| | - Thida San
- 3 Yangon Children's Hospital , Department of Medical Services, Ministry of Health and Sports, Yangon, Myanmar
| | - Noriko Urushibara
- 1 Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| | - Mitsuyo Kawaguchiya
- 1 Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| | - Ayako Sumi
- 1 Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| | - Nobumichi Kobayashi
- 1 Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
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