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Pitart C, Piquet M, Burgwinkel T, Arazo Del Pino R, Rubio M, Aguilar M, De Gea S, Pulgarín A, Campo I, Torralbo B, Parejo R, Valls S, Fortes I, Santana G, Rubio E, Vilella A, Del Río A, Martínez JA, Miró E, Navarro F, Espasa M, Casals-Pascual C, Vila J, Higgins PG, Roca I. Early identification of the nosocomial spread of vancomycin-resistant Enterococcus faecium by Fourier-transform infrared spectroscopy and performance comparison with PFGE and WGS. Emerg Microbes Infect 2024; 13:2392659. [PMID: 39137261 PMCID: PMC11346335 DOI: 10.1080/22221751.2024.2392659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/10/2024] [Accepted: 08/11/2024] [Indexed: 08/15/2024]
Abstract
Early detection of disseminating vancomycin-resistant Enterococcus faecium (VREfm) in ICU wards is crucial for outbreak identification and the implementation of prompt infection control measures. Genotypic methods like pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) are costly and time-consuming, hindering rapid response due to batch dependency. Fourier-transform infrared spectroscopy (FT-IR) offers the potential for real-time outbreak detection and reliable strain typing. We utilized FT-IR to identify clonal VREfm dissemination and compared its performance to PFGE and WGS. Between February through October 2023, an unusually high number of VREfm were recovered at a tertiary hospital in Barcelona. Isolates were examined for antimicrobial susceptibility, carriage of vanA/vanB genes and clonality was also studied using FT-IR, PFGE, and WGS. Routine FT-IR inspections revealed recurring VREfm clustering during the outbreak's initial weeks. In total, 104 isolates were recovered from 75 patients and from multiple wards. However, only one isolate was recovered from an environmental sample, suggesting the absence of environmental reservoirs. An ST80 vancomycin-resistant (vanA) E. faecium strain was the main strain responsible for the outbreak, although a few additional VREfm strains were also identified, all belonging to CC17. PFGE and cgMLST (WGS) yielded identical clustering results to FT-IR, and WGS confirmed vanA/vanB gene carriage in all VREfm isolates. Infection control measures led to a rapid decline in VREfm isolates, with no isolates detected in November. FT-IR spectroscopy offers rapid turnaround times, sensitivity, and reproducibility, comparable to standard typing methods. It proved as an effective tool for monitoring VREfm dissemination and early outbreak detection.
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Affiliation(s)
- Cristina Pitart
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Maria Piquet
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Tessa Burgwinkel
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner site Bonn–Cologne, Cologne, Germany
| | - Rocío Arazo Del Pino
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner site Bonn–Cologne, Cologne, Germany
| | - Marc Rubio
- Department of Microbiology, Institut d’Investigació Biomèdica Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Mireia Aguilar
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Sergi De Gea
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Andrea Pulgarín
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Irene Campo
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Blanca Torralbo
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Romina Parejo
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Silvia Valls
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Isabel Fortes
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Gemina Santana
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Elisa Rubio
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Molecular Core Facility, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Anna Vilella
- Department of Preventive Medicine and Epidemiology, Hospital Clínic–Universitat de Barcelona, Barcelona, Spain
| | - Ana Del Río
- Department of Infectious Diseases, Hospital Clínic–IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - José Antonio Martínez
- Department of Infectious Diseases, Hospital Clínic–IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Elisenda Miró
- Department of Microbiology, Institut d’Investigació Biomèdica Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ferran Navarro
- Department of Microbiology, Institut d’Investigació Biomèdica Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mateu Espasa
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Climent Casals-Pascual
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Vila
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner site Bonn–Cologne, Cologne, Germany
| | - Ignasi Roca
- Department of Microbiology, Biomedical Diagnostic Center (CDB) and ISGlobal, Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Kavanagh NL, Kinnevey PM, Egan SA, McManus BA, O'Connell B, Brennan GI, Coleman DC. Protracted transmission and persistence of ST80 vancomycin-resistant Enterococcus faecium clonal complex types CT2933, CT2932 and CT1916 in a large Irish hospital: a 39-month whole-genome sequencing study. J Hosp Infect 2024; 151:11-20. [PMID: 38944282 DOI: 10.1016/j.jhin.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/23/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Sequence type (ST) 80 vanA-encoding VREfm predominate in Irish hospitals, but their transmission is poorly understood. AIMS To investigate transmission and persistence of predominant complex type (CT) VREfm in two wards of an Irish hospital (H1) using whole-genome sequencing, and their intra- and inter-hospital dissemination. METHODS Rectal screening (N = 330, September 2019 to December 2022) and environmental (N = 48, November 2022 to December 2022) E. faecium were investigated. Isolate relatedness was assessed by core-genome multi-locus sequence typing (cgMLST) and core-genome single nucleotide polymorphism (cgSNP) analysis. Likely transmission chains were identified using SeqTrack (https://graphsnp.fordelab.com/graphsnp) using cgSNP data and recovery location. Well-characterized E. faecium (N = 908) from seven Irish hospitals including H1 (June 2017 to July 2022) were also investigated. FINDINGS Conventional MLST assigned isolates to nine STs (ST80, 82%). cgMLST identified three predominant ST80 CTs (CT2933, CT2932 and CT1916) (55% of isolates) of related isolates (≤20 allelic differences). cgSNP analysis differentiated these CTs into multiple distinct closely related genomic clusters (≤10 cgSNPs). Parisimonious network construction identified 55 likely inter- and intra-ward transmissions with epidemiological support between patients ≤30 days involving 73 isolates (≤10 cgSNPs) from seven genomic clusters. Numerous other likely transmissions over longer time periods without evident epidemiological links were identified, suggesting persistence and unidentified reservoirs contribute to dissemination. The three CTs predominated among E. faecium (N = 1286) in seven hospitals, highlighting inter-hospital spread without known epidemiological links. CONCLUSION This study revealed the long-term intra- and inter-hospital dominance of three major CT ST80 VREfm lineages, widespread transmission and persistence, implicating unidentified reservoirs.
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Affiliation(s)
- N L Kavanagh
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - P M Kinnevey
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - S A Egan
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - B A McManus
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - B O'Connell
- Department of Clinical Microbiology, St James's Hospital, Dublin, Ireland; National MRSA Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - G I Brennan
- Department of Clinical Microbiology, St James's Hospital, Dublin, Ireland; National MRSA Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - D C Coleman
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland.
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Segawa T, Masuda K, Hisatsune J, Ishida-Kuroki K, Sugawara Y, Kuwabara M, Nishikawa H, Hiratsuka T, Aota T, Tao Y, Iwahashi Y, Ueda K, Mae K, Masumoto K, Kitagawa H, Komatsuzawa H, Ohge H, Sugai M. Genomic analysis of inter-hospital transmission of vancomycin-resistant Enterococcus faecium sequence type 80 isolated during an outbreak in Hiroshima, Japan. Antimicrob Agents Chemother 2024; 68:e0171623. [PMID: 38506550 PMCID: PMC11064488 DOI: 10.1128/aac.01716-23] [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: 12/28/2023] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.
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Affiliation(s)
- Takaya Segawa
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Kanako Masuda
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Kasumi Ishida-Kuroki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Masao Kuwabara
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
| | - Hideki Nishikawa
- Hiroshima Prefectural Center for Disease Control and Prevention, Hiroshima, Japan
| | - Takahiro Hiratsuka
- Hiroshima Prefectural Technology Research Institute, Public Health and Environment Center, Hiroshima, Japan
| | - Tatsuaki Aota
- Hiroshima City Institute of Public Health, Hiroshima, Japan
| | - Yasuo Tao
- Hiroshima City Public Health Center, Hiroshima, Japan
| | | | - Kuniko Ueda
- Hiroshima City Public Health Center, Hiroshima, Japan
| | - Kaori Mae
- Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
| | - Ken Masumoto
- Hiroshima City Medical Association Clinical Laboratory, Hiroshima, Japan
| | - Hiroki Kitagawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Hitoshi Komatsuzawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
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Fukuda A, Nakajima C, Suzuki Y, Usui M. Transferable linezolid resistance genes (optrA and poxtA) in enterococci derived from livestock compost at Japanese farms. J Glob Antimicrob Resist 2024; 36:336-344. [PMID: 38336229 DOI: 10.1016/j.jgar.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
OBJECTIVES Linezolid is a last-resort antimicrobial in human clinical settings to treat multidrug-resistant Gram-positive bacterial infections. Mobile linezolid resistance genes (optrA, poxtA, and cfr) have been detected in various sources worldwide. However, the presence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in Japan remains uncertain. Therefore, we clarified the existence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in farm environments in Japan. METHODS Enterococci isolates from faeces compost collected from 10 pig and 11 cattle farms in Japan in 2021 were tested for antimicrobial susceptibility and possession of mobile linezolid resistance genes. Whole-genome sequencing of optrA and/or poxtA genes positive-enterococci was performed. RESULTS Of 103 enterococci isolates, 12 from pig farm compost were not-susceptible (2 resistant and 10 intermediate) to linezolid. These 12 isolates carried mobile linezolid resistance genes on plasmids or chromosomes (5 optrA-positive Enterococcus faecalis, 6 poxtA-positive E. hirae or E. thailandicus, and 1 optrA- and poxtA-positive E. faecium). The genetic structures of optrA- and poxA-carrying plasmids were almost identical to those reported in other countries. These plasmids were capable of transferring among E. faecium and E. faecalis strains. The optrA- and poxtA-positive E. faecium belonged to ST324 (clade A2), a high-risk multidrug-resistant clone. The E. faecalis carrying optrA gene on its chromosome was identified as ST593. CONCLUSIONS Although linezolid is not used in livestock, linezolid-not-susceptible enterococci could be indirectly selected by frequently used antimicrobials, such as phenicols. Moreover, various enterococci species derived from livestock compost may serve as reservoirs of linezolid resistance genes carried on globally disseminated plasmids and multidrug-resistant high-risk clones.
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Affiliation(s)
- Akira Fukuda
- Department of Health and Environmental Sciences, Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | - Masaru Usui
- Department of Health and Environmental Sciences, Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan.
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Kim E, Yang SM, Kwak HS, Moon BY, Lim SK, Kim HY. Genomic characteristics of cfr and fexA carrying Staphylococcus aureus isolated from pig carcasses in Korea. Vet Res 2024; 55:21. [PMID: 38365748 PMCID: PMC10874063 DOI: 10.1186/s13567-024-01278-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
The emergence of transferable linezolid resistance genes poses significant challenges to public health, as it does not only confer linezolid resistance but also reduces susceptibility to florfenicol, which is widely used in the veterinary field. This study evaluated the genetic characteristics of linezolid-resistant Staphylococcus aureus strains isolated from pig carcasses and further clarified potential resistance and virulence mechanisms in a newly identified sequence type. Of more than 2500 strains isolated in a prior study, 15 isolated from pig carcasses exhibited linezolid resistance (minimum inhibitory concentration ≥ 8 mg/L). The strains were characterized in detail by genomic analysis. Linezolid-resistant S. aureus strains exhibited a high degree of genetic lineage diversity, with one strain (LNZ_R_SAU_64) belonging to ST8004, which has not been reported previously. The 15 strains carried a total of 21 antibiotic resistance genes, and five carried mecA associated with methicillin resistance. All strains harbored cfr and fexA, which mediate resistance to linezolid, phenicol, and other antibiotics. Moreover, the strains carried enterotoxin gene clusters, including the hemolysin, leukotoxin, and protease genes, which are associated with humans or livestock. Some genes were predicted to be carried in plasmids or flanked by ISSau9 and the transposon Tn554, thus being transmittable between staphylococci. Strains carrying the plasmid replicon repUS5 displayed high sequence similarity (99%) to the previously reported strain pSA737 in human clinical samples in the United States. The results illustrate the need for continuous monitoring of the prevalence and transmission of linezolid-resistant S. aureus isolated from animals and their products.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hyo-Sun Kwak
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bo-Youn Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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Torabi M, Faghri J, Poursina F. Detection of Genes Related to Linezolid Resistance ( poxtA, cfr, and optrA) in Clinical Isolates of Enterococcus spp. from Humans: A First Report from Iran. Adv Biomed Res 2023; 12:205. [PMID: 37694234 PMCID: PMC10492618 DOI: 10.4103/abr.abr_74_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 09/12/2023] Open
Abstract
Background Enterococci may develop resistance to linezolid through chromosomal mutations that involve specific linezolid resistance genes, such as cfr, optrA, and poxtA. The objective of this study was to evaluate the antibiotic susceptibility of enterococcal isolates and identify cfr, optrA, and poxtA genes in MDR isolates. Materials and Methods Enterococcal isolates were collected from various clinical specimens at Al-Zahra, Amin, and Khorshid Hospitals in Isfahan. The Enterococcus isolates were identified as belonging to the E. faecalis and E. faecium species by using specific gene (D alanine D alanine ligase ddl) sets in PCR. To detect cfr, optrA, and poxtA genes among the species, a multiplex-PCR assay was performed. Results Out of 175 isolates, E. faecalis predominated 129/175 (73.7%). Furthermore, the prevalence of vancomycin-resistant Enterococci (VRE) and linezolid-resistant Enterococci (LRE) was 29.7% and 4%, respectively. The overall prevalence of MDR was 91.1%, 68.9%, and 66.6% of E. faecium, E. faecalis, and other Enterococcus spp., respectively. Interestingly, the frequency of optrA (71.4%) in E. faecium and poxtA and crf (42.8%) in E. faecalis were detected among LRE species. A statistically significant relationship (P < 0.05) was found between the presence of the three genes and the occurrence of LRE. Conclusion This is the first study to report the detection of linezolid resistance genes (cfr, optrA, and poxtA) in clinical Enterococcus spp. isolates from Iran, conducted at Isfahan University of Medical Sciences hospitals. The emergence of enterococcal strains that resist linezolid is concerning as it can lead to the spread of resistant strains among patients, resulting in treatment failure.
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Affiliation(s)
- Majid Torabi
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jamshid Faghri
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farkhondeh Poursina
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Nüesch-Inderbinen M, Biggel M, Haussmann A, Treier A, Heyvaert L, Cernela N, Stephan R. Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter. Front Microbiol 2023; 14:1150070. [PMID: 37389336 PMCID: PMC10301837 DOI: 10.3389/fmicb.2023.1150070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
Background Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes. Objective This study aimed to assess the occurrence of cfr, optrA, and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland. Methods A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA, and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS). Results Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr. Isolates included for AST and WGS analysis were Enterococcus (E.) faecalis (n = 14), E. faecium (n = 12), E. dispar (n = 1), E. durans (n = 2), E. gallinarum (n = 1), Vagococcus (V.) lutrae (n = 2), Aerococcus (A.) urinaeequi (n = 1), and Companilactobacillus (C.) farciminis (n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA-harboring plasmids, with rep9 (RepA_N) plasmids dominating in optrA-harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA-carrying E. faecium. Conclusion Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA. The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi, and the probiotic C. farciminis in food-producing animals is a public health concern.
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Affiliation(s)
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Adrian Haussmann
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Andrea Treier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Lore Heyvaert
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, University of Ghent, Ghent, Belgium
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Rodríguez-Lucas C, Ladero V. Enterococcal Phages: Food and Health Applications. Antibiotics (Basel) 2023; 12:antibiotics12050842. [PMID: 37237745 DOI: 10.3390/antibiotics12050842] [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: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Enterococcus is a diverse genus of Gram-positive bacteria belonging to the lactic acid bacteria (LAB) group. It is found in many environments, including the human gut and fermented foods. This microbial genus is at a crossroad between its beneficial effects and the concerns regarding its safety. It plays an important role in the production of fermented foods, and some strains have even been proposed as probiotics. However, they have been identified as responsible for the accumulation of toxic compounds-biogenic amines-in foods, and over the last 20 years, they have emerged as important hospital-acquired pathogens through the acquisition of antimicrobial resistance (AMR). In food, there is a need for targeted measures to prevent their growth without disturbing other LAB members that participate in the fermentation process. Furthermore, the increase in AMR has resulted in the need for the development of new therapeutic options to treat AMR enterococcal infections. Bacteriophages have re-emerged in recent years as a precision tool for the control of bacterial populations, including the treatment of AMR microorganism infections, being a promising weapon as new antimicrobials. In this review, we focus on the problems caused by Enterococcus faecium and Enterococcus faecalis in food and health and on the recent advances in the discovery and applications of enterococcus-infecting bacteriophages against these bacteria, with special attention paid to applications against AMR enterococci.
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Affiliation(s)
- Carlos Rodríguez-Lucas
- Microbiology Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Translational Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Victor Ladero
- Department of Technology and Biotechnology of Dairy Products, Dairy Research Institute, IPLA CSIC, 33300 Villaviciosa, Spain
- Molecular Microbiology Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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9
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Vancomycin-Resistant Enterococcus faecium and the emergence of new Sequence Types associated with Hospital Infection. Res Microbiol 2023; 174:104046. [PMID: 36858192 DOI: 10.1016/j.resmic.2023.104046] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023]
Abstract
Enterococcus faecium is a major cause of vancomycin-resistant enterococcal (VRE) infection. New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection of a vancomycin variable enterococcal (VVE) variant of ST1421 in Europe that exhibits a vancomycin-susceptible phenotype but which can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.
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10
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Vuichard-Gysin D, Sommerstein R, Kronenberg A, Buetti N, Eder M, Piezzi V, Gardiol C, Schlegel M, Harbarth S, Widmer A. High adherence to national IPC guidelines as key to sustainable VRE control in Swiss hospitals: a cross-sectional survey. Antimicrob Resist Infect Control 2022; 11:19. [PMID: 35090563 PMCID: PMC8795934 DOI: 10.1186/s13756-022-01051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background Vancomycin resistant enterococci (VRE) are on the rise in many European hospitals. In 2018, Switzerland experienced its largest nosocomial VRE outbreak. The national center for infection prevention (Swissnoso) elaborated recommendations for controlling this outbreak and published guidelines to prevent epidemic and endemic VRE spread. The primary goal of this study was to evaluate adherence to this new guideline and its potential impact on the VRE epidemiology in Swiss acute care hospitals. Methods In March 2020, Swissnoso distributed a survey among all Swiss acute care hospitals. The level of adherence as well as changes of infection prevention and control (IPC) strategies in the years 2018 and 2019 after publication of the national guidelines were asked along with an inventory on VRE surveillance and outbreaks. Results Data of 97/146 (66%) participants were available, representing 81.6% of all acute care beds operated in Switzerland in 2019. The vast majority—72/81 (88%) responding hospitals—have entirely or largely adopted our new national guideline. 38/51 (74.5%) hospitals which experienced VRE cases were significantly more likely to have changed their IPC strategies than those 19/38 (50%) hospitals without VRE cases p = 0.017). The new IPC guidelines included (1) introduction of targeted admission screening in 89.5%, (2) screening of close contacts of VRE cases in 56%, and (3) contact precaution for suspected VRE cases 58% of these hospitals. 52 (54%) hospitals reported 569 new VRE cases in 2018 including 14 bacteremia, and 472 new cases in 2019 with 10 bacteremia. The ten largest outbreaks encountered between 2018 and 2019 included 671 VRE cases, of which most (93.4%) consisted of colonization events, 29 (4.3%) infections and 15 (2.2%) bacteremia. Conclusion Wide adoption of this VRE control guideline seemed to have a positive effect on VRE containment in Swiss acute care hospitals over two years, even if its long-term impact on the VRE epidemiology remains to be evaluated. Broad dissemination and strict implementation of a uniform national guideline may therefore serve as model for other countries to fight VRE epidemics on a national level. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01051-9.
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11
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Investigation of a vanA linezolid- and vancomycin-resistant Enterococcus faecium outbreak in the Southwest Indian Ocean (Reunion Island). Int J Antimicrob Agents 2022; 60:106686. [PMID: 36503708 DOI: 10.1016/j.ijantimicag.2022.106686] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/09/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Dual resistance to linezolid and glycopeptides is a milestone reached by certain extensively drug-resistant (XDR) enterococci. This paper describes the molecular and epidemiological investigations of a linezolid-resistant and vancomycin-resistant Enterococcus faecium (E. faecium) (LVREf) outbreak in the French overseas territory of Reunion Island (Indian Ocean). METHODS All vancomycin-resistant Enterococcus (VRE) isolates detected on Reunion Island between 2015 and 2019 were included in the study. The VRE isolates were phenotypically characterised and genetically explored by whole-genome sequencing (WGS). RESULTS Sixteen vancomycin-resistant E. faecium (VREf) isolates were retrieved between 2015 and 2019. Seven isolates obtained in 2019 were involved in the outbreak. These seven LVREf isolates from the 2019 outbreak at the University Hospital of Reunion Island (UHRI) were suspected to be related to a linezolid-susceptible VREf strain imported from India. An epidemiological link was highlighted for six of the seven outbreak cases. All the LVREf outbreak isolates were obtained from rectal swabs (colonisation) and resistant to vancomycin (MIC > 128 mg/L) and linezolid (MIC 8-32 mg/L); one isolate was also resistant to daptomycin (MIC 8 mg/L). The seven outbreak isolates were positive for the vanA and optrA genes and belonged to ST761. CONCLUSIONS These results argue for the strict application of control and prevention measures for VRE clones at high risk of spread, particularly in areas such as Reunion Island where the risk of importation from the Indian subcontinent is high. The regional spread of optrA linezolid-resistance genes in VRE isolates is a matter of concern, due to possibility of treatment failure.
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12
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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13
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Brenciani A, Morroni G, Schwarz S, Giovanetti E. Oxazolidinones: mechanisms of resistance and mobile genetic elements involved. J Antimicrob Chemother 2022; 77:2596-2621. [PMID: 35989417 DOI: 10.1093/jac/dkac263] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The oxazolidinones (linezolid and tedizolid) are last-resort antimicrobial agents used for the treatment of severe infections in humans caused by MDR Gram-positive bacteria. They bind to the peptidyl transferase centre of the bacterial ribosome inhibiting protein synthesis. Even if the majority of Gram-positive bacteria remain susceptible to oxazolidinones, resistant isolates have been reported worldwide. Apart from mutations, affecting mostly the 23S rDNA genes and selected ribosomal proteins, acquisition of resistance genes (cfr and cfr-like, optrA and poxtA), often associated with mobile genetic elements [such as non-conjugative and conjugative plasmids, transposons, integrative and conjugative elements (ICEs), prophages and translocatable units], plays a critical role in oxazolidinone resistance. In this review, we briefly summarize the current knowledge on oxazolidinone resistance mechanisms and provide an overview on the diversity of the mobile genetic elements carrying oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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14
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Habib I, Lakshmi GB, Mohamed MYI, Ghazawi A, Khan M, Li D. Enumeration, Antimicrobial Resistance, and Virulence Genes Screening of Enterococcus spp. Isolated from Retail Chicken Carcasses in the United Arab Emirates. Foodborne Pathog Dis 2022; 19:590-597. [PMID: 35749143 DOI: 10.1089/fpd.2022.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Enterococci have recently emerged as nosocomial pathogens worldwide. Their ubiquitous nature determines their frequent finding in foods as contaminants. In this study, we aimed to determine the counts, species diversity, antimicrobial resistance profile, and to screen for a set of virulence genes among enterococci. Enterococcus were identified from 75.7% (125/165) of chilled chicken carcasses, belonging to seven companies, sampled from retail markets in Abu Dhabi Emirate, United Arab Emirates (U.A.E.). Overall, the samples, with a mean Enterococcus count of 2.58 log10 colony-forming unit (CFU)/g with a standard deviation of ±1.17 log10 CFU/g. Among the characterized Enterococcus isolates (n = 90), Enterococcus faecalis was the predominant species (51.1%), followed by Enterococcus faecium (37.8%). Using Vitek2 automated antimicrobial sensitivity panel, we found none of the E. faecalis nor E. faecium to be resistant to ampicillin, teicoplanin, vancomycin, or tigecycline. A third of the E. faecalis (28.3%) and E. faecium (35.3%) were resistant to high-level gentamicin. Over half of E. faecalis (54.3%) were resistant to ciprofloxacin, and the same was in about a third of E. faecium isolates (29.4%). Linezolid resistance was identified in 10 E. faecalis and 7 E. faecium isolates belonging to samples from three companies. All of the linezolid-resistant isolates harbored oxazolidinone resistance optrA gene. Virulence-associated genes (asa1 and gelE) were significantly (p < 0.05) more detected among E. faecalis compared to E. faecium isolates recovered in this study. Over half of the E. faecalis (25/46) and E. faecium (20/34) isolates were identified as multidrug-resistant. This study provides further insight into virulence genes and their association with the dissemination of multidrug-resistant E. faecalis and E. faecium in supermarket chicken meat in the U.A.E. This is probably the first description of the optrA gene in enterococci from supermarket chicken meat in the U.A.E. and from Arab countries. This study adds to the regional and global understanding of antimicrobial resistance spread in foods of animal origin.
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Affiliation(s)
- Ihab Habib
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab of Emirates University, Al Ain, United Arab Emirates.,Department of Environmental Health, High Institute of Public Health, Alexandria University, Alexandria, Egypt.,School of Veterinary Medicine, Murdoch University, Perth, Australia
| | - Glindya Bhagya Lakshmi
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab of Emirates University, Al Ain, United Arab Emirates
| | - Mohamed-Yousif Ibrahim Mohamed
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab of Emirates University, Al Ain, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mushtaq Khan
- Department of Medical Microbiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Dan Li
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore
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15
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Nüesch-Inderbinen M, Haussmann A, Treier A, Zurfluh K, Biggel M, Stephan R. Fattening Pigs Are a Reservoir of Florfenicol-Resistant Enterococci Harboring Oxazolidinone Resistance Genes. J Food Prot 2022; 85:740-746. [PMID: 35258564 DOI: 10.4315/jfp-21-431] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT The use of florfenicol in farm animals may select enterococci that carry resistance genes that confer resistance to linezolid, a critically important oxazolidinone antibiotic used in human medicine. This cross-sectional study aimed to assess the occurrence of oxazolidinone resistance genes in florfenicol-resistant enterococci from fattening pigs in Switzerland and to characterize a subset of the isolates using whole genome sequencing. A total of 31 florfenicol-resistant enterococcal isolates were obtained from 27 (5%) of 565 cecal samples of fattening pigs from seven (11%) of 62 farms. Screening by PCR revealed the presence of cfr-poxtA in 1 of 31, optrA in 15 of 31, and poxtA in 15 of 31 enterococcal isolates. One randomly selected isolate per PCR-positive Enterococcus species and positive farm was selected for further analysis (n = 10). In nine of the 10 isolates, the presence of oxazolidinone resistance genes did not result in phenotypic resistance. Whole genome sequencing analysis showed the presence of E. faecalis (n = 1), E. faecium (n = 1), and E. hirae (n = 1), harboring optrA18, optrA7, and a new optrA allele, respectively. E. durans (n = 1), E. faecium (n = 4), and E. hirae (n = 1) carried the wild-type poxtA, and E. faecalis (n = 1) coharbored cfr(D) and poxtA2. Except for optrA7, all oxazolidinone resistance genes were found on plasmids. Multilocus sequence typing analysis identified E. faecalis ST19 and ST376, E. faecium ST80 belonging to hospital-adapted clade A1, and E. faecium ST21, ST55, ST269, and ST416 belonging to clade A2, which represents human commensals and animal strains. The occurrence of cfr(D), optrA, and poxtA in various porcine Enterococcus spp. demonstrates the spread of oxazolidinone resistance genes among enterococci from fattening pigs in Switzerland. The presence in one sample of poxtA-carrying E. faecium ST80 emphasizes the potential risk to human health through dissemination of strains carrying oxazolidinone resistance genes into the food chain. HIGHLIGHTS
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Affiliation(s)
| | - Adrian Haussmann
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
| | - Andrea Treier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
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16
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Jozefíková A, Valček A, Šoltys K, Nováková E, Bujdáková H. Persistence and multi-ward dissemination of vancomycin resistant Enterococcus faecium ST17 clone in hospital settings in Slovakia from 2017 to 2020. Int J Antimicrob Agents 2022; 59:106561. [PMID: 35271995 DOI: 10.1016/j.ijantimicag.2022.106561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/19/2022] [Accepted: 02/27/2022] [Indexed: 11/16/2022]
Abstract
Hospital vancomycin-resistant Enterococcus faecium (VREfm) were evaluated in term of resistance and phylogenetic relatedness to estimate the location and possible route of transmission of resistance determinants. Hospital VREfm (n=49) were collected in the northern part of Slovakia during the years 2017 to 2020. The collection was analyzed for the presence of the van operon and 10 representatives were subjected to whole-genome sequencing using Illumina MiSeq platform. Obtained sequences were de novo assembled and the draft genome assemblies were analyzed with respect to sequence type (ST), plasmid content, resistance and virulence genes, and the phylogenetic relatedness in single nucleotide polymorphisms (SNP). All strains possessed the vanA operon. Ten selected evaluated isolates belonged to the clinically relevant clonal complex (CC) 17 and carried the vanHAX gene cluster conferring vancomycin resistance on mobile genetic elements, except for the isolate M17773 carrying the vanHAX gene cluster chromosomally. All isolates encoded resistance to quinolones (gyrA and parC mutations) and aminoglycosides [aac(6')-aph(2'')]. Four isolates from different wards and patients belonging to ST17 were closely related (6 - 50 SNP), suggesting a long-term persistence of VREfm ST17 in the hospital settings. VREfm proved to harbor many genetic determinants of antimicrobial resistance. The plasmids carrying the vanA genes belonged to the conjugative broad-host families Inc18 and RepA_N posing a threat to human health, especially in hospital settings. Moreover, 4 clinical isolates were phylogenetically related pointing towards a stable circulation of ST17 VREfm clone in the hospital setting underlining the necessity of continuous surveillance of glycopeptide-resistant pathogens.
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Affiliation(s)
- Anna Jozefíková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia
| | - Adam Valček
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia; Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Katarína Šoltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia
| | - Elena Nováková
- Institute of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia
| | - Helena Bujdáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia.
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17
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McHugh MP, Parcell BJ, Pettigrew KA, Toner G, Khatamzas E, El Sakka N, Karcher AM, Walker J, Weir R, Meunier D, Hopkins KL, Woodford N, Templeton KE, Gillespie SH, Holden MTG. Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35130141 PMCID: PMC8941993 DOI: 10.1099/mic.0.001137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transferable linezolid resistance due to optrA, poxtA, cfr and cfr-like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showed the isolates were genetically distinct (>13900 core SNPs) and belonged to different MLST sequence types. Plasmid contents were examined using hybrid assembly of short and long read (Oxford Nanopore MinION) sequencing technologies. The optrA gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to optrA dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to optrA-positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn6993 transposon in pWE0254-1 carrying linezolid (optrA), macrolide (ermB) and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0–20 residues. We report multiple variants of optrA on distinct plasmids in diverse strains of E. faecalis. It is important to identify the selection pressures driving the emergence and maintenance of resistance against linezolid to retain the clinical utility of this antibiotic.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK.,NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Benjamin J Parcell
- School of Medicine, University of St Andrews, St Andrews, UK.,Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK.,Present address: Medical Microbiology, Ninewells Hospital, Dundee, UK
| | - Kerry A Pettigrew
- School of Medicine, University of St Andrews, St Andrews, UK.,Present address: School of Social and Behavioural Sciences, Erasmus University, Rotterdam, Netherlands
| | - Geoff Toner
- NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Elham Khatamzas
- NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK.,Present address: Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Noha El Sakka
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Anne Marie Karcher
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK.,Present address: Medical Microbiology, Ninewells Hospital, Dundee, UK
| | - Joanna Walker
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Robert Weir
- Medical Microbiology, Forth Valley Royal Hospital, Larbert, UK
| | - Danièle Meunier
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Kate E Templeton
- NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK
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18
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Egan SA, Kavanagh NL, Shore AC, Mollerup S, Samaniego Castruita JA, O’Connell B, McManus BA, Brennan GI, Pinholt M, Westh H, Coleman DC. Genomic analysis of 600 vancomycin-resistant Enterococcus faecium reveals a high prevalence of ST80 and spread of similar vanA regions via IS1216E and plasmid transfer in diverse genetic lineages in Ireland. J Antimicrob Chemother 2022; 77:320-330. [PMID: 34747439 PMCID: PMC8809189 DOI: 10.1093/jac/dkab393] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vancomycin-resistant Enterococcus faecium (VREfm) cause a wide range of hospital infections. Ireland has had one of the highest invasive VREfm infection rates in Europe over the last decade, yet little is known about Irish VREfm. OBJECTIVES To investigate the population structure of Irish VREfm, explore diversity by analysing the vanA transposon region and compare Irish, Danish and global isolates. METHODS E. faecium (n = 648) from five Irish hospitals were investigated, including VREfm [547 rectal screening and 53 bloodstream infection (BSI)] isolates and 48 vancomycin-susceptible (VSEfm) BSI isolates recovered between June 2017 and December 2019. WGS and core-genome MLST (cgMLST) were used to assess population structure. Genetic environments surrounding vanA were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences. RESULTS All isolates belonged to hospital-adapted clade A1 and the majority (435/648) belonged to MLST ST80. The population structure was highly polyclonal; cgMLST segregated 603/648 isolates into 51 clusters containing mixtures of screening and BSI isolates, isolates from different hospitals, and VREfm and VSEfm. Isolates within clusters were closely related (mean average ≤16 allelic differences). The majority (96.5%) of VREfm harboured highly similar vanA regions located on circular or linear plasmids with multiple IS1216E insertions, variable organization of vanA operon genes and 78.6% harboured a truncated tnpA transposase. Comparison of 648 Irish isolates with 846 global E. faecium from 30 countries using cgMLST revealed little overlap. CONCLUSIONS Irish VREfm are polyclonal, yet harbour a characteristic plasmid-located vanA region with multiple IS1216E insertions that may facilitate spread.
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Affiliation(s)
- Sarah A. Egan
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College, Lincoln Place, Dublin 2, Ireland
| | - Nicole L. Kavanagh
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College, Lincoln Place, Dublin 2, Ireland
| | - Anna C. Shore
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College, Lincoln Place, Dublin 2, Ireland
| | - Sarah Mollerup
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | | | - Brian O’Connell
- Department of Clinical Microbiology, School of Medicine, University of Dublin, Trinity College Dublin, St. James’s Hospital, Dublin 8, Ireland
- National MRSA Reference Laboratory, St. James’s Hospital, James’s Street, Dublin 8, Ireland
| | - Brenda A. McManus
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College, Lincoln Place, Dublin 2, Ireland
| | - Grainne I. Brennan
- National MRSA Reference Laboratory, St. James’s Hospital, James’s Street, Dublin 8, Ireland
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - David C. Coleman
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College, Lincoln Place, Dublin 2, Ireland
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19
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Greninger AL, Zerr DM. NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology. J Pediatric Infect Dis Soc 2021; 10:S88-S95. [PMID: 34951469 PMCID: PMC8755322 DOI: 10.1093/jpids/piab074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Corresponding Author: Alexander L. Greninger MD, PhD, MS, MPhil, 1616 Eastlake Ave East Suite 320, Seattle, WA 98102, USA. E-mail:
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington, USA,Division of Infectious Diseases, Seattle Children’s Hospital, Seattle, Washington, USA
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20
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Patekar MR, Medhane V, Jadhav G, Thakare M, Deshmukh D. Synthesis of (s)‐1‐{3‐[4‐(4‐benzo[d]isothiazol‐3‐yl‐piperazin‐1‐yl)‐3‐fluoro‐phenyl]‐2‐oxo‐oxazolidin‐5‐ylmetyl}‐3‐substituted‐urea derivatives as antibacterial agents. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mukunda R. Patekar
- Chemistry Research Centre, Post Graduate Department of Chemistry KTHM College, Affiliated to SP Pune University Nashik India
| | - Vijay Medhane
- Chemistry Research Centre, Post Graduate Department of Chemistry KTHM College, Affiliated to SP Pune University Nashik India
- Department of Chemistry SVKT College, Deolali Camp, Affiliated to SP Pune University Nashik India
| | - Ghanshyam Jadhav
- Chemistry Research Centre, Post Graduate Department of Chemistry KTHM College, Affiliated to SP Pune University Nashik India
| | - Mayur Thakare
- Post Graduate Department of Microbiology KTHM College, Affiliated to SP Pune University Nashik India
| | - Dattatray Deshmukh
- Chemistry Research Centre, Post Graduate Department of Chemistry KTHM College, Affiliated to SP Pune University Nashik India
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21
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Rodríguez-Lucas C, Fernández J, Raya C, Bahamonde A, Quiroga A, Muñoz R, Rodicio MR. Establishment and Persistence of Glycopeptide-Resistant Enterococcus faecium ST80 and ST117 Clones Within a Health Care Facility Located in a Low-Prevalence Geographical Region. Microb Drug Resist 2021; 28:217-221. [PMID: 34705570 DOI: 10.1089/mdr.2021.0171] [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] [Indexed: 12/13/2022] Open
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is one of the most important nosocomial pathogens with limited therapeutic alternatives. In this study, we followed the trends of VREfm and E. faecium causing bloodstream infections (BSIs) in a Spanish hospital, from 2011 to 2020. During this period, 832 E. faecium strains were isolated and 121 (14.5%) were vancomycin resistant. Nineteen of 101 BSIs (18.8%) caused by E. faecium were due to VREfm. The number of BSI-producing E. faecium isolates increased significantly over the past 5 years, with the percentage of invasive VREfm isolates being substantially higher than the average values in Europe and especially in Spain (<3%). VREfm isolates recovered in 2018 (28) and BSI-producing isolates from 2019 (3) and 2020 (2) were molecularly characterized. All were positive for vanA and belonged to sequence type (ST) 80 (28) or ST117 (5), within clonal complex 17. The isolates were only susceptible to linezolid, although most of them were also susceptible (dose dependent) to daptomycin. We report for the first time the establishment and persistence of the VREfm ST80 and ST117 clones in a Spanish hospital. The spread and establishment of hospital-adapted, multidrug-resistant VREfm clones in health care settings are cause for concern and may precede an increment in the BSIs caused by them.
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Affiliation(s)
- Carlos Rodríguez-Lucas
- Servicio de Microbiología, Hospital Universitario de Cabueñes, Gijón, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain.,Research and Innovation, Artificial Intelligence and Statistics Department, Pragmatech AI Solutions, Oviedo, Spain
| | - Carmen Raya
- Unidad de Microbiología, Hospital El Bierzo, Ponferrada, Spain
| | | | - Antonio Quiroga
- Servicio de Medicina Preventiva, Hospital El Bierzo, Ponferrada, Spain
| | - Rosario Muñoz
- Unidad de Enfermería Servicio de Medicina Interna, Hospital El Bierzo, Ponferrada, Spain
| | - María Rosario Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain
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22
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Papan C, Schröder M, Hoffmann M, Knoll H, Last K, Albrecht F, Geisel J, Fink T, Gärtner BC, Mellmann A, Volk T, Berger FK, Becker SL. Combined antibiotic stewardship and infection control measures to contain the spread of linezolid-resistant Staphylococcus epidermidis in an intensive care unit. Antimicrob Resist Infect Control 2021; 10:99. [PMID: 34193293 PMCID: PMC8242281 DOI: 10.1186/s13756-021-00970-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/13/2021] [Indexed: 11/24/2022] Open
Abstract
Background The unrestricted use of linezolid has been linked to the emergence of linezolid-resistant Staphylococcus epidermidis (LRSE). We report the effects of combined antibiotic stewardship and infection control measures on the spread of LRSE in an intensive care unit (ICU). Methods Microbiological data were reviewed to identify all LRSE detected in clinical samples at an ICU in southwest Germany. Quantitative data on the use of antibiotics with Gram-positive coverage were obtained in defined daily doses (DDD) per 100 patient-days (PD). In addition to infection control measures, an antibiotic stewardship intervention was started in May 2019, focusing on linezolid restriction and promoting vancomycin, wherever needed. We compared data from the pre-intervention period (May 2018–April 2019) to the post-intervention period (May 2019–April 2020). Whole-genome sequencing (WGS) was performed to determine the genetic relatedness of LRSE isolates. Results In the pre-intervention period, LRSE were isolated from 31 patients (17 in blood cultures). The average consumption of linezolid and daptomycin decreased from 7.5 DDD/100 PD and 12.3 DDD/100 PD per month in the pre-intervention period to 2.5 DDD/100 PD and 5.7 DDD/100 PD per month in the post-intervention period (p = 0.0022 and 0.0205), respectively. Conversely, vancomycin consumption increased from 0.2 DDD/100 PD per month to 4.7 DDD/100 PD per month (p < 0.0001). In the post-intervention period, LRSE were detected in 6 patients (4 in blood cultures) (p = 0.0065). WGS revealed the predominance of one single clone. Conclusions Complementing infection control measures by targeted antibiotic stewardship interventions was beneficial in containing the spread of LRSE in an ICU. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00970-3.
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Affiliation(s)
- Cihan Papan
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg, Germany.
| | - Matthias Schröder
- Department of Anesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center, Homburg, Germany
| | | | - Heike Knoll
- Department of Anesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center, Homburg, Germany
| | - Katharina Last
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg, Germany
| | - Frederic Albrecht
- Department of Anesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center, Homburg, Germany
| | - Jürgen Geisel
- Department of Clinical Chemistry and Laboratory Medicine, Saarland University, Homburg, Germany
| | - Tobias Fink
- Department of Anesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center, Homburg, Germany
| | - Barbara C Gärtner
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg, Germany
| | | | - Thomas Volk
- Department of Anesthesiology, Intensive Care and Pain Therapy, Saarland University Medical Center, Homburg, Germany
| | - Fabian K Berger
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg, Germany
| | - Sören L Becker
- Center for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Strasse, Building 43, 66421, Homburg, Germany
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23
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Schwarz S, Zhang W, Du XD, Krüger H, Feßler AT, Ma S, Zhu Y, Wu C, Shen J, Wang Y. Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 PMCID: PMC8262807 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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Affiliation(s)
- Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Henrike Krüger
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Shizhen Ma
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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24
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Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L. Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain. EFSA J 2021; 19:e06651. [PMID: 34178158 PMCID: PMC8210462 DOI: 10.2903/j.efsa.2021.6651] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
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25
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Turner AM, Lee JYH, Gorrie CL, Howden BP, Carter GP. Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus. Front Microbiol 2021; 12:637656. [PMID: 33796088 PMCID: PMC8007764 DOI: 10.3389/fmicb.2021.637656] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 12/17/2022] Open
Abstract
Multidrug-resistant Staphylococcus and vancomycin-resistant Enterococcus (VRE) are important human pathogens that are resistant to most clinical antibiotics. Treatment options are limited and often require the use of 'last-line' antimicrobials such as linezolid, daptomycin, and in the case of Staphylococcus, also vancomycin. The emergence of resistance to these last-line antimicrobial agents is therefore of considerable clinical concern. This mini-review provides an overview of resistance to last-line antimicrobial agents in Staphylococcus and VRE, with a particular focus on how genomics has provided critical insights into the emergence of resistant clones, the molecular mechanisms of resistance, and the importance of mobile genetic elements in the global spread of resistance to linezolid.
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Affiliation(s)
- Adrianna M Turner
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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26
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Kumar P, Sah AK, Tripathi G, Kashyap A, Tripathi A, Rao R, Mishra PC, Mallick K, Husain A, Kashyap MK. Role of ACE2 receptor and the landscape of treatment options from convalescent plasma therapy to the drug repurposing in COVID-19. Mol Cell Biochem 2021; 476:553-574. [PMID: 33029696 PMCID: PMC7539757 DOI: 10.1007/s11010-020-03924-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023]
Abstract
Since the first case reports in Wuhan, China, the SARS-CoV-2 has caused a pandemic and took lives of > 8,35,000 people globally. This single-stranded RNA virus uses Angiotensin-converting enzyme 2 (ACE2) as a receptor for entry into the host cell. Overexpression of ACE2 is mainly observed in hypertensive, diabetic and heart patients that make them prone to SARS-CoV-2 infection. Mitigations strategies were opted globally by the governments to minimize transmission of SARS-CoV-2 via the implementation of social distancing norms, wearing the facemasks, and spreading awareness using digital platforms. The lack of an approved drug treatment regimen, and non-availability of a vaccine, collectively posed a challenge for mankind to fight against the SARS-CoV-2 pandemic. In this scenario, repurposing of existing drugs and old treatment options like convalescent plasma therapy can be one of the potential alternatives to treat the disease. The drug repurposing provides a selection of drugs based on the scientific rationale and with a shorter cycle of clinical trials, while plasma isolated from COVID-19 recovered patients can be a good source of neutralizing antibody to provide passive immunity. In this review, we provide in-depth analysis on these two approaches currently opted all around the world to treat COVID-19 patients. For this, we used "Boolean Operators" such as AND, OR & NOT to search relevant research articles/reviews from the PUBMED for the repurposed drugs and the convalescent plasma in the COVID-19 treatment. The repurposed drugs like Chloroquine and Hydroxychloroquine, Tenofovir, Remdesivir, Ribavirin, Darunavir, Oseltamivir, Arbidol (Umifenovir), Favipiravir, Anakinra, and Baricitinib are already being used in clinical trials to treat the COVID-19 patients. These drugs have been approved for a different indication and belong to a diverse category such as anti-malarial/anti-parasitic, anti-retroviral/anti-viral, anti-cancer, or against rheumatoid arthritis. Although, the vaccine would be an ideal option for providing active immunity against the SARS-CoV-2, but considering the current situation, drug repurposing and convalescent plasma therapy and repurposed drugs are the most viable option against SARS-CoV-2.
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Affiliation(s)
- Pravindra Kumar
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, UP, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Rashmi Rao
- School of Life & Allied Health Sciences, The Glocal University, Saharanpur, UP, India
| | - Prabhu C Mishra
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India
| | - Koustav Mallick
- National Liver Disease Biobank, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research, Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research, Bhopal, India
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Manesar, Gurugram, Haryana, 122413, India.
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27
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Enterococci, from Harmless Bacteria to a Pathogen. Microorganisms 2020; 8:microorganisms8081118. [PMID: 32722391 PMCID: PMC7463792 DOI: 10.3390/microorganisms8081118] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Enterococci are gastrointestinal commensals whose hardiness allowed them to colonize very diverse environments, including soils, water, food, and feed. This ability to overcome adverse conditions makes enterococci problematic once they colonize hospital niches. Together with the malleability of their genomes, the capacity to acquire and disseminate determinants of antibiotic resistance has contributed to converting what was once just another opportunistic pathogen into a first-class clinical problem. This review discusses the dimension of the emergence of enterococcal resistance to key antimicrobial agents, the dissemination of this resistance, and its significance in terms of public health, with the aim of raising awareness of the need to devise and implement surveillance programs and more effective antibiotic stewardship.
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