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Boutin S, Welker S, Gerigk M, Miethke T, Heeg K, Nurjadi D. Molecular surveillance of carbapenem-resistant Enterobacterales in two nearby tertiary hospitals to identify regional spread of high-risk clones in Germany, 2019-2020. J Hosp Infect 2024; 149:126-134. [PMID: 38723905 DOI: 10.1016/j.jhin.2024.04.014] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/16/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Understanding the transmission dynamics of carbapenem-resistant Enterobacterales (CRE) is critical to addressing the escalating global threat of antimicrobial resistance (AMR). Although hospital transmission of CRE has been extensively studied, information on community transmission is lacking. AIM To identify genomic clusters of CRE from two nearby institutions that may be indicative of community or inter-facility transmission. METHODS CRE isolates between January 1st, 2019 and December 31st, 2020 from two tertiary hospitals, detected in the respective routine microbiology laboratories, were collected and characterized by short-read whole-genome sequencing. FINDINGS A total of 272 CRE were collected, with Enterobacter cloacae complex (71/192, 37%) predominant in Heidelberg and Escherichia coli (19/80, 24%) in Mannheim. The most common carbapenem resistance gene, blaOXA-48, was detected in 38% of CRE from both centres. Several putative transmission clusters were found, including six clusters of E. cloacae complex, five clusters of Klebsiella pneumoniae, four clusters of Citrobacter freundii, and two clusters each of Escherichia coli and K. aerogenes. No clusters involved isolates from both study centres, except for an ST22 C. freundii cluster. Globally circulating clones were identified between the two centres for ST131 E. coli, ST66 E. hormaechei, and ST22 C. freundii. CONCLUSION This study found no widespread transmission clusters among isolates from both centres, suggesting a hospital-specific clonal structure. This suggests that CRE clusters involving both institutions may indicate emerging or circulating clones in the community, highlighting the need for intersectoral surveillance and data sharing.
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Affiliation(s)
- S Boutin
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig Holstein Campus Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - S Welker
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - M Gerigk
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - T Miethke
- Institute of Medical Microbiology and Hygiene, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Mannheim Institute for Innate Immunoscience (MI3), Mannheim, Germany; Center of Experimental Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - K Heeg
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - D Nurjadi
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck and University Hospital Schleswig Holstein Campus Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany.
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Duque M, Bonnin RA, Dortet L. Comparison of the French novel disc diffusion-based algorithm and the current EUCAST guidelines for the screening of carbapenemase-producing Enterobacterales. J Antimicrob Chemother 2024; 79:1194-1196. [PMID: 38412338 DOI: 10.1093/jac/dkae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Affiliation(s)
- Mathilde Duque
- Team Resist UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriales, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team Resist UMR1184 Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriales, Le Kremlin-Bicêtre, France
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Reichert F, Brinkwirth S, Pfennigwerth N, Haller S, Fritsch LS, Eckmanns T, Werner G, Gatermann S, Hans JB. Prolonged carriage of OXA-244-carbapenemase-producing Escherichia coli complicates epidemiological investigations. Int J Med Microbiol 2024; 314:151595. [PMID: 38159514 DOI: 10.1016/j.ijmm.2023.151595] [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: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
The rapid increase of OXA-244-producing Escherichia coli, predominantly driven by genetically clustered isolates of sequence type (ST)38, has been observed in at least nine European countries, including Germany. However, the reasons for the spread of OXA-244-producing E. coli remain unclear. Here, we aim to evaluate the possibility of prolonged carriage. We identified a total of six different patients with repeated detection of OXA-244-producing E. coli isolates, which were subjected to both short and long-read whole-genome sequencing (WGS). Besides allelic differences using core genome multilocus sequence typing (cgMLST) analyses, we obtained numbers of single-nucleotide polymorphisms (SNPs) to calculate individual base-pair substitution (BPS) rates. To assess possible re-exposure and risk factors for prolonged carriage, case interviews were conducted. The time between detections ranged from eleven months to more than three years. Initial isolates originated in three+ out of six cases from clinical samples, whereas remaining samples were from screening, mostly in the inpatient setting. As expected, cgMLST analyses showed low numbers of allelic differences between isolates of each case ranging from 1 to 4, whereas numbers of SNPs were between 2 and 99 (mean = 36), thus clearly highlighting the discrepancy between these different bacterial typing approaches. For five out of six cases, observed BPS rates suggest that patients can be colonized with OXA-244-producing E. coli, including ST38 cluster isolates, for extensively long times. Thus, we may have previously missed the epidemiological link between cases because exposure to OXA-244-producing E. coli could have occurred in a time frame, which has not been evaluated in previous investigations. Our results may help to guide future epidemiological investigations as well as to support the interpretation of genetic diversity of OXA-244-producing E. coli, particularly among ST38 cluster isolates.
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Affiliation(s)
- Felix Reichert
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany
| | - Simon Brinkwirth
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany; Postgraduate Training for Applied Epidemiology (PAE), Robert Koch-Institute, Berlin, Germany; ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Niels Pfennigwerth
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Sebastian Haller
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany
| | - Lena Sophie Fritsch
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Tim Eckmanns
- Robert Koch Institute, Department of Infectious Disease Epidemiology, Unit 37: Healthcare-Associated Infections, Surveillance of Antibiotic Resistance and Consumption, Berlin, Germany
| | - Guido Werner
- Robert Koch Institute, Division of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode Branch, Germany
| | - Sören Gatermann
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Jörg B Hans
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany.
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Martischang R, Seth-Smith H, Verschuuren TD, Héquet D, Gaïa N, François P, Fluit AC, Kluytmans JAJW, Seiffert SN, Tacconelli E, Cherkaoui A, Harbarth S, Egli A, Kohler P. Regional spread of an atypical ESBL-producing Escherichia coli ST131H89 clone among different human and environmental reservoirs in Western Switzerland. Antimicrob Agents Chemother 2024; 68:e0092523. [PMID: 38169291 PMCID: PMC10848748 DOI: 10.1128/aac.00925-23] [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: 07/12/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
We describe the inter-regional spread of a novel ESBL-producing Escherichia coli subclone (ST131H89) in long-term care facility residents, general population, and environmental water sources in Western Switzerland between 2017 and 2020. The study highlights the importance of molecular surveillance for tracking emerging antibiotic-resistant pathogens in healthcare and community settings.
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Affiliation(s)
- Romain Martischang
- Infection Control Programme and WHO Collaborating Centre, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Helena Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, Basel University, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Tess D. Verschuuren
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Delphine Héquet
- Unité Cantonale Hygiène, Prévention et Contrôle de l’infection, Canton de Vaud, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Ad C. Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan A. J. W. Kluytmans
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Salome N. Seiffert
- Division of Human Microbiology, Centre for Laboratory Medicine, St. Gallen, Switzerland
| | - Evelina Tacconelli
- Department of Diagnostics and Public Health, Infectious Diseases, Verona University, Verona, Italy
- Department of Internal Medicine Infectious Diseases, Tübingen University, Tübingen, Germany
| | | | - Stephan Harbarth
- Infection Control Programme and WHO Collaborating Centre, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, Basel University, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland
| | - Philipp Kohler
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
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Antimicrobial consumption and resistance in bacteria from humans and food-producing animals: Fourth joint inter-agency report on integrated analysis of antimicrobial agent consumption and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals in the EU/EEA JIACRA IV - 2019-2021. EFSA J 2024; 22:e8589. [PMID: 38405113 PMCID: PMC10885775 DOI: 10.2903/j.efsa.2024.8589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
The fourth joint inter-agency report on integrated analysis of antimicrobial consumption (AMC) and the occurrence of antimicrobial resistance (AMR) in bacteria from humans and food-producing animals (JIACRA) addressed data obtained by the Agencies' EU-wide surveillance networks for 2019-2021. The analysis also sought to identify whether significant trends in AMR and AMC were concomitant over 2014-2021. AMC in both human and animal sectors, expressed in mg/kg of estimated biomass, was compared at country and European level. In 2021, the total AMC was assessed at 125.0 mg/kg of biomass for humans (28 EU/EEA countries, range 44.3-160.1) and 92.6 mg/kg of biomass for food-producing animals (29 EU/EEA countries, range 2.5-296.5). Between 2014 and 2021, total AMC in food-producing animals decreased by 44%, while in humans, it remained relatively stable. Univariate and multivariate analyses were performed to study associations between AMC and AMR for selected combinations of bacteria and antimicrobials. Positive associations between consumption of certain antimicrobials and resistance to those substances in bacteria from both humans and food-producing animals were observed. For certain combinations of bacteria and antimicrobials, AMR in bacteria from humans was associated with AMR in bacteria from food-producing animals which, in turn, was related to AMC in animals. The relative strength of these associations differed markedly between antimicrobial class, microorganism and sector. For certain antimicrobials, statistically significant decreasing trends in AMC and AMR were concomitant for food-producing animals and humans in several countries over 2014-2021. Similarly, a proportion of countries that significantly reduced total AMC also registered increasing susceptibility to antimicrobials in indicator E. coli from food-producing animals and E. coli originating from human invasive infections (i.e., exhibited 'complete susceptibility' or 'zero resistance' to a harmonised set of antimicrobials). Overall, the findings suggest that measures implemented to reduce AMC in food-producing animals and in humans have been effective in many countries. Nevertheless, these measures need to be reinforced so that reductions in AMC are retained and further continued, where necessary. This also highlights the importance of measures that promote human and animal health, such as vaccination and better hygiene, thereby reducing the need for use of antimicrobials.
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Piazza A, Corbella M, Mattioni Marchetti V, Merla C, Mileto I, Kuka A, Petazzoni G, Gaiarsa S, Migliavacca R, Baldanti F, Cambieri P. Clinical isolates of ST131 blaOXA-244-positive Escherichia coli, Italy, December 2022 to July 2023. Euro Surveill 2024; 29:2400073. [PMID: 38390649 PMCID: PMC10899817 DOI: 10.2807/1560-7917.es.2024.29.8.2400073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 02/24/2024] Open
Abstract
The dissemination of carbapenemase-producing Escherichia coli, although still at low level, should be continuously monitored. OXA-244 is emerging in Europe, mainly in E. coli. In Italy, this carbapenemase was reported from an environmental river sample in 2019. We report clinical isolates of OXA-244-producing ST131 E. coli in four patients admitted to an acute care hospital in Pavia, Italy. The association of this difficult-to-detect determinant with a globally circulating high-risk clone, ST131 E. coli, is of clinical relevance.
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Affiliation(s)
- Aurora Piazza
- IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Marta Corbella
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Vittoria Mattioni Marchetti
- Specialization School of Microbiology and Virology, University of Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Cristina Merla
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Irene Mileto
- Specialization School of Microbiology and Virology, University of Pavia, Italy
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Angela Kuka
- Specialization School of Microbiology and Virology, University of Pavia, Italy
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Greta Petazzoni
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Stefano Gaiarsa
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
| | - Roberta Migliavacca
- IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Fausto Baldanti
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
| | - Patrizia Cambieri
- Microbiology and Virology Unit, IRCCS Fondazione Policlinico San Matteo, Pavia, Italy
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Loyola-Cruz MÁ, Gonzalez-Avila LU, Martínez-Trejo A, Saldaña-Padilla A, Hernández-Cortez C, Bello-López JM, Castro-Escarpulli G. ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic. Pathogens 2023; 12:pathogens12050743. [PMID: 37242413 DOI: 10.3390/pathogens12050743] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.
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Affiliation(s)
- Miguel Ángel Loyola-Cruz
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
- División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
| | - Luis Uriel Gonzalez-Avila
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Arturo Martínez-Trejo
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
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Kaewnirat K, Chuaychob S, Chukamnerd A, Pomwised R, Surachat K, Phoo MTP, Phaothong C, Sakunrang C, Jeenkeawpiam K, Hortiwakul T, Charernmak B, Chusri S. In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring blaNDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens. Infect Drug Resist 2022; 15:1777-1791. [PMID: 35437346 PMCID: PMC9013254 DOI: 10.2147/idr.s357965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose The spread of New Delhi metallo-β-lactamase (NDM) encoded by the blaNDM gene has been a global health crisis for many years. Most of blaNDM-harboring bacteria commonly carry various antimicrobial resistance (AMR) genes on their chromosomes or plasmids, leading to limited treatment options. Thus, we aimed to evaluate the synergistic effects of fosfomycin in combination with other antimicrobial agents against blaNDM-harboring carbapenem-resistant Escherichia coli (CREC) and to characterize the whole-genome and plasmid sequences of these pathogens. Methods Thirty-eight CREC isolates were collected from patients in the Medicine Ward, Songklanagarind Hospital, Thailand. The activity of fosfomycin in combination with other antimicrobial agents against CREC isolates harboring blaNDM on the plasmid was evaluated using the checkerboard method. In this method, the serial dilutions of two antibiotics were mixed with the cultured CREC, the mixtures were incubated, and FICI was calculated to interpret the synergistic activity of the combination. The whole-genome and particular plasmids of these pathogens were sequenced using next-generation sequencing. Sequence analysis, especially on antimicrobial resistance (AMR) genes, mobile-genetic elements (MGEs), and virulence genes was performed using many bioinformatics tools. Results Of the E. coli 38 isolates, only 3 isolates contained the blaNDM-1 gene, which is located on the IncN2 plasmid. The combinations of fosfomycin with aminoglycosides, colistin, tigecycline, sitafloxacin, and ciprofloxacin were synergies against blaNDM-1-harboring CREC isolates. Genomic analysis revealed that these isolates harbored many β-lactam resistance genes and other AMR genes that may confer resistance to aminoglycoside, fluoroquinolone, rifampicin, trimethoprim, sulfonamide, tetracycline, and macrolide. Also, various MGEs, especially the blaNDM-1-bearing IncN2 plasmid, were present in these isolates. Conclusion Our study demonstrated some synergistic effects of antimicrobial combination against CREC isolates harboring blaNDM-1 on the IncN2 plasmid. Also, our data on the whole-genome and plasmid sequences might be beneficial in the control of the spread of blaNDM-1-harboring CREC isolates. The linkages between blaNDM-1-carrying plasmid, patient information, and time of collection will be elucidated to track the horizontal gene transfer in the future.
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Affiliation(s)
- Kalyarat Kaewnirat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Surachat Chuaychob
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - May Thet Paing Phoo
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Chanitnart Phaothong
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Thanaporn Hortiwakul
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Boonsri Charernmak
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Correspondence: Sarunyou Chusri, Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand, Tel +66 8 973 40446, Email
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9
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Zhang W, Li Z, Wang N, Yang Z, Li J, Li C, Han X, Liu J, Li L, Wang S, Zhan M. Clinical Distribution Characteristics of 1439 Carbapenem-Resistant Escherichia coli Strains in China: Drug Resistance, Geographical Distribution, Antibiotic MIC50/90. Infect Drug Resist 2021; 14:4717-4725. [PMID: 34795488 PMCID: PMC8594617 DOI: 10.2147/idr.s334283] [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: 08/19/2021] [Accepted: 10/08/2021] [Indexed: 01/16/2023] Open
Abstract
Purpose To explore the clinical distribution characteristics and antimicrobial susceptibilities of carbapenem-resistant Escherichia coli (CR-ECO) in Hebei Province, China, from 2017 to 2019, and provide data on the treatment of this bacterial infection and the prevention of its spread. Materials and Methods A total of 1439 CR-ECO strains were collected from 2017 to 2019 in Hebei Province, China. Drug sensitivity tests were performed using the minimum inhibitory concentration (MIC) method, and the data were analyzed statistically using WHONET5.6 software. Results A total of 54,377 strains of Escherichia coli were isolated in Hebei Province from 2017 to 2019, of which 1439 strains were CR-ECO (2.65%). The highest proportion (33.78%) of strains was isolated from urine, and the detection rate showed a slow downward trend over the past 3 years. CR-ECO was mainly detected in densely populated and economically developed areas. Of all the patients, 54.2% were from the medical ward; the ratio of male to female patients with CR-ECO infections was 1.35:1; elderly patients and adults accounted for 59.6% and 30.8%, respectively, whereas minors and newborns accounted for 4.9% and 4.7%, respectively. For CR-ECO, the drug resistance rates to β-lactams were all higher than 80% and there was an annual increasing trend, while the drug resistance rates to quinolones remained nearly unchanged. The rate of resistance to aminoglycosides was relatively low, especially to amikacin (approximately 22%). The MIC50 of other antibacterial drugs, except amikacin, was equal to or higher than the break point of drug resistance. Conclusion From 2017 to 2019, the isolation rate of CR-ECO in Hebei Province, China, remained stable; however, the drug resistance rate showed an upward trend, primarily in cases of urinary tract infections in older men; the resistance rate to amikacin was the lowest. ![]()
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Affiliation(s)
- Wei Zhang
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China.,Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhirong Li
- Clinical Laboratory, Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Na Wang
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China
| | - Zhicong Yang
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China
| | - Jia Li
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China
| | - Caiqing Li
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China
| | - Xuying Han
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China
| | - Jinlu Liu
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China
| | - Liping Li
- Clinical Laboratory, Zhangjiakou Xuan Gang Hospital, Zhangjiakou, Hebei Province, People's Republic of China
| | - Shuwang Wang
- Clinical Laboratory, Zhangjiakou Xuan Gang Hospital, Zhangjiakou, Hebei Province, People's Republic of China
| | - Minghua Zhan
- Microbiology Department, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, People's Republic of China.,Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
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Martischang R, François P, Cherkaoui A, Gaïa N, Renzi G, Agostinho A, Perez M, Graf CE, Harbarth S. Epidemiology of ESBL-producing Escherichia coli from repeated prevalence studies over 11 years in a long-term-care facility. Antimicrob Resist Infect Control 2021; 10:148. [PMID: 34666836 PMCID: PMC8527759 DOI: 10.1186/s13756-021-01013-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/25/2021] [Indexed: 12/29/2022] Open
Abstract
Background Escherichia coli sequence type (ST) 131 H30 is an emerging multidrug resistant subclone, known to spread and cause outbreaks in long-term care facilities (LTCFs). Objectives and methods From 2010 through 2020, we performed 11 yearly surveillance studies for determining the prevalence of digestive carriage of ESBL-producing E. coli (ESBL-EC) among residents in a university-affiliated LCTF. Sequencing and genotyping of selected isolates were performed to characterize temporal trends in the prevalence and epidemic potential of ESBL-EC subclones, and for evaluating a potential rebound effect following discontinuation of contact precautions for ESBL-EC carriers in January 2019. Results This study included 2′403 LTCF residents, with 252 (10.5%) positive for ESBL-EC. Among the 236 ESBL-EC isolates available for typing, 58.0% belonged to the ST131 lineage, including 94/137 (68.6%) ST131 H30 isolates. An increasing yearly prevalence was observed for ESBL-EC (from 4.6 to 9.4%; p = 0.11), but not for the ST131 H30 subclone, which peaked in 2015 and declined thereafter. Multiple previously unnoticed ESBL-EC outbreaks occurred in the LTCF. Since 2018, we noted the clonal expansion of a rare ST131 H89 subclone (O16:H5) harboring CTX-M-14 and CTX-M-24. No rebound effect was observed in ESBL-EC prevalence nor in the different subclones following discontinuation of contact precautions for ESBL-EC carriers since 2019. Conclusion Clonal fluctuation was observed for ST131 H30 ESBL-EC with a current decline in prevalence. Surveillance should include the evolution of ST131 non-H30 subclones, which may spread in LTCFs. Our findings suggest that discontinuation of contact precautions for ESBL-EC carriers in LTCFs may be safely implemented, in support of European recommendations to limit ESBL-producing Enterobacteriaceae control measures in endemic settings to non-E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-01013-7.
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Affiliation(s)
- Romain Martischang
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
| | - Patrice François
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | | | - Nadia Gaïa
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Americo Agostinho
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Monica Perez
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Christophe E Graf
- Department of Rehabilitation and Geriatrics, Geneva University Hospitals, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
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Cano-Martín E, Portillo-Calderón I, Pérez-Palacios P, Navarro-Marí JM, Fernández-Sierra MA, Gutiérrez-Fernández J. A Study in a Regional Hospital of a Mid-Sized Spanish City Indicates a Major Increase in Infection/Colonization by Carbapenem-Resistant Bacteria, Coinciding with the COVID-19 Pandemic. Antibiotics (Basel) 2021; 10:antibiotics10091127. [PMID: 34572709 PMCID: PMC8469839 DOI: 10.3390/antibiotics10091127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023] Open
Abstract
Bacterial resistance to antibiotics has proven difficult to control over the past few decades. The large group of multidrug-resistant bacteria includes carbapenemase-producing bacteria (CPB), for which limited therapeutic options and infection control measures are available. Furthermore, carbapenemases associate with high-risk clones that are defined by the sequence type (ST) to which each bacterium belongs. The objectives of this cross-sectional and retrospective study were to describe the CPB population isolated in a third-level hospital in Southern Spain between 2015 and 2020 and to establish the relationship between the ST and the epidemiological situation defined by the hospital. CPB were microbiologically studied in all rectal and pharyngeal swabs and clinical samples received between January 2015 and December 2020, characterizing isolates using MicroScan and mass spectrometry. Carbapenemases were detected by PCR and Sanger sequencing, and STs were assigned by multilocus sequence typing (MLST). Isolates were genetically related by pulsed-field gel electrophoresis using Xbal, Spel, or Apal enzymes. The episodes in which each CPB was isolated were recorded and classified as involved or non-involved in an outbreak. There were 320 episodes with CPB during the study period: 18 with K. pneumoniae, 14 with Klebisella oxytoca, 9 with Citrobacter freundii, 11 with Escherichia coli, 46 with Enterobacter cloacae, 70 with Acinetobacter baumannii, and 52 with Pseudomonas aeruginosa. The carbapenemase groups detected were OXA, VIM, KPC, and NDM with various subgroups. Synchronous relationships were notified between episodes of K. pneumoniae and outbreaks for ST15, ST258, ST307, and ST45, but not for the other CPB. There was a major increase in infections with CPB over the years, most notably during 2020, coinciding with the COVID-19 pandemic. This study highlights the usefulness of gene sequencing techniques to control the spread of these microorganisms, especially in healthcare centers. These techniques offer faster results, and a reduction in their cost may make their real-time application more feasible. The combination of epidemiological data with real-time molecular sequencing techniques can provide a major advance in the transmission control of these CPB and in the management of infected patients. Real-time sequencing is essential to increase precision and thereby control outbreaks and target infection prevention measures in a more effective manner.
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Affiliation(s)
- Estefanía Cano-Martín
- Department of Preventive Medicine and Public Health, Virgen de las Nieves University Hospital & ibs, Granada-Instituto de Investigación Biosanitaria de Granada, Avda. de las Fuerzas Armadas, 2, 18014 Granada, Spain; (E.C.-M.); (M.A.F.-S.)
| | - Inés Portillo-Calderón
- Unidad de Gestión Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena & Instituto de Biomedicina de Sevilla (IBIs), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41020 Sevilla, Spain; (I.P.-C.); (P.P.-P.)
| | - Patricia Pérez-Palacios
- Unidad de Gestión Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena & Instituto de Biomedicina de Sevilla (IBIs), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, 41020 Sevilla, Spain; (I.P.-C.); (P.P.-P.)
| | - José María Navarro-Marí
- Laboratory of Microbiology, Virgen de las Nieves University Hospital. & ibs, Granada-Instituto de Investigación Biosanitaria de Granada, Avda. de las Fuerzas Armadas, 2, 18014 Granada, Spain;
| | - María Amelia Fernández-Sierra
- Department of Preventive Medicine and Public Health, Virgen de las Nieves University Hospital & ibs, Granada-Instituto de Investigación Biosanitaria de Granada, Avda. de las Fuerzas Armadas, 2, 18014 Granada, Spain; (E.C.-M.); (M.A.F.-S.)
| | - José Gutiérrez-Fernández
- Laboratory of Microbiology, Virgen de las Nieves University Hospital. & ibs, Granada-Instituto de Investigación Biosanitaria de Granada, Avda. de las Fuerzas Armadas, 2, 18014 Granada, Spain;
- Department of Microbiology, School of Medicine, University of Granada & ibs, Granada-Instituto de Investigación Biosanitaria de Granada, Avda. de la Investigación, 11, 18016 Granada, Spain
- Correspondence:
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Kohler P, Seiffert SN, Kessler S, Rettenmund G, Lemmenmeier E, Qalla Widmer L, Nolte O, Seth-Smith HMB, Albrich WC, Babouee Flury B, Gardiol C, Harbarth S, Münzer T, Schlegel M, Petignat C, Egli A, Héquet D. Molecular Epidemiology and Risk Factors for Extended-Spectrum β-Lactamase-Producing Enterobacterales in Long-Term Care Residents. J Am Med Dir Assoc 2021; 23:475-481.e5. [PMID: 34297981 DOI: 10.1016/j.jamda.2021.06.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVES We aimed to assess the burden of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales in Swiss long-term care facilities (LTCFs) to describe the molecular epidemiology, describe the intrainstitutional and regional clusters of resistant pathogens, and identify independent institution- and resident-level factors associated with colonization. DESIGN Cross-sectional study. SETTING AND PARTICIPANTS From August to October 2019, we performed a point prevalence study among residents from 16 LTCFs in Western and Eastern Switzerland (8 per region). METHODS Residents underwent screening for ESBL-producing Enterobacterales (ESBL-E); whole-genome sequencing (WGS) was performed. We gathered institution-level (eg, number of beds, staff-resident ratio, alcoholic hand rub consumption) and resident-level [eg, anthropometric data, time in facility, dependency, health care exposure, antibiotic treatment, proton-pump inhibitor (PPI) use] characteristics. Factors associated with colonization were identified using a generalized linear model. RESULTS Among 1185 eligible residents, 606 (51%) consented to the study. ESBL-E prevalence was 11.6% (70/606), ranging from 1.9% to 33.3% between institutions, with a median of 12.5% in the West and 6.9% in the East (P = .03). Among 59 Escherichia coli (from 58 residents), multilocus sequence type (ST) 131 was most common (n = 43/59, 73%), predominantly its subclone H30R1 (n = 37/43, 86%). WGS data identified multiple intrainstitutional and regional clusters. Independent risk factors for ESBL carriage were previous ESBL colonization [adjusted odds ratio (aOR) 23.5, 95% confidence interval (CI) 6.6-83.8, P < .001), male gender (aOR 2.6, 95% CI 1.5-4.6, P = .002), and use of PPIs (aOR 2.2, 95% CI 1.2-3.8, P = .01). CONCLUSIONS AND IMPLICATIONS Overall ESBL-E prevalence in Swiss LTCF residents is low. Yet, we identified several clusters of residents with identical pathogens within the same institution. This implies that particularly affected institutions might benefit from targeted infection control interventions. PPI use was the only modifiable factor associated with carriage of ESBL producers. This study adds to the growing list of adverse outcomes associated with PPIs, calling for action to restrict their use in the long-term care setting.
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Affiliation(s)
- Philipp Kohler
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland.
| | - Salome N Seiffert
- Division of Human Microbiology, Centre for Laboratory Medicine, St Gallen, Switzerland
| | - Simone Kessler
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Gabriela Rettenmund
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Eva Lemmenmeier
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Laetitia Qalla Widmer
- Unité cantonale hygiène, prévention et contrôle de l'infection, Canton of Vaud, Switzerland
| | - Oliver Nolte
- Division of Human Microbiology, Centre for Laboratory Medicine, St Gallen, Switzerland
| | - Helena M B Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, University of Basel, Basel, Switzerland
| | - Werner C Albrich
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Baharak Babouee Flury
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | | | - Stephan Harbarth
- Division of Infectious Diseases and Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | | | - Matthias Schlegel
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Christiane Petignat
- Unité cantonale hygiène, prévention et contrôle de l'infection, Canton of Vaud, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, University of Basel, Basel, Switzerland
| | - Delphine Héquet
- Unité cantonale hygiène, prévention et contrôle de l'infection, Canton of Vaud, Switzerland
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