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Bonnin RA, Jeannot K, Henriksen AS, Quevedo J, Dortet L. In vitro activity of cefepime-enmetazobactam on carbapenem resistant Gram negatives. Clin Microbiol Infect 2024:S1198-743X(24)00478-6. [PMID: 39374655 DOI: 10.1016/j.cmi.2024.09.031] [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: 06/15/2024] [Revised: 09/12/2024] [Accepted: 09/28/2024] [Indexed: 10/09/2024]
Abstract
OBJECTIVES Cefepime-enmetazobactam is a new β-lactam-β-lactamase inhibitor (BL/BLI) combination with broad-spectrum activity against multidrug-resistant Enterobacterales including ESBL producers. This study evaluated the in vitro activity of cefepime-enmetazobactam towards a collection of carbapenem-resistant Enterobacterales (CRE), Pseudomonas aeruginosa and Acinetobacter baumannii compared to the other BL/BLI combinations. METHODS MIC of cefepime, cefepime-enmetazobactam, ceftazidime, ceftazidime-avibactam, meropenem, meropenem-vaborbactam, imipenem, imipenem-relebactam and ertapenem were determined by broth microdilution on 2,212 CRE including 2,089 carbapenemase producers (1000 OXA-48-like, 49 KPC, 697 NDM, 180 VIM, 1 IMP, 9 IMI, 158 multiple carbapenemases) and 123 non-carbapenemase producers (CRE non-CPE) received at the French National Reference Center (1st March to 31th August 2023), 50 P. aeruginosa and 30 A. baumannii. All strains were fully sequenced. RESULTS We confirmed the absence of inhibitory activity of enmetazobactam towards metallo-β-lactamases. Cefepime-enmetazobactam and ceftazidime-avibactam exhibited a similar susceptibility (96.7% vs 99.5%, respectively) on OXA-48-producers. Cefepime-enmetazobactam exhibited 66.9% and 63.3% susceptibility for CRE non-EPC and KPC while those rates rose to 96.7%/95.9%, 93.4%/95.9%, 95.9%/98.0% for ceftazidime-avibactam, imipenem-relebactam and meropenem-vaborbactam, respectively. Low MICs (≤0.25 mg/L) were obtained for ceftazidime-avibactam resistant KPC variants. Cefepime-enmetazobactam did not display a significant added value compared to cefepime alone on P. aeruginosa and A. baumannii. CONCLUSION OXA-48 producers displayed high susceptibility to cefepime-enmetazobactam which is similar to ceftazidime-avibactam, including for OXA-48 producers that co-produce a ceftazidime hydrolyzing enzyme (ESBL or AmpC). In vivo experiments have to be implemented to confim if cefepime-enmetazobactam might be a relevant alternative to ceftazidime-avibactam for the treatment of infections caused by OXA-48 producers.
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Affiliation(s)
- Rémy A Bonnin
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Katy Jeannot
- Bacteriology Unit, University hospital of Besançon, Besançon, France; Associated French National Reference Center for Antibiotic Resistance in Pseudomonas and Acinetobacter, Besançon, France
| | | | | | - Laurent Dortet
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.
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Lee YL, Wang WY, Ko WC, Hsueh PR. Global epidemiology and antimicrobial resistance of Enterobacterales harbouring genes encoding OXA-48-like carbapenemases: insights from the results of the Antimicrobial Testing Leadership and Surveillance (ATLAS) programme 2018-2021. J Antimicrob Chemother 2024; 79:1581-1589. [PMID: 38758189 DOI: 10.1093/jac/dkae140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVES The recent emergence of carbapenem-resistant Enterobacterales poses a major and escalating threat to global public health. This study aimed to analyse the global distribution and antimicrobial resistance of Enterobacterales harbouring variant OXA-48-like carbapenemase-related genes. METHODS Enterobacterales isolates were collected from the Antimicrobial Testing Leadership and Surveillance (ATLAS) programme during 2018-2021. Comprehensive antimicrobial susceptibility testing and β-lactamase gene detection were also conducted, along with statistical analysis of the collected data. RESULTS Among the 72 244 isolates, 1934 Enterobacterales isolates were identified to harbour blaOXA-48-like genes, predominantly Klebsiella spp. (86.9%). High rates of multidrug resistance were observed, with only ceftazidime/avibactam and tigecycline showing favourable susceptibility. A discrepancy between the genotype and phenotype of carbapenem resistance was evident: 16.8% (233 out of 1384) of the Enterobacterales isolates with blaOXA-48-like genes exhibited susceptibility to meropenem. Specifically, 37.4% (64/95) of Escherichia coli strains with blaOXA-48-like genes displayed meropenem susceptibility, while the corresponding percentages for Klebsiella pneumoniae and Enterobacter cloacae complex were 25.2% (160/1184) and 0% (0/36), respectively (P < 0.05). Geographical analysis revealed that the highest prevalence of blaOXA-48-like genes occurred in Asia, the Middle East and Eastern Europe. The proportion of K. pneumoniae isolates harbouring blaOXA-232 increased from 23.9% in 2018 to 56.0% in 2021. By contrast, the proportion of blaOXA-48 decreased among K. pneumoniae isolates during 2018-2021. CONCLUSIONS This study underscores the widespread and increasing prevalence of blaOXA-48-like genes in Enterobacterales and emphasizes the need for enhanced surveillance, improved diagnostic methods and tailored antibiotic stewardship to combat the spread of these resistant pathogens.
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Affiliation(s)
- Yu-Lin Lee
- Division of Infectious Disease, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- PhD Program in Medical Biotechnology, Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Wei-Yao Wang
- Division of Infectious Disease, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Wen-Chien Ko
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Chin Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- PhD Program for Ageing, School of Medicine, China Medical University, Taichung, Taiwan
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Izdebski R, Biedrzycka M, Urbanowicz P, Żabicka D, Błauciak T, Lechowicz D, Gałecka-Ziółkowska B, Gniadkowski M. Large hospital outbreak caused by OXA-244-producing Escherichia coli sequence type 38, Poland, 2023. Euro Surveill 2024; 29:2300666. [PMID: 38818748 PMCID: PMC11141128 DOI: 10.2807/1560-7917.es.2024.29.22.2300666] [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: 11/23/2023] [Accepted: 04/04/2024] [Indexed: 06/01/2024] Open
Abstract
In February 2023, Escherichia coli sequence type (ST) 38 producing oxacillinase 244 (OXA-244-Ec ST38) was detected from three patients in a hospital in western Poland. Overall, OXA-244-Ec ST38 was detected from 38 colonised patients in 13 wards between February and June 2023. The outbreak was investigated on site by an infection control team, and the bacterial isolates were characterised microbiologically and by whole genome sequencing. We could not identify the primary source of the outbreak or reconstruct the transmission sequence. In some of the 13 affected wards or their groups linked by the patients' movement, local outbreaks occurred. The tested outbreak isolates were resistant to β-lactams (penicillins, cephalosporins, aztreonam and ertapenem) and to trimethoprim-sulfamethoxazole. Consistently, apart from bla OXA-244, all isolates contained also the bla CMY-2 and bla CTX-M-14 genes, coding for an AmpC-like cephalosporinase and extended-spectrum β-lactamase, respectively, and genes conferring resistance to trimethoprim-sulfamethoxazole, sul2 and dfrA1. Genomes of the isolates formed a tight cluster, not of the major recent European Cluster A but of the older Cluster B, with related isolates identified in Germany. This outbreak clearly demonstrates that OXA-244-Ec ST38 has a potential to cause hospital outbreaks which are difficult to detect, investigate and control.
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Affiliation(s)
- Radosław Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Marta Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Paweł Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Dorota Żabicka
- National Reference Centre for Susceptibility Testing, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Teresa Błauciak
- Bacteriological and Serological Laboratory, Multispecialist Hospital, Nowa Sól, Poland
| | - Dorota Lechowicz
- Hospital Infection Control and Prevention Team, Multispecialist Hospital, Nowa Sól, Poland
| | | | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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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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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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Daaboul D, Oueslati S, Rima M, Kassem II, Mallat H, Birer A, Girlich D, Hamze M, Dabboussi F, Osman M, Naas T. The emergence of carbapenemase-producing Enterobacterales in hospitals: a major challenge for a debilitated healthcare system in Lebanon. Front Public Health 2023; 11:1290912. [PMID: 38074718 PMCID: PMC10699444 DOI: 10.3389/fpubh.2023.1290912] [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: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Background Carbapenem- and extended-spectrum cephalosporin-resistant Enterobacterales (CR-E and ESCR-E, respectively) are increasingly isolated worldwide. Information about these bacteria is sporadic in Lebanon and generally relies on conventional diagnostic methods, which is detrimental for a country that is struggling with an unprecedented economic crisis and a collapsing public health system. Here, CR-E isolates from different Lebanese hospitals were characterized. Materials and methods Non-duplicate clinical ESCR-E or CR-E isolates (N = 188) were collected from three hospitals from June 2019 to December 2020. Isolates were identified by MALDI-TOF, and their antibiotic susceptibility by Kirby-Bauer disk diffusion assay. CR-E isolates (n = 33/188) were further analyzed using Illumina-based WGS to identify resistome, MLST, and plasmid types. Additionally, the genetic relatedness of the CR-E isolates was evaluated using an Infrared Biotyper system and compared to WGS. Results Using the Kirby-Bauer disk diffusion assay, only 90 isolates out of the 188 isolates that were collected based on their initial routine susceptibility profile by the three participating hospitals could be confirmed as ESCR-E or CR-E isolates and were included in this study. This collection comprised E. coli (n = 70; 77.8%), K. pneumoniae (n = 13; 14.4%), Enterobacter spp. (n = 6; 6.7%), and Proteus mirabilis (n = 1; 1.1%). While 57 were only ESBL producers the remaining 33 isolates (i.e., 26 E. coli, five K. pneumoniae, one E. cloacae, and one Enterobacter hormaechei) were resistant to at least one carbapenem, of which 20 were also ESBL-producers. Among the 33 CR-E, five different carbapenemase determinants were identified: blaNDM-5 (14/33), blaOXA-244 (10/33), blaOXA-48 (5/33), blaNDM-1 (3/33), and blaOXA-181 (1/33) genes. Notably, 20 CR-E isolates were also ESBL-producers. The analysis of the genetic relatedness revealed a substantial genetic diversity among CR-E isolates, suggesting evolution and transmission from various sources. Conclusion This study highlighted the emergence and broad dissemination of blaNDM-5 and blaOXA-244 genes in Lebanese clinical settings. The weak AMR awareness in the Lebanese community and the ongoing economic and healthcare challenges have spurred self-medication practices. Our findings highlight an urgent need for transformative approaches to combat antimicrobial resistance in both community and hospital settings.
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Affiliation(s)
- Dina Daaboul
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Saoussen Oueslati
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Paris, France
| | - Mariam Rima
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
| | - Issmat I. Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, United States
| | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Aurélien Birer
- French National Reference Center for Antibiotic Resistance, Clermont-Ferrand, France
| | - Delphine Girlich
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, United States
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, United States
| | - Thierry Naas
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Paris, France
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Biguenet A, Bordy A, Atchon A, Hocquet D, Valot B. Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST. Microb Genom 2023; 9. [PMID: 37966168 DOI: 10.1099/mgen.0.001126] [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] [Indexed: 11/16/2023] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome database. For each gene, the first allele is aligned against the bacterial genome of interest using BLAT. Incomplete genes are aligned using MAFT. All data are stored in a SQLite database. pyMLST accepts assembly genomes or raw data (with the option pyMLST-KMA) as input. To evaluate our new tool, we selected three genome collections of major bacterial pathogens (Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus) and compared them with pyMLST, pyMLST-KMA, ChewBBACA, SeqSphere and the variant calling approach. We compared the sensitivity, precision and false-positive rate for each method with those of the variant calling approach. Minimal spanning trees were generated with each type of software to evaluate their interest in the context of a bacterial outbreak. We found that pyMLST-KMA is a convenient screening method to avoid assembling large bacterial collections. Our data showed that pyMLST (free, open source, available in Galaxy and pipeline ready) performed similarly to the commercial SeqSphere and performed better than ChewBBACA and pyMLST-KMA.
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Affiliation(s)
- Adrien Biguenet
- CHU de Besançon, Hygiène Hospitalière, F-25030 Besançon, France
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
| | - Augustin Bordy
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
| | - Alban Atchon
- Bioinformatique et Big Data Au Service de La Santé, Université de Franche-Comté, F-25000 Besançon, France
| | - Didier Hocquet
- CHU de Besançon, Hygiène Hospitalière, F-25030 Besançon, France
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
| | - Benoit Valot
- Université de Franche-Comté, CNRS, Chrono-environnement, F-25000 Besançon, France
- Bioinformatique et Big Data Au Service de La Santé, Université de Franche-Comté, F-25000 Besançon, France
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Lindemann PC, Pedersen T, Oma DH, Janice J, Grøvan F, Chedid GM, Hafne LJ, Josefsen EH, Kacelnik O, Sundsfjord A, Samuelsen Ø. Intraregional hospital outbreak of OXA-244-producing Escherichia coli ST38 in Norway, 2020. Euro Surveill 2023; 28:2200773. [PMID: 37410380 PMCID: PMC10370041 DOI: 10.2807/1560-7917.es.2023.28.27.2200773] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Infections with OXA-244-carbapenemase-producing Escherichia coli with sequence type (ST)38 have recently increased in Europe. Due to its low-level activity against carbapenems, OXA-244 can be difficult to detect. Previous assessments have not revealed a clear source and route of transmission for OXA-244-producing E. coli, but there are indications of non-healthcare related sources and community spread. Here we report a hospital-associated outbreak of OXA-244-producing E. coli ST38 involving three hospitals in Western Norway in 2020. The outbreak occurred over a 5-month period and included 12 cases identified through clinical (n = 6) and screening (n = 6) samples. The transmission chain was unclear; cases were identified in several wards and there was no clear overlap of patient stay. However, all patients had been admitted to the same tertiary hospital in the region, where screening revealed an outbreak in one ward (one clinical case and five screening cases). Outbreak control measures were instigated including contact tracing, isolation, and screening; no further cases were identified in 2021. This outbreak adds another dimension to the spread of OXA-244-producing E. coli ST38, illustrating this clone's ability to establish itself in the healthcare setting. Awareness of challenges concerning OXA-244-producing E. coli diagnostic is important to prevent further spread.
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Affiliation(s)
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Dorthea Hagen Oma
- Division of Patient Safety, Haukeland University Hospital, Bergen, Norway
| | - Jessin Janice
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | | | | | - Liv Jorunn Hafne
- Department of Microbiology, Haugesund Hospital, Haugesund, Norway
| | - Ellen H Josefsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Oliver Kacelnik
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
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9
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van Soest TM, Søndermølle MB, Brouwer MC, Chekrouni N, Larsen AR, Petersen A, van Sorge NM, Nielsen H, van de Beek D, Bodilsen J. Community-acquired Staphylococcus aureus meningitis in adults. J Infect 2023; 86:239-244. [PMID: 36682629 DOI: 10.1016/j.jinf.2023.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND Staphylococcus aureus is an uncommon cause of community-acquired bacterial meningitis. We aimed to describe patients with this disease. METHODS We evaluated clinical characteristics and outcome of adults with community-acquired S. aureus meningitis from prospective nationwide cohort studies from Denmark (2015-2020) and the Netherlands (2006-2021). Whole genome sequencing of S. aureus isolates was performed to evaluate the potential association between clonal complex and clinical characteristics. RESULTS We evaluated 111 episodes of community-acquired S. aureus meningitis: 65 from Denmark and 46 from the Netherlands. The median age was 66 years (interquartile range [IQR] 50-74) and 43 of 111 patients were female (39%). Concomitant infectious foci were found in 95 of 107 patients (89%), most commonly endocarditis (53 of 109 [49%]) and spondylodiscitis (43 of 109 [39%]). The triad of neck stiffness, altered mental status (Glasgow Coma Scale score <14), and fever was present in only 18 of 108 patients (17%). Surgery was performed in 14 of 33 patients (42%) with spondylodiscitis and 26 of 52 (50%) with endocarditis. A favorable outcome (Glasgow Outcome Scale score 5) occurred in 26 of 111 patients (23%), while 39 (35%) died. The most common bacterial clonal complexes (CC) were CC30 (16 [17%]), CC45 (16 [17%]), CC5 (12 [13%], and CC15 (10 [11%]); no associations between CCs and concomitant foci or outcome were found. CONCLUSIONS Community-acquired S. aureus meningitis is a severe disease with a high case fatality rate, occurring mainly in patients with concomitant endocarditis or spondylodiscitis.
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Affiliation(s)
- Thijs M van Soest
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | - Maria Birgitte Søndermølle
- European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland; Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, Aalborg 9000, Denmark
| | - Matthijs C Brouwer
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | - Nora Chekrouni
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | | | | | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Henrik Nielsen
- European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland; Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, Aalborg 9000, Denmark
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Neurosciences, Neuroinfection and - Inflammation, Amsterdam, the Netherlands; European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland
| | - Jacob Bodilsen
- European Society for Clinical Microbiology and Infectious Disease (ESCMID) Study Group on Infections of the Brain (ESGIB), Basel, Switzerland; Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, Aalborg 9000, Denmark.
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10
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Alfifi A, Christensen JP, Hounmanou YMG, Sandberg M, Dalsgaard A. Characterization of Escherichia coli and other bacteria isolated from condemned broilers at a Danish abattoir. Front Microbiol 2022; 13:1020586. [PMID: 36439808 PMCID: PMC9686377 DOI: 10.3389/fmicb.2022.1020586] [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] [Received: 08/16/2022] [Accepted: 10/19/2022] [Indexed: 10/17/2023] Open
Abstract
Meat inspection is important to ensure food safety and protect public health. Visual inspection of slaughtered carcasses for pathological changes should be supported by bacteriological analysis to determine whether the entire carcass or parts of it should be condemned. The aim of this study was to determine the bacterial species present in different sample types from condemned broiler carcasses. Furthermore, we investigated the genetic characteristics, zoonotic potential, and relatedness of Escherichia coli, the predominant bacterial species isolated from the carcasses. A total of 400 broiler carcasses condemned because of cellulitis (100), scratches (100), hepatitis (100), and healthy control carcasses (100) were selected. Samples of meat, pathological lesion, and bone marrow of each carcass were obtained for microbial analysis. From the analyzed samples, 469 bacterial isolates were recovered with E. coli accounting for 45.8%, followed by Aeromonas spp. (27.9%), in particular A. veronii. The highest rate of bacterial isolation was observed in carcasses condemned with cellulitis, whereas carcasses with hepatitis had the lowest rate of bacterial isolation. Forty-four E. coli isolates originating from different sample types were selected for whole genome sequencing. A clonal relationship was shown between E. coli from different sample types of the same carcass condemned with cellulitis and scratches. A major clade of E. coli was found in carcasses condemned with cellulitis with isolates containing mdf(A), tet(A), and bla TEM-1B genes that confer resistance to macrolides, tetracycline, and ampicillin, respectively. E. coli in this clade all belonged to ST117 and clustered with E. coli isolates previously collected from dead chickens and carcasses condemned due to cellulitis in Denmark, Finland, and the United Kingdom. Bacterial evaluation results of carcasses condemned with cellulitis, scratches (moderate to severe skin lesion), and acute hepatitis confirmed the need for total condemnation of carcasses with these pathological findings. A similar evaluation should be done for carcasses affected with chronic hepatitis, and minor scratches lesions.
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Affiliation(s)
- Ahmed Alfifi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Jens P. Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Marianne Sandberg
- National Food Institute, Danish Technical University, Lyngby, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
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11
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Notermans DW, Schoffelen AF, Landman F, Wielders CCH, Witteveen S, Ganesh VA, van Santen-Verheuvel M, de Greeff SC, Kuijper EJ, Hendrickx APA. A genetic cluster of OXA-244 carbapenemase-producing Escherichia coli ST38 with putative uropathogenicity factors in the Netherlands. J Antimicrob Chemother 2022; 77:3205-3208. [PMID: 36171716 PMCID: PMC9616543 DOI: 10.1093/jac/dkac307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Daan W Notermans
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Annelot F Schoffelen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Fabian Landman
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Cornelia C H Wielders
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Sandra Witteveen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Varisha A Ganesh
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Marga van Santen-Verheuvel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Sabine C de Greeff
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Ed J Kuijper
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Antoni P A Hendrickx
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
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12
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Zhao X, Zhao H, Zhou Z, Miao Y, Li R, Yang B, Cao C, Xiao S, Wang X, Liu H, Wang J, Yang Z. Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates That Cause Diarrhea in Sheep in Northwest China. Microbiol Spectr 2022; 10:e0159522. [PMID: 35943154 PMCID: PMC9431196 DOI: 10.1128/spectrum.01595-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022] Open
Abstract
Development of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli is one the greatest threats faced by mankind. Among animals, chickens, pigs, and cattle are reservoirs of these pathogens worldwide. Nevertheless, there is a knowledge gap on ESBL-producing E. coli from small ruminants (i.e., sheep and goats) in China. The aim of this study was to identify and characterize the resistance profiles, resistomes, and sequence features of 67 ESBL-producing E. coli isolates from sheep in northwest China. The findings showed that blaCTX-M and blaTEM were the most prevalent. Interestingly, we found that the resistance gene mcr-1 was widespread in sheep merely from Shaanxi areas, accounting for 19.2% (5/26). The highly prevalent serotypes and FumC-FimH (CH) typing isolates were O8 and C4H32, respectively. High-risk E. coli clones, such as sequence type 10 (ST10), ST23, ST44, and ST58, were also found in China's sheep population. A total of 67 ESBL-producing isolates were divided into five phylogenetic groups, namely, B1 (n = 47, 70.1%), B2 (n = 1, 1.5%), C (n = 14, 20.9%), E (n = 1, 1.5%), and F (n = 1, 1.5%), with the phylogenetic groups for 3 isolates (4.5%) remaining unknown. Moreover, ESBL-producing E. coli isolates were also characterized by the abundance and diversity of biocide/metal resistance genes and insert sequences. We found that in ESBL-producing E. coli isolates, there were two different types of isolates, those containing ESBL genes or not, which led to large discrepancies between resistance phenotypes and resistomes. In summary, our study provides a comprehensive overview of resistance profiles and genome sequence features in ESBL-producing E. coli and highlights the possible role of sheep as antibiotic resistance gene disseminators into humans. IMPORTANCE Antimicrobial resistance (AMR), especially the simultaneous resistance to several antibiotics (multidrug resistance [MDR]), is one of the greatest threats to global public health in the 21st century. Among animals, chickens, pigs, and cattle are reservoirs of these pathogens worldwide. Nevertheless, there is a knowledge gap on ESBL-producing E. coli from small ruminants in China. This study is the largest and most comprehensive analysis of ESBL-producing E. coli isolates from sheep, including antibiotic resistance profiles, phylogenetic groups, serotypes, multilocus sequence types (MLST), insert sequences (IS), antibiotic resistance genes, disinfectant resistance genes, and heavy metal resistance genes. We recommend extending the surveillance of AMR of sheep-origin E. coli to prevent future public health risks.
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Affiliation(s)
- Xueliang Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Haoyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Zilian Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongqiang Miao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Chenyang Cao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Sa Xiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Haijin Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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13
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Sadek M, Ortiz de la Rosa JM, Ramadan M, Nordmann P, Poirel L. Molecular Characterization of Extended-Spectrum ß-lactamase Producers, Carbapenemase Producers, Polymyxin-Resistant, and Fosfomycin-Resistant Enterobacterales Among Pigs from Egypt. J Glob Antimicrob Resist 2022; 30:81-87. [PMID: 35667645 DOI: 10.1016/j.jgar.2022.05.022] [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] [Received: 03/15/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To perform the first prospective surveillance evaluating the occurrence of genes encoding colistin resistance, fosfomycin resistance, carbapenemase or extended-spectrum ß-lactamases (ESBLs) among Enterobacterial isolates recovered from the gut flora of pigs from Egypt. METHODS Between February and April 2020, eighty-one rectal swabs were collected from pigs in a slaughterhouse, Cairo, Egypt. Samples were screened for different resistance mechanisms using SuperPolymyxin, ChromID ESBL, SuperFOS, SuperCarba selective agar plates. Antimicrobial susceptibility testing was performed for all isolates using disk diffusion and broth microdilution techniques. PCR screening was performed for ESBLs, carbapenemases, mcr, and fosA genes. Mating-out assays, multilocus sequence typing analysis and plasmid typing were also performed. RESULTS A high prevalence of ESBLs, carbapenemases, fosfomycin and colistin resistance genes was evidenced among those isolates. The predominant ESBL identified was blaCTX-M-15, followed by blaCTX-M-9. We also identified blaNDM-5 and blaOXA-244. fosA3, fosA4, and fosA6 were identified in E. coli isolates. In addition, eleven MCR-1 producers were recovered. Notably, co-occurrence of ESBL genes and mcr or fosA genes was observed. MLST analysis revealed a high clonal diversity, ruling out the dissemination of one major clone. IncFIB-type was predominantly present among ESBL- and FosA-producers. The blaNDM-5 gene was carried on an IncX4-type, although the blaOXA-244 gene was chromosomally located. The mcr-1 gene was carried on a diversity of plasmids (IncI2, IncX4, and IncHI2). CONCLUSIONS These results raise serious public health concerns as Egyptian pig meat could serve as a reservoir for the antimicrobial resistance genes (ARGs) leading to worldwide dissemination.
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Affiliation(s)
- Mustafa Sadek
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt; INSERM European Unit (IAME), University of Fribourg, Fribourg
| | - José Manuel Ortiz de la Rosa
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME), University of Fribourg, Fribourg
| | | | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME), University of Fribourg, Fribourg; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg; Institute for Microbiology, University of Lausanne and University Hospital Centre, Lausanne, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME), University of Fribourg, Fribourg; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg.
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14
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Larsen SAH, Kyhl K, Baig S, Petersen A, av Steinum MR, Clemmensen S, Jensen E, á Steig T, Gaini S. Life-Threatening Necrotizing Pneumonia with Panton-Valentine Leukocidin-Producing, Methicillin-Sensitive Staphylococcus aureus in a Healthy Male Co-Infected with Influenza B. Infect Dis Rep 2021; 14:12-19. [PMID: 35076575 PMCID: PMC8788275 DOI: 10.3390/idr14010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
A previously healthy male was rushed into a hospital critically ill with confusion, sepsis, and acute respiratory distress syndrome only 43 h after having a normal chest X-ray and with blood samples showing only minimally elevated C-reactive protein. Two days earlier, the patient had returned to his home country, the Faroe Islands, from a 10-day work trip aboard a Scandinavian ship in Colombia. The diagnosis turned out to be an influenza B infection and necrotizing pneumonia with Panton-Valentine leukocidin (PVL)-producing methicillin-sensitive Staphylococcus aureus (MSSA). It was influenza season in Colombia but not in the Faroe Islands. The frequency of MSSA with PVL-encoding genes among pediatric infection patients is very low in the Kingdom of Denmark and Faroe Islands and very high in Colombia, and the frequency generally varies highly by region. The patient in this case now suffers severe sequelae from the infection. With this case, we would like to remind clinicians of this rare but severe condition. PVL-producing S. aureus pneumonia should be considered in critically ill, previously healthy patients, especially during influenza season and if the patient has been traveling in countries with high frequencies of PVL-producing S. aureus.
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Affiliation(s)
- Sara Agnete Hjort Larsen
- Medical Department, National Hospital Faroe Islands, 100 Tórshavn, Faroe Islands; (K.K.); (M.R.a.S.); (T.á.S.); (S.G.)
| | - Kasper Kyhl
- Medical Department, National Hospital Faroe Islands, 100 Tórshavn, Faroe Islands; (K.K.); (M.R.a.S.); (T.á.S.); (S.G.)
- Department of Cardiology, Copenhagen University Hospital, 2100 Rigshospitalet, Denmark
| | - Sharmin Baig
- Bacteria, Parasites & Fungi, Statens Serum Institute, 2300 Copenhagen, Denmark; (S.B.); (A.P.)
| | - Andreas Petersen
- Bacteria, Parasites & Fungi, Statens Serum Institute, 2300 Copenhagen, Denmark; (S.B.); (A.P.)
| | | | - Sissal Clemmensen
- Department of Radiology, National Hospital Faroe Islands, 100 Tórshavn, Faroe Islands;
| | - Elin Jensen
- Department of Intensive Care and Anesthesiology, National Hospital Faroe Islands, 100 Tórshavn, Faroe Islands;
| | - Torkil á Steig
- Medical Department, National Hospital Faroe Islands, 100 Tórshavn, Faroe Islands; (K.K.); (M.R.a.S.); (T.á.S.); (S.G.)
| | - Shahin Gaini
- Medical Department, National Hospital Faroe Islands, 100 Tórshavn, Faroe Islands; (K.K.); (M.R.a.S.); (T.á.S.); (S.G.)
- Infectious Diseases Research Unit, Odense University Hospital, University of Southern Denmark, 5000 Odense, Denmark
- Centre of Health Research, Department of Science and Technology, University of the Faroe Islands, 100 Tórshavn, Faroe Islands
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15
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Halimeh FB, Rafei R, Osman M, Kassem II, Diene SM, Dabboussi F, Rolain JM, Hamze M. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol 2021; 52:2043-2055. [PMID: 34524650 PMCID: PMC8441030 DOI: 10.1007/s42770-021-00573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.
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Affiliation(s)
- Fatima Bachir Halimeh
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14850, USA
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA
| | - Seydina M Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
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16
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Eriksen HB, Petersen A, Pedersen M, Overballe-Petersen S, Larsen AR, Holzknecht BJ. Possible misinterpretation of penicillin susceptibility in Staphylococcus aureus blood isolate due to in vitro loss of the blaZ gene. Eur J Clin Microbiol Infect Dis 2021; 41:163-167. [PMID: 34529167 DOI: 10.1007/s10096-021-04344-w] [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: 06/01/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
We describe a case of recurrent catheter-related blood stream infections (BSI) with Staphylococcus aureus, in which the first isolate tested susceptible to penicillin, while subsequent isolates were resistant. Phenotypic susceptibility correlated with the absence/presence of the blaZ gene. The in vitro stability of penicillin resistance was investigated by subculturing single colonies. In two out of five colonies, phenotypical resistance was lost after a single subculture, which correlated with loss of the blaZ gene. This in vitro phenomenon probably resulted in a very major error in the microbiology report of the first BSI, where penicillin had been recommended as treatment.
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Affiliation(s)
- Helle Brander Eriksen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Borgmester Ib Juuls Vej 52, 5., 2730, Copenhagen, Herlev, Denmark.
| | - Andreas Petersen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Pedersen
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Søren Overballe-Petersen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance, Statens Serum Institut, Copenhagen, Denmark
| | - Barbara Juliane Holzknecht
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Borgmester Ib Juuls Vej 52, 5., 2730, Copenhagen, Herlev, Denmark
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17
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Rima M, Emeraud C, Bonnin RA, Gonzalez C, Dortet L, Iorga BI, Oueslati S, Naas T. Biochemical characterization of OXA-244, an emerging OXA-48 variant with reduced β-lactam hydrolytic activity. J Antimicrob Chemother 2021; 76:2024-2028. [PMID: 33993262 DOI: 10.1093/jac/dkab142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND OXA-48-producing Enterobacterales have widely disseminated globally with an increasing number of variants identified. Among them, OXA-244 is increasingly reported, despite detection difficulties. OBJECTIVES To determine the steady-state kinetic parameters of OXA-244. METHODS The blaOXA-244 gene was amplified, cloned into plasmids p-TOPO and pET41b+, and transformed into Escherichia coli TOP10 for MIC determination and E. coli BL21 DE3 for purification. Steady-state kinetic parameters and IC50s of clavulanic acid, tazobactam and NaCl were determined using purified OXA-244. Molecular modelling was also performed. RESULTS A reduction in MICs of temocillin and carbapenems was observed in E. coli expressing OXA-244 as compared with OXA-48. The kinetic parameters revealed a reduced carbapenemase activity of OXA-244 as compared with OXA-48, especially for imipenem, which was 10-fold lower. Similarly, catalytic efficiency (kcat/Km) was reduced by 4-fold and 20-fold for ampicillin and temocillin, respectively. Kinetic parameters for cephalosporins were, however, similar. Molecular modelling studies evidenced the key role of R214 in OXA-48, establishing salt bridges with D159 and with the carboxylate group of the R1 substituent of temocillin. These interactions are not possible with G214 in OXA-244, explaining the reduced affinity of temocillin for this enzyme. The R214G mutation in OXA-244 is also likely to induce changes in the active site's water network that would explain the decrease in the hydrolysis rate of carbapenems. CONCLUSIONS Our data confirm that the R214G mutation (present in OXA-244) results in reduced carbapenem- and temocillin-hydrolysing activity, confirming the crucial role of residue 214 in the hydrolysis of these substrates by OXA-48-like β-lactamases.
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Affiliation(s)
- Mariam Rima
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France
| | - Cecile Emeraud
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Camille Gonzalez
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Saoussen Oueslati
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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18
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Emeraud C, Girlich D, Bonnin RA, Jousset AB, Naas T, Dortet L. Emergence and Polyclonal Dissemination of OXA-244-Producing Escherichia coli, France. Emerg Infect Dis 2021; 27:1206-1210. [PMID: 33755001 PMCID: PMC8007313 DOI: 10.3201/eid2704.204459] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Since 2016, OXA-244-producing Escherichia coli has been increasingly isolated in France. We sequenced 97 OXA-244-producing E. coli isolates and found a wide diversity of sequence types and a high prevalence of sequence type 38. Long-read sequencing demonstrated the chromosomal location of blaOXA-244 inside the entire or truncated Tn51098.
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19
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Welker S, Boutin S, Miethke T, Heeg K, Nurjadi D. Emergence of carbapenem-resistant ST131 Escherichia coli carrying bla OXA-244 in Germany, 2019 to 2020. ACTA ACUST UNITED AC 2021; 25. [PMID: 33213685 PMCID: PMC7678038 DOI: 10.2807/1560-7917.es.2020.25.46.2001815] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The dissemination of carbapenem-producing Gram-negative bacteria is a major public health concern. We report the first detection of OXA-244-producing ST131 O16:H5 Escherichia coli in three patients from two tertiary hospitals in the south-west of Germany. OXA-244 is emerging in Europe. Because of detection challenges, OXA-244-producing E. coli may be under-reported. The emergence of carbapenem resistance in a globally circulating high-risk clone, such as ST131 E. coli is of clinical relevance and should be monitored closely.
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Affiliation(s)
- Sybille Welker
- Institute for Medical Microbiology and Hygiene, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Sébastien Boutin
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Miethke
- Institute for Medical Microbiology and Hygiene, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Klaus Heeg
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Nurjadi
- Medical Microbiology and Hygiene, Department of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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20
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Chudejova K, Kraftova L, Mattioni Marchetti V, Hrabak J, Papagiannitsis CC, Bitar I. Genetic Plurality of OXA/NDM-Encoding Features Characterized From Enterobacterales Recovered From Czech Hospitals. Front Microbiol 2021; 12:641415. [PMID: 33633720 PMCID: PMC7900173 DOI: 10.3389/fmicb.2021.641415] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/20/2021] [Indexed: 01/24/2023] Open
Abstract
The aim of this study was to characterize four Enterobacterales co-producing NDM- and OXA-48-like carbapenemases from Czech patients with travel history or/and previous hospitalization abroad. Klebsiella pneumoniae isolates belonged to “high risk” clones ST147, ST11, and ST15, while the Escherichia coli isolate was assigned to ST167. All isolates expressed resistance against most β-lactams, including carbapenems, while retaining susceptibility to colistin. Furthermore, analysis of WGS data showed that all four isolates co-produced OXA-48- and NDM-type carbapenemases, in different combinations (Kpn47733: blaNDM–5 + blaOXA–181; Kpn50595: blaNDM–1 + blaOXA–181; Kpn51015: blaNDM–1 + blaOXA–244; Eco52418: blaNDM–5 + blaOXA–244). In Kpn51015, the blaOXA–244 was found on plasmid p51015_OXA-244, while the respective gene was localized in the chromosomal contig of E. coli Eco52418. On the other hand, blaOXA–181 was identified on a ColKP3 plasmid in isolate Kpn47733, while a blaOXA–181-carrying plasmid being an IncX3-ColKP3 fusion was identified in Kpn50595. The blaNDM–1 gene was found on two different plasmids, p51015_NDM-1 belonging to a novel IncH plasmid group and p51015_NDM-1 being an IncFK1-FIB replicon. Furthermore, the blaNDM–5 was found in two IncFII plasmids exhibiting limited nucleotide similarity to each other. In both plasmids, the genetic environment of blaNDM–5 was identical. Finally, in all four carbapenemase-producing isolates, a diverse number of additional replicons, some of these associated with important resistance determinants, like blaCTX–M–15, arr-2 and ermB, were identified. In conclusion, this study reports the first description of OXA-244-producing Enterobacterales isolated from Czech hospitals. Additionally, our findings indicated the genetic plurality involved in the acquisition and dissemination of determinants encoding OXA/NDM carbapenemases.
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Affiliation(s)
- Katerina Chudejova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Lucie Kraftova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Vittoria Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Costas C Papagiannitsis
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia.,Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
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21
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First Report of Multidrug-Resistant Carbapenemase-Producing Bacteria Coharboring mcr-9 Associated with Respiratory Disease Complex in Pets: Potential of Animal-Human Transmission. Antimicrob Agents Chemother 2020; 65:AAC.01890-20. [PMID: 33139280 DOI: 10.1128/aac.01890-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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22
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Kremer K, Kramer R, Neumann B, Haller S, Pfennigwerth N, Werner G, Gatermann S, Schroten H, Eckmanns T, Hans JB. Rapid spread of OXA-244-producing Escherichia coli ST38 in Germany: insights from an integrated molecular surveillance approach; 2017 to January 2020. Euro Surveill 2020; 25:2000923. [PMID: 32613940 PMCID: PMC7331143 DOI: 10.2807/1560-7917.es.2020.25.25.2000923] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Annually, increasing numbers of OXA-244-producing Escherichia coli in 13 German federal states prompted us to initiate an outbreak investigation. Whole genome sequencing revealed that among 148 isolates analysed, most belonged to sequence type 38 with 62 isolates forming a genetically distinct cluster. Although no epidemiological link could be identified between cases, ongoing investigations suggest non-healthcare associated transmission. A screening-PCR was developed facilitating early detection of ST38 cluster isolates to identify the source and transmission route.
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Affiliation(s)
- Katrin Kremer
- Robert Koch-Institute, Department for Infectious Disease Epidemiology, Berlin, Germany,Postgraduate Training for Applied Epidemiology (PAE), Robert Koch-Institute, Berlin, Germany,These authors contributed equally to this manuscript
| | - Rolf Kramer
- Robert Koch-Institute, Department for Infectious Disease Epidemiology, Berlin, Germany,These authors contributed equally to this manuscript
| | - Bernd Neumann
- Robert Koch Institute, Division of Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| | - Sebastian Haller
- Robert Koch-Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
| | - Niels Pfennigwerth
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Ruhr University Bochum, Bochum, Germany
| | - Guido Werner
- Robert Koch Institute, Division of Nosocomial Pathogens and Antibiotic Resistance, Wernigerode, Germany
| | - Sören Gatermann
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Ruhr University Bochum, Bochum, Germany
| | - Horst Schroten
- Department of Pediatrics, Pediatric Infectious Diseases, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tim Eckmanns
- Robert Koch-Institute, Department for Infectious Disease Epidemiology, Berlin, Germany
| | - Jörg B Hans
- National Reference Centre for multidrug-resistant Gram-negative bacteria, Ruhr University Bochum, Bochum, Germany
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