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Schechner V, Levytskyi K, Shalom O, Yalek A, Adler A. A hospital-wide outbreak of IMI-17-producing Enterobacter ludwigii in an Israeli hospital. Antimicrob Resist Infect Control 2021; 10:166. [PMID: 34844659 PMCID: PMC8630898 DOI: 10.1186/s13756-021-01036-0] [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: 11/01/2020] [Accepted: 11/21/2021] [Indexed: 11/11/2022] Open
Abstract
Background To describe the course and intervention of an hospital-wide IMI-Producing Enterobacter ludwigii outbreak. Methods This was an outbreak interventional study, done at a tertiary care center in Tel-Aviv, Israel. Data was collected on the course of the outbreak and the demographic and clinical characteristics of all patients involved in the outbreak. The intervention measures included patients’ cohorting, contact isolation precautions, environmental cleaning and screening of contacts. The molecular features and phylogeny of outbreak-related isolates were studied by whole-genome based analysis. Results The outbreak included 34 patients that were colonized by IMI-Producing E. ludwigii and were identified in 24 wards throughout the hospital. Colonization was identified in the first 72 h of admission in 13/34 patients (38.2%). Most patients (91.2%) were admitted from home and had relatively low level of comorbidities. The majority of them (88%) had no recent use of invasive catheters and none had previous carriage of other multi-drug resistant bacteria. All available isolates harbored the blaIMI-17 allele and belonged to Sequence-Type 385. With the exception of two isolates, all isolates were closely related with less than a 20-SNP difference between them. Conclusions This outbreak had most likely originated in the community and subsequently disseminated inside our institution. More studies are required in order to elucidate the epidemiology of IMI-Producing E. ludwigii and the possible role of environmental sources in its dissemination.
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Affiliation(s)
- Vered Schechner
- Section of Epidemiology and Preventative Medicine, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, 6 Weizmann Street, 6423906, Tel-Aviv, Israel
| | - Katya Levytskyi
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Ohad Shalom
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Alexander Yalek
- Department of Pediatrics, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Amos Adler
- Sackler Faculty of Medicine, Tel-Aviv University, 6 Weizmann Street, 6423906, Tel-Aviv, Israel. .,Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.
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Multiplex Real-Time PCR Assay for Six Major Carbapenemase Genes. Pathogens 2021; 10:pathogens10030276. [PMID: 33804402 PMCID: PMC7999841 DOI: 10.3390/pathogens10030276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/08/2021] [Accepted: 02/26/2021] [Indexed: 11/17/2022] Open
Abstract
The global dissemination of carbapenemase-producing Enterobacteriaceae (CPE) is a major concern in public health. Due to the existence of the diversity of carbapenemases, development of an easily available, cost-effective multiplex detection assay for CPE is required worldwide. Using clinically available and reliable equipment, COBAS® z480 (Roche Diagnostics K.K., Tokyo, Japan), we developed a multiplex real-time PCR assay for the detection of two combinations of carbapenemases; first, blaNDM, blaKPC, and blaIMP (Set 1), and second, blaGES, blaOXA-48, and blaVIM (Set 2). We constructed standard curves for each carbapenemase gene using serial dilutions of DNA standards, then applied reference or clinical isolates with each carbapenemase gene to this assay. The multiplex assay showed satisfactory accuracy to detect CPE genes, with the correlation coefficients of greater than 0.99 for all genotypes. The assay appropriately differentiated the reference or clinical strains harboring each carbapenemase gene without cross reactivity. Lastly, the assay successfully detected multiple genes without false-positive reactions by applying six clinical isolates carrying both NDM and OXA-48-like carbapenemase genes. Major advantages of our assay include multiplicity, simple operation, robustness, and speed (1 h). We believe that the multiplex assay potentially contributes to early diagnosis of CPE with a diverse genetic background.
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Implementation and evaluation of a novel real-time multiplex assay for SARS-CoV-2: in-field learnings from a clinical microbiology laboratory. Pathology 2020; 52:754-759. [PMID: 32943228 PMCID: PMC7462582 DOI: 10.1016/j.pathol.2020.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
Abstract
The unprecedented scale of testing required to effectively control the coronavirus disease (COVID-19) pandemic has necessitated urgent implementation of rapid testing in clinical microbiology laboratories. To date, there are limited data available on the analytical performance of emerging commercially available assays for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and integration of these assays into laboratory workflows. Here, we performed a prospective validation study of a commercially available assay, the AusDiagnostics Coronavirus Typing (8-well) assay. Respiratory tract samples for SARS-CoV-2 testing were collected between 1 March and 25 March 2020. All positive samples and a random subset of negative samples were sent to a reference laboratory for confirmation. In total, 2673 samples were analysed using the Coronavirus Typing assay. The predominant sample type was a combined nasopharyngeal/throat swab (2640/2673; 98.8%). Fifty-four patients were positive for SARS-CoV-2 (2.0%) using the Coronavirus Typing assay; 53/54 (98.1%) positive results and 621/621 (100%) negative results were concordant with the reference laboratory. Compared to the reference laboratory gold standard, sensitivity of the Coronavirus Typing assay for SARS-CoV-2 was 100% (95% CI 93.2–100%), specificity 99.8% (95% CI 99.1–100%), positive predictive value 98.1% (95% CI 90.2–99.7%) and negative predictive value 100% (95% CI 99.4–100%). In many countries, standard regulatory requirements for the introduction of new assays have been replaced by emergency authorisations and it is critical that laboratories share their post-market validation experiences, as the consequences of widespread introduction of a suboptimal assay for SARS-CoV-2 are profound. Here, we share our in-field experience, and encourage other laboratories to follow suit.
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Cusack TP, Phimolsarnnousith V, Duangmala K, Phoumin P, Turton J, Hopkins KL, Woodford N, Shetty N, Stoesser N, Phan HTT, Dance DAB. Molecular characterization of carbapenem-resistant Escherichia coli and Acinetobacter baumannii in the Lao People's Democratic Republic. J Antimicrob Chemother 2020; 74:2810-2821. [PMID: 31167025 PMCID: PMC6736291 DOI: 10.1093/jac/dkz234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Tomas-Paul Cusack
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.,National Infection Service, Public Health England, London, UK
| | - Vilayouth Phimolsarnnousith
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Khuanta Duangmala
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Phonelavanh Phoumin
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Jane Turton
- National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- National Infection Service, Public Health England, London, UK
| | - Nandini Shetty
- National Infection Service, Public Health England, London, UK
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, UK
| | - Hang T T Phan
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, UK
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Basile K, Rahman H, Carter I, Donovan L, Kumar S, Tran T, Ko D, Alderson S, Sivaruban T, Eden JS, Rockett R, O'Sullivan MV, Sintchenko V, Chen SCA, Maddocks S, Dwyer DE, Kok J. Response. J Clin Virol 2020; 130:104484. [PMID: 32777760 PMCID: PMC7273136 DOI: 10.1016/j.jcv.2020.104484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 11/27/2022]
Affiliation(s)
- K Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia.
| | - H Rahman
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - I Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - L Donovan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - S Kumar
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - T Tran
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - D Ko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - S Alderson
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - T Sivaruban
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - J-S Eden
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - R Rockett
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - M V O'Sullivan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - V Sintchenko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - S C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - S Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - D E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead NSW 2145 Australia
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