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Marinelli TM, Dolan L, Jenkins F, Lee A, Davis RJ, Crawford S, Nield B, Ronnachit A, Van Hal SJ. The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19). Infect Control Hosp Epidemiol 2023; 44:1116-1120. [PMID: 36082784 DOI: 10.1017/ice.2022.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE We aimed to demonstrate the role of real-time, on-site, whole-genome sequencing (WGS) of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in the management of hospital outbreaks of coronavirus disease 2019 (COVID-19). DESIGN This retrospective study was undertaken at our institutions in Sydney, New South Wales, Australia, between July 2021 and April 2022. We included SARS-CoV-2 outbreaks due to SARS-CoV-2 δ (delta) and ο (omicron) variants. All unexpected SARS-CoV-2-positive cases identified within the hospital were managed by the infection control team. An outbreak was defined as 2 or more cases acquired on a single ward. We included only outbreaks with 2 or more suspected transmission events in which WGS was utilized to assist with outbreak assessment and management. RESULTS We studied 8 outbreaks involving 266 patients and 486 staff, of whom 73 (27.4%) and 39 (8.0%), respectively, tested positive for SARS-CoV-2 during the outbreak management. WGS was used to evaluate the source of the outbreak, to establish transmission chains, to highlight deficiencies in infection control practices, and to delineate between community and healthcare acquired infection. CONCLUSIONS Real-time, on-site WGS combined with epidemiologic assessment is a useful tool to guide management of hospital SARS-CoV-2 outbreaks. WGS allowed us (1) to establish likely transmission events due to personal protective equipment (PPE) breaches; (2) to detect inadequacies in infection control infrastructure including ventilation; and (3) to confirm multiple viral introductions during periods of high community SARS-CoV-2 transmission. Insights gained from WGS-guides outbreak management directly influenced policy including modifying PPE requirements, instituting routine inpatient SARS-CoV-2 surveillance, and confirmatory SARS-CoV-2 testing prior to placing patients in a cohort setting.
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Affiliation(s)
- Tina M Marinelli
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Leanne Dolan
- Infection Prevention and Control Unit, Royal Prince Alfred Hospital, Sydney, Australia
| | - Frances Jenkins
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Andie Lee
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Department of Medicine, The University of Sydney, Sydney, Australia
| | - Rebecca J Davis
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Department of Medicine, The University of Sydney, Sydney, Australia
| | - Simeon Crawford
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Blake Nield
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Amrita Ronnachit
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Department of Medicine, The University of Sydney, Sydney, Australia
| | - Sebastiaan J Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Department of Medicine, The University of Sydney, Sydney, Australia
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Henderson A, Cheng MP, Chew KL, Coombs GW, Davis JS, Grant JM, Gregson D, Giulieri SG, Howden BP, Lee TC, Nguyen V, Mora JM, Morpeth SC, Robinson JO, Tong SYC, Van Hal SJ. A multi-site, international laboratory study to assess the performance of penicillin susceptibility testing of Staphylococcus aureus. J Antimicrob Chemother 2023; 78:1499-1504. [PMID: 37071589 PMCID: PMC10232234 DOI: 10.1093/jac/dkad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/29/2023] [Indexed: 04/19/2023] Open
Abstract
OBJECTIVES There is clinical uncertainty over the optimal treatment for penicillin-susceptible Staphylococcus aureus (PSSA) infections. Furthermore, there is concern that phenotypic penicillin susceptibility testing methods are not reliably able to detect some blaZ-positive S. aureus. METHODS Nine S. aureus isolates, including six genetically diverse strains harbouring blaZ, were sent in triplicate to 34 participating laboratories from Australia (n = 14), New Zealand (n = 6), Canada (n = 12), Singapore (n = 1) and Israel (n = 1). We used blaZ PCR as the gold standard to assess susceptibility testing performance of CLSI (P10 disc) and EUCAST (P1 disc) methods. Very major errors (VMEs), major error (MEs) and categorical agreement were calculated. RESULTS Twenty-two laboratories reported 593 results according to CLSI methodology (P10 disc). Nineteen laboratories reported 513 results according to the EUCAST (P1 disc) method. For CLSI laboratories, the categorical agreement and calculated VME and ME rates were 85% (508/593), 21% (84/396) and 1.5% (3/198), respectively. For EUCAST laboratories, the categorical agreement and calculated VME and ME rates were 93% (475/513), 11% (84/396) and 1% (3/198), respectively. Seven laboratories reported results for both methods, with VME rates of 24% for CLSI and 12% for EUCAST. CONCLUSIONS The EUCAST method with a P1 disc resulted in a lower VME rate compared with the CLSI methods with a P10 disc. These results should be considered in the context that among collections of PSSA isolates, as determined by automated MIC testing, less than 10% harbour blaZ. Furthermore, the clinical relevance of phenotypically susceptible, but blaZ-positive S. aureus, remains unclear.
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Affiliation(s)
- Andrew Henderson
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Matthew P Cheng
- Department of Medicine, and Laboratory Medicine, McGill University Health Centre, Montreal, Canada
| | - Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Geoffrey W Coombs
- Department of Antimicrobial Resistance, and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, Australia
| | - Joshua S Davis
- Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
- Department of Infectious Diseases, John Hunter Hospital, Newcastle, Australia
| | - Jennifer M Grant
- Department of Medicine, Vancouver Coastal Health, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Dan Gregson
- Department of Pathology, Laboratory Medicine, and Medicine, Cummings School of Medicine at The University of Calgary, Calgary, Canada
| | - Stefano G Giulieri
- Department of Microbiology, and Immunology, The University of Melbourne, Melbourne, Australia
- Victorian Infectious Diseases Services, The Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Hospital, Heidelberg, Australia
| | - Todd C Lee
- Department of Medicine, McGill University, Montreal, Canada
| | - Vi Nguyen
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jocelyn M Mora
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Susan C Morpeth
- Microbiology Laboratory, Middlemore Hospital (Counties Manukau Te Whatu Ora), Otahuhu, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - James O Robinson
- Department of Infectious Diseases, Royal Perth Hospital, Perth, Australia
- Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Services, The Royal Melbourne Hospital, Melbourne, Australia
| | - Sebastiaan J Van Hal
- Department of Microbiology, and Infectious Diseases, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Sydney, Australia
- School of Medicine, The University of Sydney, Sydney, Australia
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Foster CSP, Bull RA, Tedla N, Santiago F, Agapiou D, Adhikari A, Walker GJ, Shrestha LB, Van Hal SJ, Kim KW, Rawlinson WD. Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak. Viruses 2023; 15:v15020522. [PMID: 36851735 PMCID: PMC9966144 DOI: 10.3390/v15020522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. A 17-nucleotide frameshift-inducing deletion in ORF7a rapidly became represented at the consensus level (Delta-ORF7aΔ17del) in most Australian outbreak cases. Studies from early in the COVID-19 pandemic suggest that frameshift-inducing deletions in ORF7a do not persist for long in the population; therefore, Delta-ORF7aΔ17del genomes should have disappeared early in the Australian outbreak. In this study, we conducted a retrospective analysis of global Delta genomes to characterise the dynamics of Delta-ORF7aΔ17del over time, determined the frequency of all ORF7a deletions worldwide, and compared global trends with those of the Australian Delta outbreak. We downloaded all GISAID clade GK Delta genomes and scanned them for deletions in ORF7a. For each deletion we identified, we characterised its frequency, the number of countries it was found in, and how long it persisted. Of the 4,018,216 Delta genomes identified globally, 134,751 (~3.35%) possessed an ORF7a deletion, and ORF7aΔ17del was the most common. ORF7aΔ17del was the sole deletion in 28,014 genomes, of which 27,912 (~99.6%) originated from the Australian outbreak. During the outbreak, ~87% of genomes were Delta-ORF7aΔ17del, and genomes with this deletion were sampled until the outbreak's end. These data demonstrate that, contrary to suggestions early in the COVID-19 pandemic, genomes with frameshifting deletions in ORF7a can persist over long time periods. We suggest that the proliferation of Delta-ORF7aΔ17del genomes was likely a chance founder effect. Nonetheless, the frequency of ORF7a deletions in SARS-CoV-2 genomes worldwide suggests they might have some benefit for virus transmission.
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Affiliation(s)
- Charles S. P. Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- Correspondence:
| | - Rowena A. Bull
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicodemus Tedla
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Fernando Santiago
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - David Agapiou
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anurag Adhikari
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences, Lalitpur 44700, Province Bagmati, Nepal
| | - Gregory J. Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Lok Bahadur Shrestha
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sebastiaan J. Van Hal
- Department of Infectious Diseases and Microbiology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
- Central Clinical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Ki Wook Kim
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Women’s and Children’s Health, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - William D. Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- School of Biomedical Sciences, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- School of Women’s and Children’s Health, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW 2052, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
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Foster CS, Madden M, Chan R, Agapiou D, Bull RA, Rawlinson WD, Van Hal SJ. SARS-CoV-2 N-gene mutation leading to Xpert Xpress SARS-CoV-2 assay instability. Pathology 2022; 54:499-501. [PMID: 35440368 PMCID: PMC9012949 DOI: 10.1016/j.pathol.2022.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 11/21/2022]
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Gosbell IB, Van Hal SJ, Spencer PM, Chang Y, Collett PW. Comparison of adult patients hospitalised with pandemic (H1N1) 2009 influenza and seasonal influenza during the “PROTECT” phase of the pandemic response. Med J Aust 2010. [DOI: 10.5694/j.1326-5377.2010.tb03546.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Van Hal SJ, Frostis V, Miyakis S, Marriott D, Harkness J. Prevalence and significance of coagulase-negative staphylococci isolated from blood cultures in a tertiary hospital. ACTA ACUST UNITED AC 2008; 40:551-4. [PMID: 18584546 DOI: 10.1080/00365540701877304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Blood cultures (BC) are the most important tool in the diagnosis of bloodstream infections. However, false positive results are associated with increased laboratory costs and inappropriate antibiotic use. In order to determine the prevalence and location of blood cultures contaminated with coagulase-negative staphylococci (CNS), we performed a retrospective analysis of all blood cultures performed at St. Vincent's Hospital, Sydney during a 6-month period. From a total of 4234 patients with BC collected, CNS was isolated from 109 patients (2.6%). 94% of all CNS isolates (101/109) were contaminants. In the emergency department (ED), CNS isolates were significantly more likely to be contaminants (62/63, p<0.02) compared with the rest of the hospital, representing a 3.3% patient BC contamination rate. Treatment for a contaminant with vancomycin was significantly more likely to occur in ward patients (14/28, p<0.01) compared to the rest of the hospital. Duration of therapy did not differ across the hospital. Strategies to reduce the numbers of contaminants should be directed at medical staff in ED. Inappropriate vancomycin therapy could be curtailed by greater clinical microbiology liaison and vancomycin stewardship.
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Affiliation(s)
- Sebastiaan J Van Hal
- Department of Microbiology and Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia.
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