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van Hal SJ, Jensen SO, Tong SYC, Bentley S, Holden MT. Unravelling the complex interplay between antibiotic consumption and adaptive changes in methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother 2024; 79:891-896. [PMID: 38412336 DOI: 10.1093/jac/dkae048] [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] [Received: 10/19/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
OBJECTIVES This study aims to elucidate the genomic dynamics driving the emergence of antimicrobial resistance (AMR), with a specific focus on the interplay between AMR and antimicrobial usage. METHODS We conducted a comprehensive analysis using a ST239 methicillin-resistant Staphylococcus aureus (MRSA) dataset over a continuous 12-year period from a single hospital. Genomic analyses were performed tracking the changes in MRSA populations, particularly the emergence of reduced vancomycin susceptibility, and assessing the impact of glycopeptide use on these emergence events. RESULTS Our findings reveal a significant correlation between hospital glycopeptide usage and the selection of MRSA strains with reduced vancomycin susceptibility. Genomic analyses provided insights into the molecular mechanisms driving resistance emergence, including the slowing of the molecular clock rate in response to heightened antimicrobial consumption. CONCLUSIONS In conclusion, this study the highlights the complex dynamics between AMR and antimicrobial use at the hospital level. The observed correlation between antimicrobial consumption and the development of less susceptible MRSA strains underscores the importance of antimicrobial stewardship programmes and the establishment of optimal consumption thresholds for mitigating AMR effectively.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Slade O Jensen
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Stephen Y C Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Stephen Bentley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew T Holden
- School of Medicine, University of St Andrews, St Andrews, Fife KY16 9TF, UK
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2
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Lee AS, Dolan L, Jenkins F, Crawford B, van Hal SJ. Active surveillance of carbapenemase-producing Enterobacterales using genomic sequencing for hospital-based infection control interventions. Infect Control Hosp Epidemiol 2024; 45:137-143. [PMID: 37702063 PMCID: PMC10877539 DOI: 10.1017/ice.2023.205] [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] [Received: 03/26/2023] [Revised: 06/12/2023] [Accepted: 07/30/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) is increasingly used to characterize hospital outbreaks of carbapenemase-producing Enterobacterales (CPE). However, access to WGS is variable and testing is often centralized, leading to delays in reporting of results. OBJECTIVE We describe the utility of a local sequencing service to promptly respond to facility needs over an 8-year period. METHODS The study was conducted at Royal Prince Alfred Hospital in Sydney, Australia. All CPE isolated from patient (screening and clinical) and environmental samples from 2015 onward underwent prospective WGS. Results were notified to the infection control unit in real time. When outbreaks were identified, WGS reports were also provided to senior clinicians and the hospital executive administration. Enhanced infection control interventions were refined based on the genomic data. RESULTS In total, 141 CPE isolates were detected from 123 patients and 5 environmental samples. We identified 9 outbreaks, 4 of which occurred in high-risk wards (intensive care unit and/or solid-organ transplant ward). The largest outbreak involved Enterobacterales containing an NDM gene. WGS detected unexpected links among patients, which led to further investigation of epidemiological data that uncovered the outpatient setting and contaminated equipment as reservoirs for ongoing transmission. Targeted interventions as part of outbreak management halted further transmission. CONCLUSIONS WGS has transitioned from an emerging technology to an integral part of local CPE control strategies. Our results show the value of embedding this technology in routine surveillance, with timely reports generated in clinically relevant timeframes to inform and optimize local control measures for greatest impact.
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Affiliation(s)
- Andie S. Lee
- Departments of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Leanne Dolan
- Infection Control Unit, Royal Prince Alfred Hospital, Sydney, Australia
| | - Frances Jenkins
- Department of Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Sebastiaan J. van Hal
- Departments of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
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3
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Jenkins F, Le T, Farhat R, Pinto A, Anzari A, Bonsall D, Golubchik T, Bowden R, Lee FJ, van Hal SJ. Validation of an HIV whole genome sequencing method for HIV drug resistance testing in an Australian clinical microbiology laboratory. J Med Virol 2023; 95:e29273. [PMID: 38050831 DOI: 10.1002/jmv.29273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023]
Abstract
Detection of HIV drug resistance (HIVDR) is vital to successful anti-retroviral therapy (ART). HIVDR testing to determine drug-resistance mutations is routinely performed in Australia to guide ART choice in newly diagnosed people living with HIV or in cases of treatment failure. In 2022, our clinical microbiology laboratory sought to validate a next-generation sequencing (NGS)-based HIVDR assay to replace the previous Sanger-sequencing (SS)-based ViroSeq. NGS solutions for HIVDR offer higher throughput, lower costs and higher sensitivity for variant detection. We sought to validate the previously described low-cost probe-based NGS method (veSEQ-HIV) for whole-genome recovery and HIVDR-testing in a diagnostic setting. veSEQ-HIV displayed 100% and 98% accuracy in major and minor mutation detection, respectively, and 100% accuracy of subtyping (provided > 1000 mapped reads were obtained). Pairwise comparison exhibited low inter-and intrarun variability across the whole-genome (Jaccard index [J] = 0.993; J = 0.972) and the Pol gene (J = 0.999; J = 0.999), respectively. veSEQ-HIV met all our pre-set criteria based on WHO recommendations and successfully replaced ViroSeq in our laboratory. Scaling-down veSEQ-HIV to a limited batch size and sequencing on Illumina iSeq. 100, allowed easy implementation of the assay into the workflow of a small sequencing laboratory with minimal staff and equipment and the ability to meet clinically relevant test turn-around times. As HIVDR-testing moves from SS- to NGS-based methods and new ART drugs come to market (particularly those with targets outside the Pol region), whole-genome recovery using veSEQ-HIV provides a robust, cost-effective and "future-proof" NGS method for HIVDR-testing.
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Affiliation(s)
- Frances Jenkins
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Thomas Le
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Rima Farhat
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Angie Pinto
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- The Kirby Institute, UNSW Australia, Sydney, Australia
| | - Azim Anzari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Department of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Advanced Genomics Facility, Melbourne, Australia
| | - Frederick J Lee
- Department of Clinical Immunology and Allergy, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Sebastiaan J van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
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4
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Stoler S, van Hal SJ, Chadban S, Le T, Torzillo P, Scarlato RM, Wyburn K, Perkins GB, Marinelli T. Protracted COVID-19 pneumonitis early post-ABO incompatible kidney transplantation: Management considerations and the role of whole genome sequencing. Nephrology (Carlton) 2023; 28:639-643. [PMID: 37635271 DOI: 10.1111/nep.14235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
We present the case of a recent ABO incompatible kidney transplant recipient with persistent SARS-CoV-2 infection and pneumonitis. Serial whole genome sequencing confirmed intra-host viral evolution, which was used as a surrogate to confirm active viral replication and support re-treatment with antivirals, late in the course of infection. A prolonged course of remdesivir combined with immunosuppression modulation resulted in successful clearance of virus and clinical improvement. The diagnostic process undertaken in this case provides a useful guide for other clinicians when approaching similar patients.
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Affiliation(s)
- Sara Stoler
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sebastiaan J van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Steve Chadban
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Kidney Node, Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Le
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred, Sydney, New South Wales, Australia
| | - Paul Torzillo
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Rose-Marie Scarlato
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Kate Wyburn
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Kidney Node, Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Griffith B Perkins
- Central and Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
- Immunology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - Tina Marinelli
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred, Sydney, New South Wales, Australia
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5
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Ouk V, Pham CD, Wi T, van Hal SJ, Lahra MM. The Enhanced Gonococcal Surveillance Programme, Cambodia. Lancet Infect Dis 2023; 23:e332-e333. [PMID: 37549683 DOI: 10.1016/s1473-3099(23)00479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/09/2023]
Affiliation(s)
- Vichea Ouk
- National Center for HIV/AIDS, Dermatology and Sexually Transmitted Diseases, Phnom Penh, Cambodia
| | - Cau Dinh Pham
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Teodora Wi
- Global HIV, Hepatitis and STI Programmes, WHO, Geneva Switzerland
| | - Sebastiaan J van Hal
- New South Wales Health Pathology, Microbiology, Royal Prince Alfred Hospital Camperdown, NSW, Australia
| | - Monica M Lahra
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, New South Wales Health Pathology, Microbiology, The Prince of Wales Hospital Randwick, NSW, Australia.
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6
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Whiley DM, Tickner JA, Kundu RL, Hogan TR, van Hal SJ, Lahra MM. Selection of Neisseria gonorrhoeae ceftriaxone resistance using doxycycline post-exposure prophylaxis. Lancet Infect Dis 2023:S1473-3099(23)00359-6. [PMID: 37321241 DOI: 10.1016/s1473-3099(23)00359-6] [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] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Affiliation(s)
- David M Whiley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Pathology Queensland Central Laboratory, Queensland Health, Brisbane, Queensland, Australia.
| | - Jacob A Tickner
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Ratan L Kundu
- World Health Organization Collaborating Centre for STI and AMR, New South Wales Health Pathology Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Tiffany R Hogan
- World Health Organization Collaborating Centre for STI and AMR, New South Wales Health Pathology Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, 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
| | - Monica M Lahra
- World Health Organization Collaborating Centre for STI and AMR, New South Wales Health Pathology Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, Australia; Faculty of Medicine, The University of New South Wales, Sydney, New South Wales, Australia
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7
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Tong SYC, Mora J, Bowen AC, Cheng MP, Daneman N, Goodman AL, Heriot GS, Lee TC, Lewis RJ, Lye DC, Mahar RK, Marsh J, McGlothlin A, McQuilten Z, Morpeth SC, Paterson DL, Price DJ, Roberts JA, Robinson JO, van Hal SJ, Walls G, Webb SA, Whiteway L, Yahav D, Davis JS. The Staphylococcus aureus Network Adaptive Platform Trial Protocol: New Tools for an Old Foe. Clin Infect Dis 2022; 75:2027-2034. [PMID: 35717634 PMCID: PMC9710697 DOI: 10.1093/cid/ciac476] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Indexed: 01/17/2023] Open
Abstract
Staphylococcus aureus bloodstream (SAB) infection is a common and severe infectious disease, with a 90-day mortality of 15%-30%. Despite this, <3000 people have been randomized into clinical trials of treatments for SAB infection. The limited evidence base partly results from clinical trials for SAB infections being difficult to complete at scale using traditional clinical trial methods. Here we provide the rationale and framework for an adaptive platform trial applied to SAB infections. We detail the design features of the Staphylococcus aureus Network Adaptive Platform (SNAP) trial that will enable multiple questions to be answered as efficiently as possible. The SNAP trial commenced enrolling patients across multiple countries in 2022 with an estimated target sample size of 7000 participants. This approach may serve as an exemplar to increase efficiency of clinical trials for other infectious disease syndromes.
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Affiliation(s)
- Steven Y C Tong
- Department of Infectious Diseases University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jocelyn Mora
- Department of Infectious Diseases University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Asha C Bowen
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Matthew P Cheng
- Divisions of Infectious Diseases and Medical Microbiology, McGill University Health Centre, Montreal, Canada
| | - Nick Daneman
- Division of Infectious Diseases, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - Anna L Goodman
- Medical Research Council Clinical Trials Unit, University College London, London, United Kingdom.,Department of Infection, St Thomas Hospital, Guy's and St Thomas NHS Foundation Trust, London, United Kingdom
| | - George S Heriot
- Department of Infectious Diseases University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Todd C Lee
- Clinical Practice Assessment Unit and Division of Infectious Diseases, McGill University, Montreal, Canada
| | - Roger J Lewis
- Berry Consultants, LLC, Austin, Texas, USA.,Department of Emergency Medicine, Harbor-UCLA Medical Center, Torrance, California, USA.,Department of Emergency Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - David C Lye
- National Centre for Infectious Diseases, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,Yong Loo Lin School of Medicine, Singapore.,Lee Kong Chian School of Medicine, Singapore
| | - Robert K Mahar
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Australia.,Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Parkville, Australia
| | - Julie Marsh
- Telethon Kids Institute, Perth Children's Hospital, Perth, Australia
| | | | - Zoe McQuilten
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia.,Department of Haematology, Monash Health, Melbourne, Australia
| | - Susan C Morpeth
- Department of Infectious Diseases, Middlemore Hospital, Auckland, New Zealand
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - David J Price
- Department of Infectious Diseases University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Australia
| | - Jason A Roberts
- University of Queensland Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia.,Departments of Pharmacy and Intensive Care Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - J Owen Robinson
- Department of Infectious Diseases, Royal Perth Hospital, Perth, Australia.,Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Australia.,PathWest Laboratory Medicine, Perth, Australia.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases Royal Prince Alfred Hospital, Sydney, Australia.,School of Medicine, University of Sydney, Sydney, Australia
| | - Genevieve Walls
- Department of Infectious Diseases, Middlemore Hospital, Auckland, New Zealand
| | - Steve A Webb
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Australia
| | - Lyn Whiteway
- Freelance Health Consumer Advocate, Adealide, South Australia, Australia
| | - Dafna Yahav
- Infectious Diseases Unit, Rabin Medical Center, Beilinson Hospital, Petah-Tikva, Israel
| | - Joshua S Davis
- School of Medicine and Public Health and Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
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8
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Keighley C, Gall M, van Hal SJ, Halliday CL, Chai LYA, Chew KL, Biswas C, Slavin MA, Meyer W, Sintchenko V, Chen SCA. Whole Genome Sequencing Shows Genetic Diversity, as Well as Clonal Complex and Gene Polymorphisms Associated with Fluconazole Non-Susceptible Isolates of Candida tropicalis. J Fungi (Basel) 2022; 8:jof8090896. [PMID: 36135621 PMCID: PMC9505729 DOI: 10.3390/jof8090896] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
Resistance to azoles in Candida tropicalis is increasing and may be mediated by genetic characteristics. Using whole genome sequencing (WGS), we examined the genetic diversity of 82 bloodstream C. tropicalis isolates from two countries and one ATCC strain in a global context. Multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogenies were generated. Minimum inhibitory concentrations (MIC) for antifungal agents were determined using Sensititre YeastOne YO10. Eleven (13.2%) isolates were fluconazole-resistant and 17 (20.5%) were classified as fluconazole-non susceptible (FNS). Together with four Canadian isolates, the genomes of 12 fluconazole-resistant (18 FNS) and 69 fluconazole-susceptible strains were examined for gene mutations associated with drug resistance. Fluconazole-resistant isolates contained a mean of 56 non-synonymous SNPs per isolate in contrast to 36 SNPs in fluconazole-susceptible isolates (interquartile range [IQR] 46−59 vs. 31−48 respectively; p < 0.001). Ten of 18 FNS isolates contained missense ERG11 mutations (amino acid substitutions S154F, Y132F, Y257H). Two echinocandin-non susceptible isolates had homozygous FKS1 mutations (S30P). MLST identified high genetic diversity with 61 diploid sequence types (DSTs), including 53 new DSTs. All four isolates in DST 773 were fluconazole-resistant within clonal complex 2. WGS showed high genetic variation in invasive C. tropicalis; azole resistance was distributed across different lineages but with DST 773 associated with in vitro fluconazole resistance.
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Affiliation(s)
- Caitlin Keighley
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology, Sydney Institute for Infectious Diseases, The University of Sydney, Westmead Hospital, Sydney, NSW 2145, Australia
- Correspondence: (C.K.); (M.G.)
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW 2145, Australia
- Correspondence: (C.K.); (M.G.)
| | - Sebastiaan J. van Hal
- Department of Infectious Diseases and Microbiology, New South Wales Health Pathology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW 2145, Australia
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Kean Lee Chew
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Department of Laboratory Medicine, National University Health System, Singapore 119074, Singapore
| | - Chayanika Biswas
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW 2145, Australia
| | - Monica A. Slavin
- Department of Infectious Diseases, National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Wieland Meyer
- Centre for Infectious Diseases and Microbiology, Sydney Institute for Infectious Diseases, The University of Sydney, Westmead Hospital, Sydney, NSW 2145, Australia
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Research and Education Network, Western Sydney Local Health District, Westmead Hospital, Westmead, NSW 2145, Australia
- Curtin Medical School, Curtin University, Bentley, WA 6102, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology, Sydney Institute for Infectious Diseases, The University of Sydney, Westmead Hospital, Sydney, NSW 2145, Australia
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Sharon C. A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology, Sydney Institute for Infectious Diseases, The University of Sydney, Westmead Hospital, Sydney, NSW 2145, Australia
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9
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Kazmer ST, Hartel G, Robinson H, Richards RS, Yan K, van Hal SJ, Chan R, Hind A, Bradley D, Zieschang F, Rawle DJ, Le TT, Reid DW, Suhrbier A, Hill MM. Pathophysiological Response to SARS-CoV-2 Infection Detected by Infrared Spectroscopy Enables Rapid and Robust Saliva Screening for COVID-19. Biomedicines 2022; 10:biomedicines10020351. [PMID: 35203562 PMCID: PMC8962262 DOI: 10.3390/biomedicines10020351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/10/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Fourier transform infrared (FTIR) spectroscopy provides a (bio)chemical snapshot of the sample, and was recently used in proof-of-concept cohort studies for COVID-19 saliva screening. However, the biological basis of the proposed technology has not been established. To investigate underlying pathophysiology, we conducted controlled infection experiments on Vero E6 cells in vitro and K18-hACE2 mice in vivo. Potentially infectious culture supernatant or mouse oral lavage samples were treated with ethanol or 75% (v/v) Trizol for attenuated total reflectance (ATR)-FTIR spectroscopy and proteomics, or RT-PCR, respectively. Controlled infection with UV-inactivated SARS-CoV-2 elicited strong biochemical changes in culture supernatant/oral lavage despite a lack of viral replication, determined by RT-PCR or a cell culture infectious dose 50% assay. Nevertheless, SARS-CoV-2 infection induced additional FTIR signals over UV-inactivated SARS-CoV-2 infection in both cell and mouse models, which correspond to aggregated proteins and RNA. Proteomics of mouse oral lavage revealed increased secretion of kallikreins and immune modulatory proteins. Next, we collected saliva from a cohort of human participants (n = 104) and developed a predictive model for COVID-19 using partial least squares discriminant analysis. While high sensitivity of 93.48% was achieved through leave-one-out cross-validation, COVID-19 patients testing negative on follow-up on the day of saliva sampling using RT-PCR was poorly predicted in this model. Importantly, COVID-19 vaccination did not lead to the misclassification of COVID-19 negatives. Finally, meta-analysis revealed that SARS-CoV-2 induced increases in the amide II band in all arms of this study and in recently published cohort studies, indicative of altered β-sheet structures in secreted proteins. In conclusion, this study reveals a consistent secretory pathophysiological response to SARS-CoV-2, as well as a simple, robust method for COVID-19 saliva screening using ATR-FTIR.
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Affiliation(s)
- Seth T. Kazmer
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
| | - Gunter Hartel
- Biostatistics Unit, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia;
| | - Harley Robinson
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
| | - Renee S. Richards
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
| | - Kexin Yan
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
| | - Sebastiaan J. van Hal
- New South Wales Health Pathology-Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (S.J.v.H.); (R.C.)
| | - Raymond Chan
- New South Wales Health Pathology-Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; (S.J.v.H.); (R.C.)
| | - Andrew Hind
- Agilent Technologies Australia, Mulgrave, VIC 3170, Australia; (A.H.); (D.B.); (F.Z.)
| | - David Bradley
- Agilent Technologies Australia, Mulgrave, VIC 3170, Australia; (A.H.); (D.B.); (F.Z.)
| | - Fabian Zieschang
- Agilent Technologies Australia, Mulgrave, VIC 3170, Australia; (A.H.); (D.B.); (F.Z.)
| | - Daniel J. Rawle
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
| | - Thuy T. Le
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
| | - David W. Reid
- Lung Inflammation & Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia;
- The Prince Charles Hospital, Chermside, QLD 4032, Australia
| | - Andreas Suhrbier
- Inflammation Biology Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (K.Y.); (D.J.R.); (T.T.L.); (A.S.)
- Australian Infectious Disease Research Centre, GVN Centre of Excellence, Brisbane, QLD 4029, Australia
| | - Michelle M. Hill
- Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.T.K.); (H.R.); (R.S.R.)
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
- Correspondence:
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10
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van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Pinholt M, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, Bowden R. The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis. Lancet Microbe 2022; 3:e133-e141. [PMID: 35146465 PMCID: PMC8810393 DOI: 10.1016/s2666-5247(21)00236-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups-A and B-corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. METHODS We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. FINDINGS We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. INTERPRETATION A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital. FUNDING Wellcome Trust.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia,Central Clinical School, University of Sydney, Sydney, NSW, Australia,Correspondence to: Sebastiaan J van Hal, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute, Madrid, Spain,Network Research Centre for Epidemiology and Public Health, Madrid, Spain
| | | | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North-Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA, USA
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway,Parasites and Microbes, Wellcome Sanger Institute, Saffron Walden, UK
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia,Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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11
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Pratama R, Beukers AG, McIver CJ, Keighley CL, Taylor PC, van Hal SJ. A vanA vancomycin-resistant Enterococcus faecium ST80 outbreak resulting from a single importation event. J Antimicrob Chemother 2021; 77:31-37. [PMID: 34718605 DOI: 10.1093/jac/dkab379] [Citation(s) in RCA: 1] [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] [Received: 05/10/2021] [Accepted: 09/24/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND A marked genotype shift among vancomycin-resistant Enterococcus faecium (VREfm) from vanB to vanA in Australia between 2011 and 2015 is a well-known phenomenon. It is hypothesized that this was caused by multiple independent clones emerging simultaneously in different settings and/or regions. OBJECTIVES To gain insights into the circumstances surrounding the shift from vanB to vanA VREfm in one Australian hospital. METHODS The genomes of 69 vanA VREfm isolates from St George Hospital collected between 2009 and 2018 were studied. An expansion of ST80 vanA VREfm was noted following a single introduction. ST80 isolates were thus further characterized using hybrid sequencing and contextualized through comparisons with other published Australian ST80 isolates. Phylogenies were constructed with plasmid sequences compared with the index isolate. RESULTS The 2011 expansion of ST80 vanA VREfm isolates in our institution originated from the 2009 index isolate, from a patient transferred from overseas. Phylogenetic analysis with other Australian ST80 vanA VREfm isolates showed that the 2011 expansion event was unique, with limited spread to adjacent local health districts. Plasmid analysis showed multiple variants, which can also be traced back to the 2009 isolate, consistent with ongoing plasmid adaptation over time. CONCLUSIONS These findings confirm an expansion event following a VREfm introduction event leading to a sustained clonal and plasmid outbreak over several years. Moreover, it demonstrates the complexity of countrywide replacement events. This study also highlights the use of hybrid sequencing in establishing an epidemiological relationship to the index isolate that was initially inapparent.
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Affiliation(s)
- Ryanbi Pratama
- Department of Microbiology, NSW Health Pathology, St George Hospital, Kogarah, Sydney, NSW 2217, Australia
| | - Alicia G Beukers
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, Sydney, NSW 2050, Australia
| | - Christopher J McIver
- Department of Microbiology, NSW Health Pathology, St George Hospital, Kogarah, Sydney, NSW 2217, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Caitlin L Keighley
- Department of Microbiology, NSW Health Pathology, St George Hospital, Kogarah, Sydney, NSW 2217, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Peter C Taylor
- Department of Microbiology, NSW Health Pathology, St George Hospital, Kogarah, Sydney, NSW 2217, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Camperdown, Sydney, NSW 2050, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
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12
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Drennan PG, Thoma Y, Barry L, Matthey J, Sivam S, van Hal SJ. Bayesian Forecasting for Intravenous Tobramycin Dosing in Adults With Cystic Fibrosis Using One Versus Two Serum Concentrations in a Dosing Interval. Ther Drug Monit 2021; 43:505-511. [PMID: 33941739 DOI: 10.1097/ftd.0000000000000900] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/05/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Intravenous tobramycin treatment requires therapeutic drug monitoring (TDM) to ensure safety and efficacy when used for prolonged treatment, as in infective exacerbations of cystic fibrosis. The 24-hour area under the concentration-time curve (AUC24) is widely used to guide dosing; however, there remains variability in practice around methods for its estimation. The objective of this study was to determine the potential for a sparse-sampling strategy using a single postinfusion tobramycin concentration and Bayesian forecasting to assess the AUC24 in routine practice. METHODS Adults with cystic fibrosis receiving once-daily tobramycin had paired concentrations measured 2 hours (c1) and 6 hours (c2) after the end of infusion as routine monitoring. AUC24 exposures were estimated using Tucuxi, a Bayesian forecasting application that incorporates a validated population pharmacokinetic model. Simulations were performed to estimate AUC24 using the full data set using c1 and c2, compared with estimates using depleted data sets (c1 or c2 only), with and without concentration data from earlier in the course. The agreement between each simulation condition and the reference was assessed graphically and numerically using the median difference (∆) AUC24 and (relative) root mean square error (rRMSE) as measures of bias and accuracy, respectively. RESULTS A total of 55 patients contributed 512 concentrations from 95 tobramycin courses and 256 TDM episodes. Single concentration methods performed well, with median ∆AUC24 <2 mg·h·L-1 and rRMSE of <15% for sequential c1 and c2 conditions. CONCLUSIONS Bayesian forecasting implemented in Tucuxi, using single postinfusion concentrations taken 2-6 hours after tobramycin administration, yield similar exposure estimates to more intensive (two-sample) methods and are suitable for routine TDM practice.
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Affiliation(s)
- Philip G Drennan
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, Australia
| | - Yann Thoma
- School of Management and Engineering Vaud (HEIG-VD), University of Applied Science Western Switzerland (HES-SO), Yverdon-les-Bains, Switzerland
| | - Lucinda Barry
- Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, Australia; and
| | - Johan Matthey
- School of Management and Engineering Vaud (HEIG-VD), University of Applied Science Western Switzerland (HES-SO), Yverdon-les-Bains, Switzerland
| | - Sheila Sivam
- Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, Australia; and
- University of Sydney Central Clinical School, University of Sydney, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, Australia
- University of Sydney Central Clinical School, University of Sydney, Australia
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13
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Lane CR, Sherry NL, Porter AF, Duchene S, Horan K, Andersson P, Wilmot M, Turner A, Dougall S, Johnson SA, Sait M, Gonçalves da Silva A, Ballard SA, Hoang T, Stinear TP, Caly L, Sintchenko V, Graham R, McMahon J, Smith D, Leong LEX, Meumann EM, Cooley L, Schwessinger B, Rawlinson W, van Hal SJ, Stephens N, Catton M, Looker C, Crouch S, Sutton B, Alpren C, Williamson DA, Seemann T, Howden BP. Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study. Lancet Public Health 2021; 6:e547-e556. [PMID: 34252365 PMCID: PMC8270762 DOI: 10.1016/s2468-2667(21)00133-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia. METHODS In this observational, genomic epidemiological study, we did genomic sequencing of all laboratory-confirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK. FINDINGS Between Jan 25, 2020, and Jan 31, 2021, there were 20 451 laboratory-confirmed cases of COVID-19 in Victoria, Australia, of which 15 431 were submitted for sequencing, and 11 711 met all quality control metrics and were included in our analysis. We identified 595 genomic clusters, with a median of five cases per cluster (IQR 2-11). Overall, samples from 11 503 (98·2%) of 11 711 cases clustered with another sample in Victoria, either within a genomic cluster or transmission network. Genomic analysis revealed that 10 426 cases, including 10 416 (98·4%) of 10 584 locally acquired cases, diagnosed during the second wave (between June and October, 2020) were derived from a single incursion from hotel quarantine, with the outbreak lineage (transmission network G, lineage D.2) rapidly detected in other Australian states and territories. Phylodynamic analyses indicated that the epidemic growth rate of the outbreak lineage in Victoria during the initial growth phase (samples collected between June 4 and July 9, 2020; 47·4 putative transmission events, per branch, per year [1/years; 95% credible interval 26·0-85·0]), was similar to that of other reported variants, such as B.1.1.7 in the UK (mean approximately 71·5 1/years). Strict interventions were implemented, and the outbreak lineage has not been detected in Australia since Oct 29, 2020. Subsequent cases represented independent international or interstate introductions, with limited local spread. INTERPRETATION Our study highlights how rapid escalation of clonal outbreaks can occur from a single incursion. However, strict quarantine measures and decisive public health responses to emergent cases are effective, even with high epidemic growth rates. Real-time genomic surveillance can alter the way in which public health agencies view and respond to COVID-19 outbreaks. FUNDING The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.
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Affiliation(s)
- Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ashleigh F Porter
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mathilda Wilmot
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Sally Dougall
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Sandra A Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Sydney, NSW, Australia,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Rikki Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Jamie McMahon
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - David Smith
- Department of Microbiology, PathWest Laboratory Medicine, QEII Medical Centre, Perth, WA, Australia,School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Lex EX Leong
- Public Health Laboratory, Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA, Australia
| | - Ella M Meumann
- Territory Pathology, Royal Darwin Hospital, Darwin, NT, Australia,Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Louise Cooley
- Royal Hobart Hospital, Hobart, TAS, Australia,School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | | | - William Rawlinson
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Infectious Disease and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nicola Stephens
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Mike Catton
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Clare Looker
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Simon Crouch
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Brett Sutton
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Charles Alpren
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia,Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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14
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Beukers AG, Newton P, Hudson B, Ross K, Gottlieb T, O'Sullivan M, Daley DA, Pang S, Coombs GW, van Hal SJ. A multicentre outbreak of ST45 MRSA containing deletions in the spa gene in New South Wales, Australia. J Antimicrob Chemother 2021; 75:1112-1116. [PMID: 32016400 DOI: 10.1093/jac/dkz560] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/01/2019] [Accepted: 12/16/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Early identification of MRSA by diagnostic medical microbiology laboratories enables improved antimicrobial choice and outcomes. The Cepheid Xpert® MRSA/SA BC test rapidly identifies Staphylococcus aureus bloodstream infections through spa gene detection and methicillin resistance via mecA gene detection. Recent emergence of S. aureus with deletions in the spa gene has resulted in false-negative results for this test, leading to misidentification of infections with this organism, particularly MRSA ST45. OBJECTIVES To investigate the emergence and prevalence of ST45 MRSA in New South Wales (NSW), Australia. METHODS WGS read data from six NSW hospitals were collected for 131 ST45 MRSA isolates and analysed. RESULTS Of the 131 ST45 MRSA investigated, 88.5% (116/131) contained a deletion in the spa gene that appeared to have arisen once in approximately 2010 followed by clonal expansion. Given the successful establishment of this 'spa-deletion' MRSA clone, the Cepheid Xpert® MRSA/SA BC test became unreliable for confirming S. aureus bacteraemia in NSW. Subsequently, the algorithm used by this test has been updated and evaluated to take into account the presence of S. aureus with either a spa deletion or SCCmec target variations. CONCLUSIONS This study highlighted the applied use of WGS for assessing diagnostic assays and informing necessary changes to ensure the viability of the Cepheid Xpert® MRSA/SA BC test in the context of the new 'spa-deletion' MRSA clone. It demonstrated how continued surveillance through WGS can reveal evolutionary events that may impact diagnostic assays, allowing corrective modifications to be made in real time.
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Affiliation(s)
- Alicia G Beukers
- NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Peter Newton
- NSW Health Pathology, Microbiology, Wollongong Hospital, Wollongong, NSW, Australia
| | - Bernard Hudson
- NSW Health Pathology, Microbiology and Infectious Diseases, Royal North Shore Private Hospital, St Leonards, NSW, Australia
| | - Kimberly Ross
- NSW Health Pathology, Microbiology, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Thomas Gottlieb
- NSW Health Pathology, Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, NSW, Australia
| | - Matthew O'Sullivan
- NSW Health Pathology, Microbiology Department, Westmead Hospital, Westmead, NSW, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Perth, WA, Australia
| | - Stanley Pang
- Australian Group on Antimicrobial Resistance, Perth, WA, Australia.,Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
| | - Geoffrey W Coombs
- Australian Group on Antimicrobial Resistance, Perth, WA, Australia.,Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
| | - Sebastiaan J van Hal
- NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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15
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Beukers AG, Jenkins F, van Hal SJ. Centralised or Localised Pathogen Whole Genome Sequencing: Lessons Learnt From Implementation in a Clinical Diagnostic Laboratory. Front Cell Infect Microbiol 2021; 11:636290. [PMID: 34094996 PMCID: PMC8169965 DOI: 10.3389/fcimb.2021.636290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
Whole genome sequencing (WGS) has had widespread use in the management of microbial outbreaks in a public health setting. Current models encompass sending isolates to a central laboratory for WGS who then produce a report for various levels of government. This model, although beneficial, has multiple shortcomings especially for localised infection control interventions and patient care. One reason for the slow rollout of WGS in clinical diagnostic laboratories has been the requirement for professionally trained personal in both wet lab techniques and in the analysis and interpretation of data, otherwise known as bioinformatics. A further bottleneck has been establishment of regulations in order to certify clinical and technical validity and demonstrate WGS as a verified diagnostic test. Nevertheless, this technology is far superior providing information that would normally require several diagnostic tests to achieve. An obvious barrier to informed outbreak tracking is turnaround time and requires isolates to be sequenced in real-time to rapidly identify chains of transmission. One way this can be achieved is through onsite hospital sequencing with a cumulative analysis approach employed. Onsite, as opposed to centralised sequencing, has added benefits including the increased agility to combine with local infection control staff to iterate through the data, finding links that aide in understanding transmission chains and inform infection control strategies. Our laboratory has recently instituted a pathogen WGS service within a diagnostic laboratory, separate to a public health laboratory. We describe our experience, address the challenges faced and demonstrate the advantages of de-centralised sequencing through real-life scenarios.
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Affiliation(s)
- Alicia G Beukers
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Frances Jenkins
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,Faculty of Medicine, University of Sydney, Sydney, NSW, Australia
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16
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van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Westh HT, Howden BP, Malhotra-Kumar S, Werner G, Yanagihara K, Earl AM, Raven KE, Corander J, Bowden R. The global dissemination of hospital clones of Enterococcus faecium. Genome Med 2021; 13:52. [PMID: 33785076 PMCID: PMC8008517 DOI: 10.1186/s13073-021-00868-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood. METHODS A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled (n = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes. RESULTS Two main modes of genomic evolution continue to shape E. faecium: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes. CONCLUSIONS The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.
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Affiliation(s)
- Sebastiaan J. van Hal
- Department of Infectious Disesase and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW Australia
- University of Sydney, Sydney, NSW Australia
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrech, Utrecht, The Netherlands
| | | | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | | | - Kristin Hegstad
- Department of Microbiology and Infection Control, Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North-Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, UiT – the Arctic University of Norway, Tromsø, Norway
| | - Hendrik T. Westh
- MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Wilrijk, Belgium
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA USA
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052 Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Melbourne, Victoria Australia
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
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17
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Bull RA, Adikari TN, Ferguson JM, Hammond JM, Stevanovski I, Beukers AG, Naing Z, Yeang M, Verich A, Gamaarachchi H, Kim KW, Luciani F, Stelzer-Braid S, Eden JS, Rawlinson WD, van Hal SJ, Deveson IW. Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nat Commun 2020; 11:6272. [PMID: 33298935 PMCID: PMC7726558 DOI: 10.1038/s41467-020-20075-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/11/2020] [Indexed: 01/15/2023] Open
Abstract
Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, here we perform viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. We report that, despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >99% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.
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Affiliation(s)
- Rowena A Bull
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Thiruni N Adikari
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - James M Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jillian M Hammond
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Alicia G Beukers
- NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Zin Naing
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Malinna Yeang
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Andrey Verich
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Ki Wook Kim
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Fabio Luciani
- The Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sacha Stelzer-Braid
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity & Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Centre for Virus Research, Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - William D Rawlinson
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- NSW Health Pathology, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,Central Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia. .,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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18
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Biswas C, Wang Q, van Hal SJ, Eyre DW, Hudson B, Halliday CL, Mazsewska K, Kizny Gordon A, Lee A, Irinyi L, Heath CH, Chakrabarti A, Govender NP, Meyer W, Sintchenko V, Chen SCA. Genetic Heterogeneity of Australian Candida auris Isolates: Insights From a Nonoutbreak Setting Using Whole-Genome Sequencing. Open Forum Infect Dis 2020; 7:ofaa158. [PMID: 32500091 PMCID: PMC7255648 DOI: 10.1093/ofid/ofaa158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/29/2020] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequencing clustered Australian Candida auris isolates from sporadic cases within clade III. Case isolates were genomically distinct; however, unexpectedly, those from 1 case comprised 2 groups separated by >60 single nucleotide polymorphisms (SNPs) with no isolate being identical, in contrast to outbreaks where isolates from any 1 individual have differed by <3 SNPs. Multidrug resistance was absent. High within-host genetic heterogeneity should be considered when investigating C. auris infections.
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Affiliation(s)
- Chayanika Biswas
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, The University of Sydney, Sydney, Australia.,Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, The University of Sydney, Sydney, Australia.,Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia
| | - Sebastiaan J van Hal
- Deparment of Infectious Diseases and Microbiology, New South Wales Health Pathology, The Royal Prince Alfred Hospital, Sydney, Australia
| | - David W Eyre
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Bernard Hudson
- Department of Microbiology, Royal North Shore Hospital, New South Wales Health Pathology, Sydney, Australia
| | - Catriona L Halliday
- Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia.,Marie Bashir Institute for Emerging Infections and Biosecurity, The University of Sydney, Sydney, Australia
| | - Krystyna Mazsewska
- Marie Bashir Institute for Emerging Infections and Biosecurity, The University of Sydney, Sydney, Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School and the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Alice Kizny Gordon
- Department of Microbiology, Royal North Shore Hospital, New South Wales Health Pathology, Sydney, Australia
| | - Andie Lee
- Deparment of Infectious Diseases and Microbiology, New South Wales Health Pathology, The Royal Prince Alfred Hospital, Sydney, Australia
| | - Laszlo Irinyi
- Marie Bashir Institute for Emerging Infections and Biosecurity, The University of Sydney, Sydney, Australia.,Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Westmead Clinical School and the Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Christopher H Heath
- Department of Microbiology, Fiona Stanley Hospital Network, PathWest Laboratory Medicine, and the Department of Infectious Diseases, Fiona Stanley Hospital, Perth, Australia
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nelesh P Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service and Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Wieland Meyer
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, The University of Sydney, Sydney, Australia.,Department of Microbiology, Royal North Shore Hospital, New South Wales Health Pathology, Sydney, Australia.,Marie Bashir Institute for Emerging Infections and Biosecurity, The University of Sydney, Sydney, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, The University of Sydney, Sydney, Australia.,Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia.,Department of Microbiology, Royal North Shore Hospital, New South Wales Health Pathology, Sydney, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, The University of Sydney, Sydney, Australia.,Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia.,Department of Microbiology, Royal North Shore Hospital, New South Wales Health Pathology, Sydney, Australia.,Marie Bashir Institute for Emerging Infections and Biosecurity, The University of Sydney, Sydney, Australia
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19
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Tong SYC, Lye DC, Yahav D, Sud A, Robinson JO, Nelson J, Archuleta S, Roberts MA, Cass A, Paterson DL, Foo H, Paul M, Guy SD, Tramontana AR, Walls GB, McBride S, Bak N, Ghosh N, Rogers BA, Ralph AP, Davies J, Ferguson PE, Dotel R, McKew GL, Gray TJ, Holmes NE, Smith S, Warner MS, Kalimuddin S, Young BE, Runnegar N, Andresen DN, Anagnostou NA, Johnson SA, Chatfield MD, Cheng AC, Fowler VG, Howden BP, Meagher N, Price DJ, van Hal SJ, O’Sullivan MVN, Davis JS. Effect of Vancomycin or Daptomycin With vs Without an Antistaphylococcal β-Lactam on Mortality, Bacteremia, Relapse, or Treatment Failure in Patients With MRSA Bacteremia: A Randomized Clinical Trial. JAMA 2020; 323:527-537. [PMID: 32044943 PMCID: PMC7042887 DOI: 10.1001/jama.2020.0103] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is associated with mortality of more than 20%. Combining standard therapy with a β-lactam antibiotic has been associated with reduced mortality, although adequately powered randomized clinical trials of this intervention have not been conducted. OBJECTIVE To determine whether combining an antistaphylococcal β-lactam with standard therapy is more effective than standard therapy alone in patients with MRSA bacteremia. DESIGN, SETTING, AND PARTICIPANTS Open-label, randomized clinical trial conducted at 27 hospital sites in 4 countries from August 2015 to July 2018 among 352 hospitalized adults with MRSA bacteremia. Follow-up was complete on October 23, 2018. INTERVENTIONS Participants were randomized to standard therapy (intravenous vancomycin or daptomycin) plus an antistaphylococcal β-lactam (intravenous flucloxacillin, cloxacillin, or cefazolin) (n = 174) or standard therapy alone (n = 178). Total duration of therapy was determined by treating clinicians and the β-lactam was administered for 7 days. MAIN OUTCOMES AND MEASURES The primary end point was a 90-day composite of mortality, persistent bacteremia at day 5, microbiological relapse, and microbiological treatment failure. Secondary outcomes included mortality at days 14, 42, and 90; persistent bacteremia at days 2 and 5; acute kidney injury (AKI); microbiological relapse; microbiological treatment failure; and duration of intravenous antibiotics. RESULTS The data and safety monitoring board recommended early termination of the study prior to enrollment of 440 patients because of safety. Among 352 patients randomized (mean age, 62.2 [SD, 17.7] years; 121 women [34.4%]), 345 (98%) completed the trial. The primary end point was met by 59 (35%) with combination therapy and 68 (39%) with standard therapy (absolute difference, -4.2%; 95% CI, -14.3% to 6.0%). Seven of 9 prespecified secondary end points showed no significant difference. For the combination therapy vs standard therapy groups, all-cause 90-day mortality occurred in 35 (21%) vs 28 (16%) (difference, 4.5%; 95% CI, -3.7% to 12.7%); persistent bacteremia at day 5 was observed in 19 of 166 (11%) vs 35 of 172 (20%) (difference, -8.9%; 95% CI, -16.6% to -1.2%); and, excluding patients receiving dialysis at baseline, AKI occurred in 34 of 145 (23%) vs 9 of 145 (6%) (difference, 17.2%; 95% CI, 9.3%-25.2%). CONCLUSIONS AND RELEVANCE Among patients with MRSA bacteremia, addition of an antistaphylococcal β-lactam to standard antibiotic therapy with vancomycin or daptomycin did not result in significant improvement in the primary composite end point of mortality, persistent bacteremia, relapse, or treatment failure. Early trial termination for safety concerns and the possibility that the study was underpowered to detect clinically important differences in favor of the intervention should be considered when interpreting the findings. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02365493.
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Affiliation(s)
- Steven Y. C. Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - David C. Lye
- National Centre for Infectious Diseases, Singapore
- Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Dafna Yahav
- Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Archana Sud
- Nepean Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Kingswood, New South Wales, Australia
| | - J. Owen Robinson
- Royal Perth Hospital, Perth, Western Australia, Australia
- Fiona Stanley Hospital, Murdoch, Western Australia, Australia
- Pathwest Laboratory Medicine WA, Murdoch, Western Australia, Australia
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Jane Nelson
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Sophia Archuleta
- Division of Infectious Diseases, National University Hospital, Singapore
- Department of Medicine, National University of Singapore, Singapore
| | - Matthew A. Roberts
- Australasian Kidney Trials Network, University of Queensland, Brisbane, Australia
- Eastern Health Clinical School, Monash University, Box Hill, Victoria, Australia
| | - Alan Cass
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - David L. Paterson
- Centre for Clinical Research, University of Queensland, Herston, Australia
| | - Hong Foo
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, New South Wales, Australia
| | - Mical Paul
- Rambam Health Care Campus, Haifa, Israel
- Technion–Israel Institute of Technology, Haifa, Israel
| | - Stephen D. Guy
- Footscray Hospital, Western Health, Footscray, Victoria, Australia
| | | | - Genevieve B. Walls
- Department of Infectious Diseases, Middlemore Hospital, Auckland, New Zealand
| | - Stephen McBride
- Department of Infectious Diseases, Middlemore Hospital, Auckland, New Zealand
| | - Narin Bak
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Niladri Ghosh
- Wollongong Public Hospital, Wollongong, New South Wales, Australia
| | - Benjamin A. Rogers
- School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Monash Infectious Diseases, Monash Medical Centre, Clayton, Victoria, Australia
| | - Anna P. Ralph
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
- Division of Medicine, Royal Darwin Hospital, Tiwi, Northern Territory, Australia
| | - Jane Davies
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
- Division of Medicine, Royal Darwin Hospital, Tiwi, Northern Territory, Australia
| | - Patricia E. Ferguson
- Department of Infectious Diseases, Blacktown Hospital, Blacktown, New South Wales, Australia
| | - Ravindra Dotel
- Department of Infectious Diseases, Blacktown Hospital, Blacktown, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Genevieve L. McKew
- Department of Microbiology and Infectious Diseases, Concord Repatriation General Hospital, Concord, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Timothy J. Gray
- Department of Microbiology and Infectious Diseases, Concord Repatriation General Hospital, Concord, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Natasha E. Holmes
- Department of Infectious Diseases, Austin Health, Austin Centre for Infection Research, Heidelberg, Victoria, Australia
| | - Simon Smith
- Cairns Hospital, Cairns, Queensland, Australia
| | - Morgyn S. Warner
- The Queen Elizabeth Hospital, Woodville, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
| | - Barnaby E. Young
- National Centre for Infectious Diseases, Singapore
- Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore
| | - Naomi Runnegar
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Southern Clinical School, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - David N. Andresen
- St Vincent’s Public Hospital Sydney, Darlinghurst, New South Wales, Australia
- School of Medicine, University of Notre Dame, Darlinghurst, New South Wales, Australia
| | | | - Sandra A. Johnson
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark D. Chatfield
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
- Centre for Clinical Research, University of Queensland, Herston, Australia
| | - Allen C. Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
- Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina
| | - Benjamin P. Howden
- Department of Infectious Diseases, Austin Health, Austin Centre for Infection Research, Heidelberg, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Niamh Meagher
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, Royal Melbourne Hospital, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David J. Price
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, Royal Melbourne Hospital, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastiaan J. van Hal
- Department of Microbiology and Infectious Disease, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Matthew V. N. O’Sullivan
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- New South Wales Health Pathology, Westmead Hospital, Westmead, Australia
| | - Joshua S. Davis
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
- Department of Infectious Diseases, John Hunter Hospital, Newcastle, New South Wales, Australia
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20
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New D, Beukers AG, Kidd SE, Merritt AJ, Weeks K, van Hal SJ, Arthur I. Identification of multiple species and subpopulations among Australian clinical Sporothrix isolates using whole genome sequencing. Med Mycol 2020; 57:905-908. [PMID: 30500920 DOI: 10.1093/mmy/myy126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/28/2018] [Accepted: 11/02/2018] [Indexed: 12/25/2022] Open
Abstract
Whole genome sequencing (WGS) was used to demonstrate the wide genetic variability within Sporothrix schenckii sensu lato and establish that there are two main species of Sporothrix within Australian clinical isolates-S. schenckii sensu stricto and Sporothrix globosa. We also demonstrated southwest Western Australia contained genetically similar S. schenckii ss strains that are distinct from strains isolated in the eastern and northern states of Australia. Some genetic clustering by region was also noted for northern NSW, Queensland, and Northern Territory. Phylogenetic analysis of WGS data provided greater phylogenetic resolution compared to analysis of the calmodulin gene alone.
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Affiliation(s)
- David New
- PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Alicia G Beukers
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Sarah E Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, SA, Australia
| | - Adam J Merritt
- PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Kerry Weeks
- Mycology Laboratory (Microbiology Department), NSW Health Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Ian Arthur
- PathWest Laboratory Medicine WA, Nedlands, WA, Australia
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21
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Burgard M, Sandaradura I, van Hal SJ, Stacey S, Hennig S. Evaluation of Tobramycin Exposure Predictions in Three Bayesian Forecasting Programmes Compared with Current Clinical Practice in Children and Adults with Cystic Fibrosis. Clin Pharmacokinet 2019; 57:1017-1027. [PMID: 29134570 DOI: 10.1007/s40262-017-0610-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Bayesian forecasting (BF) methods for tobramycin dose individualisation has not seen widespread clinical adoption, despite being endorsed by clinical practice guidelines. Several freeware and commercial programmes using BF methods are available to support personalised dosing. This study evaluated exposure estimates, dose recommendations, and predictive performance compared with current clinical practice. METHODS Data from 105 patients (50 adults and 55 children) with cystic fibrosis who received intravenous tobramycin treatment and had paired concentration-time measurements were analysed using (1) log-linear regression analysis, and (2) three BF programmes: TDMx, InsightRX, and DoseMe. Exposure estimates and dose recommendations were compared using the Wilcoxon signed-rank test and Bland-Altman analysis. Predictive performance of BF programmes was compared based on bias and imprecision. RESULTS Median estimated tobramycin exposure with current clinical practice was significantly lower (87.8 vs. 92.5, 94.0 and 90.3 mg h l-1; p ≤ 0.01), hence median subsequent dose recommendations were significantly higher (10.1 vs. 9.4, 9.4 and 9.2 mg kg-1; p ≤ 0.01) compared with BF programmes. Furthermore, median relative dose-adjustment differences were higher in adults (> 10%) compared with children (4.4-7.8%), and differences in individual dose recommendations were > 20% on 19.1-27.4% of occasions. BF programmes showed low bias (< 7%) and imprecision (< 20%), and none of the programmes made consistently significantly different recommendations compared with each other. CONCLUSIONS On average, the predictions made by the BF programmes were similar, however substantial individual differences were observed for some patients. This suggests the need for detailed investigations of true tobramycin exposure.
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Affiliation(s)
- Marc Burgard
- School of Pharmacy, Pharmacy Australia Centre of Excellence, University of Queensland, 20 Cornwall Street, Woolloongabba, Brisbane, QLD, 4102, Australia
| | - Indy Sandaradura
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Sonya Stacey
- School of Pharmacy, Pharmacy Australia Centre of Excellence, University of Queensland, 20 Cornwall Street, Woolloongabba, Brisbane, QLD, 4102, Australia.,Pharmacy Department, Children's Health Queensland Hospital and Health Service, Lady Cilento Children's Hospital, South Brisbane, QLD, Australia
| | - Stefanie Hennig
- School of Pharmacy, Pharmacy Australia Centre of Excellence, University of Queensland, 20 Cornwall Street, Woolloongabba, Brisbane, QLD, 4102, Australia.
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22
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van Hal SJ, Beukers AG, Timms VJ, Ellem JA, Taylor P, Maley MW, Newton PJ, Ferguson JK, Lee A, Chen SCA, Sintchenko V. Relentless spread and adaptation of non-typeable vanA vancomycin-resistant Enterococcus faecium: a genome-wide investigation. J Antimicrob Chemother 2019; 73:1487-1491. [PMID: 29566173 DOI: 10.1093/jac/dky074] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/09/2018] [Indexed: 12/17/2022] Open
Abstract
Background VRE are prevalent among patients in ICUs. Non-typeable vanA VRE, due to loss of one of the genes used for MLST (pstS), have increased in Australia, suggestive of a new, hospital-acquired lineage. Objectives To understand the significance of this lineage and its transmission using WGS of strains isolated from patients in ICUs across New South Wales, Australia. Methods A total of 240 Enterococcus faecium isolates collected between February and May 2016, and identified by conventional PCR as vanA positive, were sequenced. Isolates originated from 12 ICUs in New South Wales, grouped according to six local health districts, and represented both rectal screening swab (n = 229) and clinical (n = 11) isolates. Results ST analysis revealed the absence of the pstS gene in 84.2% (202 of 240) of vanA isolates. Two different non-typeable STs were present based on different allelic backbone patterns. Loss of the pstS gene appeared to be the result of multiple recombination events across this region. Evidence for pstS-negative lineage spread across all six local health districts was observed suggestive of inter-hospital transmission. In addition, multiple outbreaks were detected, some of which were protracted and lasted for the duration of the study. Conclusions These findings confirmed the evolution, emergence and dissemination of non-typeable vanA E. faecium. This study has highlighted the utility of WGS when attempting to describe accurately the hospital-based pathogen epidemiology, which in turn will continue to inform optimal infection control measures necessary to halt the spread of this important nosocomial organism.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Alicia G Beukers
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Verlaine J Timms
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia
| | - Justin A Ellem
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia
| | - Peter Taylor
- Department of Microbiology, NSW Health Pathology, St George Hospital, Kogarah, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Michael W Maley
- School of Medical Sciences, University of New South Wales, Sydney, Australia.,Department of Microbiology and Infectious Diseases, South Western Sydney LHD and NSW Health Pathology - Liverpool, Sydney, Australia
| | - Peter J Newton
- NSW Health Pathology, Microbiology, Wollongong Hospital, Wollongong, NSW, Australia
| | - John K Ferguson
- Department of Microbiology, NSW Health Pathology, John Hunter Hospital, University of Newcastle, Newcastle, Australia
| | - Andie Lee
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Sydney, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
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23
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Nield B, Larsen SR, van Hal SJ. Clinical experience with new formulation SUBA®-itraconazole for prophylaxis in patients undergoing stem cell transplantation or treatment for haematological malignancies. J Antimicrob Chemother 2019; 74:3049-3055. [DOI: 10.1093/jac/dkz303] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/01/2019] [Accepted: 06/14/2019] [Indexed: 01/09/2023] Open
Abstract
AbstractBackgroundSUper BioAvailability-itraconazole (SUBA®-itraconazole) was introduced into Australia in April 2014 as a substitute for standard itraconazole on the basis of improved bioavailability, tolerance and interpatient variability. Shortly after its introduction, our centre converted to the novel formulation for mould prophylaxis in patients undergoing allogeneic HSCT, autologous HSCT or treatment for haematological malignancies with an intermediate/high risk of invasive fungal infection (IFI).MethodsA single-institution, investigator-initiated retrospective cohort study was conducted between June 2016 and April 2018 to assess therapeutic drug concentrations, safety and tolerability of a standard prophylactic dose of SUBA®-itraconazole.ResultsA total of 74 patients were assessed across 98 admissions with 178 measured itraconazole trough concentrations. The median duration of prophylaxis was 15.5 (1–59) days. No significant correlation was identified between trough concentrations and patient demographics including gender and weight. Drug concentrations were reduced by gastric acid suppression and diarrhoea. Therapeutic itraconazole trough concentrations (≥0.5 mg/L) were achieved at a median of 7 (95% CI = 6–8) days, with 87% of patients achieving therapeutic concentrations at day 14 (expected steady-state). One (1%) proven/probable IFI and 5 (5%) possible breakthrough IFIs were identified. Although adverse events were experienced by 42% of the cohort, only a single event was directly attributable to SUBA®-itraconazole, resulting in change of prophylactic agent.ConclusionsSUBA®-itraconazole achieved rapid therapeutic trough concentrations, was associated with low rates of IFI and was well tolerated in the study population. This formulation should be considered a realistic and safe first-line agent for the prevention of IFIs in those undergoing HSCT and intermediate/high-risk therapy for haematological malignancies.
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Affiliation(s)
- Blake Nield
- Department of Microbiology and Infectious Disease, Royal Prince Alfred Hospital, Sydney, Australia
| | - Stephen R Larsen
- Institute of Haematology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Disease, Royal Prince Alfred Hospital, Sydney, Australia
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24
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Abstract
Cronobacter sakazakii neonatal infections are often epidemiologically linked to the consumption of contaminated powdered infant formula. We describe a case resulting from consumption of contaminated expressed breast milk, as confirmed by whole-genome sequencing. This case highlights potential risks associated with storage and acquisition of expressed breast milk.
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van Hal SJ, Ip CLC, Ansari MA, Wilson DJ, Espedido BA, Jensen SO, Bowden R. Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance. Microb Genom 2018; 2. [PMID: 27713836 PMCID: PMC5049587 DOI: 10.1099/mgen.0.000048] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Enterococcus faecium, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E. faecium population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of E. faecium nosocomial infections and establishing routes of transmission. Several forms of the Tn1549-like element–vanB gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of in situ evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible E. faecium with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant E. faecium patient transmission events, underlining the need for careful consideration before modifying current E. faecium infection control strategies.
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Affiliation(s)
- Sebastiaan J van Hal
- 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,1 Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Camilla L C Ip
- 3 Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M Azim Ansari
- 4 Oxford Martin School, University of Oxford, 34 Broad Street, Oxford, UK
| | - Daniel J Wilson
- 5 Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bjorn A Espedido
- 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,6 Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - Slade O Jensen
- 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,6 Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - Rory Bowden
- 3 Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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26
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van Hal SJ, Steinig EJ, Andersson P, Holden MTG, Harris SR, Nimmo GR, Williamson DA, Heffernan H, Ritchie SR, Kearns AM, Ellington MJ, Dickson E, de Lencastre H, Coombs GW, Bentley SD, Parkhill J, Holt DC, Giffard PM, Tong SYC. Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia. Front Microbiol 2018; 9:1453. [PMID: 30038600 PMCID: PMC6047344 DOI: 10.3389/fmicb.2018.01453] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/11/2018] [Indexed: 11/13/2022] Open
Abstract
Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas. Results: Comparisons with other S. aureus genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973-1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome mec (SCCmec) IVa expanding and spreading to Australia's east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations. Conclusion: ST93 has a highly recombinant genome including portions derived from an early diverging S. aureus population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.
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Affiliation(s)
- Sebastiaan J. van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Eike J. Steinig
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia
- Australian Institute of Tropical Health and Medicine, Townsville, QLD, Australia
| | - Patiyan Andersson
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Matthew T. G. Holden
- School of Medicine, University of St. Andrews, Fife, United Kingdom
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Simon R. Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Graeme R. Nimmo
- Pathology Queensland Central Laboratory and Griffith University School of Medicine, Queensland Health, Brisbane, QLD, Australia
| | - Deborah A. Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen Heffernan
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - S. R. Ritchie
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Angela M. Kearns
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Matthew J. Ellington
- National Infection Service, Public Health England, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Elizabeth Dickson
- Scottish MRSA Reference Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, United States
| | - Geoffrey W. Coombs
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, Fiona Stanley Hospital, Perth, WA, Australia
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Deborah C. Holt
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Phillip M. Giffard
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Steven Y. C. Tong
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, and The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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27
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Holmes NE, Robinson JO, van Hal SJ, Munckhof WJ, Athan E, Korman TM, Cheng AC, Turnidge JD, Johnson PDR, Howden BP. Morbidity from in-hospital complications is greater than treatment failure in patients with Staphylococcus aureus bacteraemia. BMC Infect Dis 2018; 18:107. [PMID: 29506483 PMCID: PMC5838938 DOI: 10.1186/s12879-018-3011-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/22/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Various studies have identified numerous factors associated with poor clinical outcomes in patients with Staphylococcus aureus bacteraemia (SAB). A new study was created to provide deeper insight into in-hospital complications and risk factors for treatment failure. METHODS Adult patients hospitalised with Staphylococcus aureus bacteraemia (SAB) were recruited prospectively into a multi-centre cohort. The primary outcome was treatment failure at 30 days (composite of all-cause mortality, persistent bacteraemia, or recurrent bacteraemia), and secondary measures included in-hospital complications and mortality at 6- and 12-months. Data were available for 222 patients recruited from February 2011 to December 2012. RESULTS Treatment failure at 30-days was recorded in 14.4% of patients (30-day mortality 9.5%). Multivariable analysis predictors of treatment failure included age > 70 years, Pitt bacteraemia score ≥ 2, CRP at onset of SAB > 250 mg/L, and persistent fevers after SAB onset; serum albumin at onset of SAB, receipt of appropriate empiric treatment, recent healthcare attendance, and performing echocardiography were protective. 6-month and 12-month mortality were 19.1% and 24.2% respectively. 45% experienced at least one in-hospital complication, including nephrotoxicity in 19.5%. CONCLUSIONS This study demonstrates significant improvements in 30-day outcomes in SAB in Australia. However, we have identified important areas to improve outcomes from SAB, particularly reducing renal dysfunction and in-hospital treatment-related complications.
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Affiliation(s)
- Natasha E Holmes
- Department of Infectious Diseases, Austin Health, Austin Centre for Infection Research, PO Box 5555, Heidelberg, VIC, 3084, Australia. .,Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia.
| | - J Owen Robinson
- Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine-WA, Royal Perth Hospital, 197 Wellington Street, Perth, WA, 6000, Australia.,Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research, School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia.,Department of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - Wendy J Munckhof
- Infection Management Services, Princess Alexandra Hospital, 199 Ipswich Road, Woolloongabba, QLD, 4102, Australia.,Department of Medicine, University of Queensland, St Lucia, QLD, Australia
| | - Eugene Athan
- Department of Infectious Diseases, University Hospital Geelong, Barwon Health, Bellerine Street, Geelong, VIC, 3220, Australia.,Department of Medicine, Deakin University, Geelong, VIC, Australia.,Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Tony M Korman
- Department of Infectious Diseases, Monash Health, 246 Clayton Road, Clayton, VIC, 3168, Australia.,Department of Medicine, Monash University, Clayton, VIC, Australia
| | - Allen C Cheng
- Department of Infectious Diseases, Alfred Hospital, 55 Commercial Road, Prahran, VIC, 3181, Australia.,Department of Epidemiology and Preventive Medicine, Monash University, Prahran, VIC, Australia
| | - John D Turnidge
- Australian Commission on Safety and Quality in Health Care, Level 5, 255 Elizabeth Street, Sydney, NSW, 2000, Australia.,Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia
| | - Paul D R Johnson
- Department of Infectious Diseases, Austin Health, Austin Centre for Infection Research, PO Box 5555, Heidelberg, VIC, 3084, Australia.,Department of Medicine, University of Melbourne, Parkville, VIC, Australia.,Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Benjamin P Howden
- Department of Infectious Diseases, Austin Health, Austin Centre for Infection Research, PO Box 5555, Heidelberg, VIC, 3084, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia.,Department of Microbiology, Monash University, Clayton, VIC, Australia.,Microbiological Diagnostic Unit, Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC, 3000, Australia
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Menon V, Davis R, Shackel N, Espedido BA, Beukers AG, Jensen SO, van Hal SJ. Failure of daptomycin β-Lactam combination therapy to prevent resistance emergence in Enterococcus faecium. Diagn Microbiol Infect Dis 2017; 90:120-122. [PMID: 29195768 DOI: 10.1016/j.diagmicrobio.2017.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022]
Abstract
Daptomycin β-Lactam combination therapy offers "protection" against daptomycin non-susceptibility (DNS) development in Enterococcus faecium. We report failure of this strategy and the importance of source control. Mutations were detected in the LiaF and cls genes in DNS isolates. A single DNS isolate contained an unrecognized mutation, which requires confirmation.
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Affiliation(s)
- Vidthiya Menon
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Rebecca Davis
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nick Shackel
- University of NSW, Gastroenterology and Liver Disease Group Ingham Institute, Department of Gastroenterology, Liverpool Hospital
| | - Bjorn A Espedido
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Western Sydney University, Sydney, NSW, Australia
| | - Alicia G Beukers
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
| | - Slade O Jensen
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Western Sydney University, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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29
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Ghabrial R, Ananda A, van Hal SJ, Thompson EO, Larsen SR, Heydon P, Gupta R, Cherepanoff S, Rodriguez M, Halmagyi GM. Invasive Fungal Sinusitis Presenting as Acute Posterior Ischemic Optic Neuropathy. Neuroophthalmology 2017; 42:209-214. [PMID: 30042790 DOI: 10.1080/01658107.2017.1392581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022] Open
Abstract
Invasive fungal sinusitis causes painful orbital apex syndrome with ophthalmoplegia and visual loss; the mechanism is unclear. We report an immunocompromised patient with invasive fungal sinusitis in whom the visual loss was due to posterior ischaemic optic neuropathy, shown on diffusion-weighted MRI, presumably from fungal invasion of small meningeal-based arteries at the orbital apex. After intensive antifungal drugs, orbital exenteration and immune reconstitution, the patient survived, but we were uncertain if the exenteration helped. We suggest that evidence of acute posterior ischaemic optic neuropathy should be a contra-indication to the need for orbital exenteration in invasive fungal sinusitis.
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Affiliation(s)
- Rafat Ghabrial
- Ophthalmology Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Arjun Ananda
- Otorhinolaryngology Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Sebastiaan J van Hal
- Microbiology and Infectious Diseases Department, Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Stephen R Larsen
- Institute of Haematology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Peter Heydon
- Ophthalmology Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Ruta Gupta
- Anatomical Pathology Department, Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Michael Rodriguez
- Anatomical Pathology Department, St Vincent's Hospital, Sydney, Australia
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van Hal SJ, Espedido BA, Coombs GW, Howden BP, Korman TM, Nimmo GR, Gosbell IB, Jensen SO. Polyclonal emergence of vanA vancomycin-resistant Enterococcus faecium in Australia. J Antimicrob Chemother 2017; 72:998-1001. [PMID: 28031272 DOI: 10.1093/jac/dkw539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Objectives To investigate the genetic context associated with the emergence of vanA VRE in Australia. Methods The whole genomes of 18 randomly selected vanA -positive Enterococcus faecium patient isolates, collected between 2011 and 2013 from hospitals in four Australian capitals, were sequenced and analysed. Results In silico typing and transposon/plasmid assembly revealed that the sequenced isolates represented (in most cases) different hospital-adapted STs and were associated with a variety of different Tn 1546 variants and plasmid backbone structures. Conclusions The recent emergence of vanA VRE in Australia was polyclonal and not associated with the dissemination of a single 'dominant' ST or vanA -encoding plasmid. Interestingly, the factors contributing to this epidemiological change are not known and future studies may need to consider investigation of potential community sources.
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Affiliation(s)
- Sebastiaan J van Hal
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Björn A Espedido
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia.,PathWest Laboratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia
| | - Benjamin P Howden
- Austin Health, Melbourne, Vic., Australia.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Vic., Australia
| | | | | | - Iain B Gosbell
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,Sydney South Western Pathology Service, NSW Pathology, Sydney, NSW, Australia
| | - Slade O Jensen
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
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Abstract
MRSA bacteraemia (MRSAB), including infective endocarditis, carries a high mortality rate, with up to 50% of patients failing initial therapy with vancomycin and requiring salvage therapy. Persistent MRSAB can be difficult to successfully eliminate, especially when source control is not possible due to an irremovable focus or the bacteraemia still persists despite surgical intervention. Although vancomycin and daptomycin are the only two antibiotics approved by the US FDA for the treatment of patients with MRSAB as monotherapy, the employment of novel strategies is required to effectively treat patients with persistent MRSAB and these may frequently involve combination drug therapy. Treatment strategies that are reviewed in this manuscript include vancomycin combined with a β-lactam, daptomycin-based therapy, ceftaroline-based therapy, linezolid-based therapy, quinupristin/dalfopristin, telavancin, trimethoprim/sulfamethoxazole-based therapy and fosfomycin-based therapy. We recommend that combination antibiotic therapy be considered for use in MRSAB salvage treatment.
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Affiliation(s)
- Ravina Kullar
- Global Center for Scientific Affairs, Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ, USA
| | - George Sakoulas
- Division of Paediatric Pharmacology & Drug Discovery, University of California San Diego School of Medicine, La Jolla, CA, USA Sharp Rees-Stealy Medical Group, San Diego, CA, USA
| | - Stan Deresinski
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Sebastiaan J van Hal
- Department of Microbiology & Infectious Diseases, Royal Prince Alfred Hospital, Camperdown, Australia
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32
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Davis JS, Sud A, O'Sullivan MVN, Robinson JO, Ferguson PE, Foo H, van Hal SJ, Ralph AP, Howden BP, Binks PM, Kirby A, Tong SYC. Combination of Vancomycin and β-Lactam Therapy for Methicillin-ResistantStaphylococcus aureusBacteremia: A Pilot Multicenter Randomized Controlled Trial. Clin Infect Dis 2015; 62:173-180. [DOI: 10.1093/cid/civ808] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/28/2015] [Indexed: 01/12/2023] Open
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Espedido BA, Dimitrijovski B, van Hal SJ, Jensen SO. The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae. J Clin Pathol 2015; 68:835-8. [PMID: 26056157 DOI: 10.1136/jclinpath-2015-203044] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/20/2015] [Indexed: 11/04/2022]
Abstract
AIMS To characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis. METHODS Kp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype. RESULTS Importantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants. CONCLUSIONS This study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.
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Affiliation(s)
- Björn A Espedido
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Borce Dimitrijovski
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sebastiaan J van Hal
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Espedido BA, Jensen SO, van Hal SJ. Ceftaroline fosamil salvage therapy: an option for reduced-vancomycin-susceptible MRSA bacteraemia. J Antimicrob Chemother 2015; 70:797-801. [PMID: 25406295 DOI: 10.1093/jac/dku455] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
OBJECTIVES To examine the activity of ceftaroline against reduced-vancomycin-susceptible MRSA isolates. METHODS One-hundred and three MRSA blood culture isolates (predominantly ST239-MRSA-III), with varying vancomycin phenotypes, had their ceftaroline MICs determined by broth microdilution and MIC Evaluator strip (Oxoid-Thermo Fisher). Statistical analyses were performed that examined relationships with vancomycin and daptomycin MICs. Mutations in mecA were also examined. RESULTS All 103 isolates (including 60 heteroresistant vancomycin-intermediate Staphylococcus aureus/vancomycin-intermediate S. aureus) were susceptible to ceftaroline, with one isolate displaying heteroresistance that may be related to a mecA mutation. Higher ceftaroline MICs were associated with vancomycin-susceptible S. aureus isolates. CONCLUSIONS This study highlights that ceftaroline fosamil is an option for salvage therapy based on in vitro activity.
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Affiliation(s)
- Björn A Espedido
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Slade O Jensen
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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Holmes NE, Tong SYC, Davis JS, van Hal SJ. Treatment of methicillin-resistant Staphylococcus aureus: vancomycin and beyond. Semin Respir Crit Care Med 2015; 36:17-30. [PMID: 25643268 DOI: 10.1055/s-0034-1397040] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
There has been a welcome increase in the number of agents available for the treatment of methicillin-resistant Staphylococcus aureus (MRSA). Vancomycin remains an acceptable treatment option, with moves toward individualized dosing to a pharmacokinetic/pharmacodynamic (PK/PD) target. Numerous practicalities, however, would need to be resolved before implementation. Lipoglycopeptides as a class show excellent in vitro potency. Their long half-lives and complex PKs may preclude these agents being used in critically ill patients. Anti-MRSA cephalosporins provide great promise in the treatment of MRSA. These agents, despite broad-spectrum activity, should be reserved for patients with MRSA infections as it is likely that usage will be associated with increased rates of resistance. Daptomycin is currently the only antibiotic to have shown noninferiority to vancomycin in the treatment of MRSA bacteremia. The results of an open-labeled trial to address the superiority of daptomycin compared with vancomycin in reduced vancomycin susceptibility infections are eagerly anticipated. No drug to date has shown superiority to vancomycin in the treatment of MRSA infections with the possible exception of linezolid in hospital-acquired pneumonia (HAP), making linezolid an important option in the treatment of MRSA-proven HAP. Whether these strengths and features are agent or class specific are unclear but will likely be answered with the marketing of tedizolid. There are insufficient data to recommend either quinupristin/dalfopristin or tigecycline, as first line in the treatment of severe MRSA infections. These agents however remain options in patients with no other alternatives.
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Affiliation(s)
- Natasha E Holmes
- Department of Infectious Diseases, Austin Centre for Infection Research, Heidelberg, Victoria, Australia
| | - Steven Y C Tong
- Department of Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Joshua S Davis
- Department of Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, Australia
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Foo H, Chater M, Maley M, van Hal SJ. Glycopeptide use is associated with increased mortality in Enterococcus faecalis bacteraemia--authors' response. J Antimicrob Chemother 2014; 69:3166. [PMID: 25118271 DOI: 10.1093/jac/dku329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hong Foo
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, Liverpool, Sydney, NSW, Australia Antibiotic Resistance and Mobile Genetic Elements Group, Microbiology and Infectious Diseases Unit, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - Mathew Chater
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, Liverpool, Sydney, NSW, Australia
| | - Michael Maley
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, Liverpool, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, Liverpool, Sydney, NSW, Australia Antibiotic Resistance and Mobile Genetic Elements Group, Microbiology and Infectious Diseases Unit, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
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van Hal SJ, Steen JA, Espedido BA, Grimmond SM, Cooper MA, Holden MTG, Bentley SD, Gosbell IB, Jensen SO. In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale? J Antimicrob Chemother 2013; 69:363-7. [PMID: 24047554 DOI: 10.1093/jac/dkt354] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure. METHODS The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed. RESULTS Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure. CONCLUSIONS This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture 'bias' and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies.
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Affiliation(s)
- Sebastiaan J van Hal
- Antibiotic Resistance & Mobile Elements Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
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Espedido BA, Steen JA, Ziochos H, Grimmond SM, Cooper MA, Gosbell IB, van Hal SJ, Jensen SO. Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumoniae isolates: the resistome and in vivo evolution. PLoS One 2013; 8:e59920. [PMID: 23555831 PMCID: PMC3612081 DOI: 10.1371/journal.pone.0059920] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022] Open
Abstract
Whole genome sequencing was used to characterize the resistome of intensive care unit (ICU) outbreak-associated carbapenem-resistant K. pneumoniae isolates. Importantly, and of particular concern, the carbapenem-hydrolyzing β-lactamase gene blaOXA-48 and the extended-spectrum β-lactamase gene blaCTX-M-14, were identified on a single broad host-range conjugative plasmid. This represents the first report of blaOXA-48 in Australia and highlights the importance of resistance gene surveillance, as such plasmids can silently spread amongst enterobacterial populations and have the potential to drastically limit treatment options. Furthermore, the in vivo evolution of these isolates was also examined after 18 months of intra-abdominal carriage in a patient that transited through the ICU during the outbreak period. Reflecting the clonality of K. pneumoniae, only 11 single nucleotide polymorphisms (SNPs) were accumulated during this time-period and many of these were associated with genes involved in tolerance/resistance to antibiotics, metals or organic solvents, and transcriptional regulation. Collectively, these SNPs are likely to be associated with changes in virulence (at least to some extent) that have refined the in vivo colonization capacity of the original outbreak isolate.
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Affiliation(s)
- Björn A. Espedido
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, New South Wales, Australia
| | - Jason A. Steen
- Queensland Centre for Medical Genomics, University of Queensland, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Helen Ziochos
- Sydney South Western Pathology Service, NSW Pathology, New South Wales, Australia
| | - Sean M. Grimmond
- Queensland Centre for Medical Genomics, University of Queensland, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Iain B. Gosbell
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, New South Wales, Australia
- Sydney South Western Pathology Service, NSW Pathology, New South Wales, Australia
| | - Sebastiaan J. van Hal
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, New South Wales, Australia
- * E-mail: (SJvH); (SOJ)
| | - Slade O. Jensen
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, New South Wales, Australia
- * E-mail: (SJvH); (SOJ)
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van Hal SJ, Fowler VG. Is it time to replace vancomycin in the treatment of methicillin-resistant Staphylococcus aureus infections? Clin Infect Dis 2013; 56:1779-88. [PMID: 23511300 DOI: 10.1093/cid/cit178] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
For more than 4 decades, vancomycin has been the antibiotic of choice for methicillin-resistant Staphylococcus aureus (MRSA) infections. Recently, infections due to isolates with high but susceptible vancomycin minimum inhibitory concentrations have been associated with additional treatment failures and patient mortality. These poorer outcomes may in part be explained by the inability of attaining appropriate vancomycin levels in these patients. However, assumptions that these poor outcomes are solely due to failure to achieve optimal serum levels of vancomycin are premature. The availability of effective alternatives further erodes the position of vancomycin as first-line therapy. The emergence of resistance and cost considerations, however, favor a more measured approach when using alternative antimicrobials. Collectively, the current available data suggest that the optimal therapy for MRSA infections remains unclear. In the absence of further data, the Infectious Diseases Society of America guidelines remain relevant and inform clinicians of best practice for treating patients with MRSA infections.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Camperdown, Sydney, Australia.
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Blyth CC, Webb SAR, Kok J, Dwyer DE, van Hal SJ, Foo H, Ginn AN, Kesson AM, Seppelt I, Iredell JR. The impact of bacterial and viral co-infection in severe influenza. Influenza Other Respir Viruses 2012; 7:168-76. [PMID: 22487223 PMCID: PMC5006004 DOI: 10.1111/j.1750-2659.2012.00360.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Many questions remain concerning the burden, risk factors and impact of bacterial and viral co-infection in patients with pandemic influenza admitted to the intensive care unit (ICU). OBJECTIVES To examine the burden, risk factors and impact of bacterial and viral co-infection in Australian patients with severe influenza. PATIENTS/METHODS A cohort study conducted in 14 ICUs was performed. Patients with proven influenza A during the 2009 influenza season were eligible for inclusion. Demographics, risk factors, clinical data, microbiological data, complications and outcomes were collected. Polymerase chain reaction for additional bacterial and viral respiratory pathogens was performed on stored respiratory samples. RESULTS Co-infection was identified in 23·3-26·9% of patients with severe influenza A infection: viral co-infection, 3·2-3·4% and bacterial co-infection, 20·5-24·7%. Staphylococcus aureus was the most frequent bacterial co-infection followed by Streptococcus pneumoniae and Haemophilus influenzae. Patients with co-infection were younger [mean difference in age = 8·46 years (95% CI: 0·18-16·74 years)], less likely to have significant co-morbidities (32·0% versus 66·2%, P = 0·004) and less frequently obese [mean difference in body mass index = 6·86 (95% CI: 1·77-11·96)] compared to those without co-infection. CONCLUSIONS Bacterial or viral co-infection complicated one in four patients admitted to ICU with severe influenza A infection. Despite the co-infected patients being younger and with fewer co-morbidities, no significant difference in outcomes was observed. It is likely that co-infection contributed to a need for ICU admission in those without other risk factors for severe influenza disease. Empiric antibiotics with staphylococcal activity should be strongly considered in all patients with severe influenza A infection.
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Affiliation(s)
- Christopher C Blyth
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research ICPMR, Westmead Hospital, Sydney, NSW, Australia.
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Abstract
INTRODUCTION Influenza virus infections cause significant morbidity, and the unique ability of these viruses to undergo antigenic drift and shift means that it is critical for current laboratory assays to keep pace with these changes for accurate diagnosis. New subtypes have the potential to evolve into pandemics hence accurate virus subtyping is also essential. AREAS COVERED In this article, the authors review the current techniques available to detect influenza virus. EXPERT OPINION The biggest gains in improving on influenza diagnostics may lie in reappraising our current approach and optimizing all existing steps in influenza detection: pre-analytical, analytical, post-analytical. In addition, we must foster close collaboration between governments, surveillance networks and frontline diagnostic laboratories, and utilize advances in information technology to facilitate these interactions and to disseminate crucial information.
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Affiliation(s)
- Matthew C Gray
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service -Liverpool , Locked Bag 7090, Liverpool BC, NSW, 1871 , Australia +0061 2 9828 5124 ; +0061 2 9828 5129 ;
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van Hal SJ, Barbagiannakos T, Jones M, Wehrhahn MC, Mercer J, Chen D, Paterson DL, Gosbell IB. Methicillin-resistant Staphylococcus aureus vancomycin susceptibility testing: methodology correlations, temporal trends and clonal patterns. J Antimicrob Chemother 2011; 66:2284-7. [PMID: 21750101 DOI: 10.1093/jac/dkr280] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the correlation between various vancomycin MIC testing methodologies and explore the phenomenon of MIC creep. METHODS A total of 417 consecutive non-duplicate methicillin-resistant Staphylococcus aureus (MRSA) bloodstream isolates from Liverpool Hospital between 1997 and 2008 were retrieved. All isolates were classified using PFGE and underwent susceptibility testing for vancomycin using a standard Etest (AB bioMérieux, Solna, Sweden), Vitek2(®) (AST-P612; bioMérieux, Inc., Durham, NC, USA) and broth microdilution (BMD) performed as per the CLSI method. RESULTS Over the 12 years, 78% (n = 326) of the isolates were multiresistant MRSA (ST239-like by PFGE, where ST stands for sequence type). The correlation between MIC testing methods was moderate with Spearman's correlation coefficients of 0.50 for BMD versus Etest (P < 0.001), 0.33 for BMD versus Vitek2(®) (P < 0.001) and 0.42 for Etest versus Vitek2(®) (P < 0.001). In general, Etest results were 1 dilution higher while the Vitek2(®) results were 1 dilution lower than the BMD MIC result. MIC creep was dependent on the MIC testing method and the measurement used for analysis (geometric mean MIC versus modal MIC versus frequency analysis), with creep detected for Etest regression analysis only. In contrast, the proportion of isolates with a BMD MIC ≥2 mg/L decreased from 16% to 9% in the latter half of the study. Modal MIC was stable over the 12 years at 1 mg/L irrespective of MIC method used. CONCLUSIONS Correlation between vancomycin MIC methodologies remains suboptimal. Temporal MIC trends should be interpreted with caution as these are dependent on the testing methodology and the measurement used for analysis.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology & Infectious Diseases, Sydney South West Pathology Service-Liverpool, South Western Sydney Local Health Network, NSW, Sydney, Australia.
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van Hal SJ, Jones M, Gosbell IB, Paterson DL. Vancomycin heteroresistance is associated with reduced mortality in ST239 methicillin-resistant Staphylococcus aureus blood stream infections. PLoS One 2011; 6:e21217. [PMID: 21713004 PMCID: PMC3119693 DOI: 10.1371/journal.pone.0021217] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 05/23/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Despite hVISA infections being associated with vancomycin treatment failure, no previous study has been able to detect a mortality difference between heteroresistant vancomycin intermediate Staphylococcus aureus (hVISA) and vancomycin susceptible Staphylococcus aureus (VSSA) bloodstream infections (BSI). METHODOLOGY Consecutive methicillin-resistant S. aureus (MRSA) BSI episodes between 1996 and 2008 were reviewed. Patient demographics, clinical presentation, treatment and overall mortality at 30 days were extracted from the medical records. All isolates underwent vancomycin minimum inhibitory concentration (VMIC) testing by broth microdilution and Etest. hVISA was confirmed by population analysis profiling using the area under the curve method (PAP-AUC). PRINCIPAL FINDINGS 401 evaluable MRSA BSI episodes were identified over the 12 years. Of these, 46 (11.5%) and 2 (0.5%) were confirmed as hVISA and VISA by PAP-AUC respectively. hVISA predominantly occurred in ST239-like MRSA isolates with high VMIC (2 mg/L). Compared to VSSA, hVISA was associated with chronic renal failure (p<0.001), device related infections (haemodialysis access) (p<0.001) and previous vancomycin usage (p = 0.004). On multivariate analysis, independent predictors of mortality included age, presence of multiple co-morbidities, principal diagnosis, transit to ICU and severity of illness while infection related surgery and hVISA phenotype were associated with increased survival. CONCLUSIONS/SIGNIFICANCE The presence of hVISA is dependent on the appropriate interplay between host and pathogen factors. hVISA in ST239 MRSA is an independent predictor of survival. Whether these findings would be replicated across all MRSA clones is unknown and warrants further study.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service-Liverpool Hospital, Sydney, New South Wales, Australia.
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Jardine A, Conaty SJ, Cretikos MA, Su WY, Gosbell IB, van Hal SJ. Influenza A testing and detection in patients admitted through emergency departments in Sydney during winter 2009: implications for rational testing. Med J Aust 2010; 193:455-9. [PMID: 20955122 DOI: 10.5694/j.1326-5377.2010.tb03999.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 08/25/2010] [Indexed: 11/17/2022]
Abstract
AIM To examine factors associated with testing and detection of influenza A in patients admitted to hospital for acute care during the winter 2009 pandemic influenza outbreak. DESIGN, SETTING AND PARTICIPANTS Retrospective observational study of patients who were tested for influenza A after being admitted to hospital through emergency departments of the Sydney South West Area Health Service from 15 June to 30 August 2009. MAIN OUTCOME MEASURES The association of factors such as age, diagnosis at admission, hospital and week of admission with rates of testing and detection of influenza A. RESULTS 17,681 patients were admitted through nine emergency departments; 1344 (7.6%) were tested for influenza A, of whom 356 (26.5%) tested positive for pandemic influenza. Testing rates were highest in 0-4-year-old children, in the peak period of the outbreak, and in patients presenting with a febrile or respiratory illness. Positive influenza test results were common across a range of diagnoses, but occurred most frequently in children aged 10-14 years (64.3%) and in patients with a diagnosis at admission of influenza-like illness (59.1%). Using multivariate logistic regression, patients with a diagnosis at admission of fever or a respiratory illness at admission were most likely to be tested (odds ratios [ORs], 15 [95% CI, 11-21] and 17 [95% CI, 15-19], respectively). These diagnoses were stronger predictors of influenza testing than the peak testing week (Week 4; OR, 7.0 [95% CI, 3.8-13]) or any age group. However, diagnosis at admission and age were significant but weak predictors of a positive test result, and the strongest predictor of a positive test result was the peak epidemic week (Week 3; OR, 120 [95% CI, 27-490]). CONCLUSION The strongest predictor of a clinician's decision to test for influenza was the diagnosis at admission, but the strongest predictor of a positive test was the week of admission. A rational approach to influenza testing for patients who are admitted to hospital for acute care could include active tracking of influenza testing and detection rates, testing patients with a strong indication for antiviral treatment, and admitting only those who test negative to "clean" wards during the peak of an outbreak.
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Affiliation(s)
- Andrew Jardine
- Public Health Unit, Sydney South West Area Health Service, Sydney, NSW, Australia
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Blyth CC, Foo H, van Hal SJ, Hurt AC, Barr IG, McPhie K, Armstrong PK, Rawlinson WD, Sheppeard V, Conaty S, Staff M, Dwyer DE. Influenza outbreaks during World Youth Day 2008 mass gathering. Emerg Infect Dis 2010; 16:809-15. [PMID: 20409371 PMCID: PMC2953988 DOI: 10.3201/eid1605.091136] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Influenza outbreaks during mass gatherings have been rarely described, and detailed virologic assessment is lacking. An influenza outbreak occurred during World Youth Day in Sydney, Australia, July 2008 (WYD2008). We assessed epidemiologic data and respiratory samples collected from attendees who sought treatment for influenza-like illness at emergency clinics in Sydney during this outbreak. Isolated influenza viruses were compared with seasonal influenza viruses from the 2008 influenza season. From 100 infected attendees, numerous strains were identified: oseltamivir-resistant influenza A (H1N1) viruses, oseltamivir-sensitive influenza A (H1N1) viruses, influenza A (H3N2) viruses, and strains from both influenza B lineages (B/Florida/4/2006-like and B/Malaysia/2506/2004-like). Novel viruses were introduced, and pre-WYD2008 seasonal viruses were amplified. Viruses isolated at mass gatherings can have substantial, complex, and unpredictable effects on community influenza activity. Greater flexibility by public health authorities and hospitals is required to appropriately manage and contain these outbreaks.
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Chang YS, van Hal SJ, Spencer PM, Gosbell IB, 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; 192:90-3. [PMID: 20078410 DOI: 10.5694/j.1326-5377.2010.tb03426.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 11/09/2009] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To compare the patient characteristics, clinical features and outcomes of adult patients hospitalised with pandemic (H1N1) 2009 influenza and seasonal influenza. DESIGN AND SETTING Retrospective medical record review of all patients admitted to Liverpool Hospital, Sydney, with laboratory-confirmed influenza from the initiation of the "PROTECT" phase of the pandemic response on 17 June until the end of our study period on 31 July 2009. MAIN OUTCOME MEASURES Severity of illness; requirement for admission to the intensive care unit (ICU) and/or invasive ventilation; mortality. RESULTS Sixty-four adults were admitted to Liverpool Hospital with influenza, 48 with pandemic (H1N1) 2009 influenza and 16 with seasonal influenza. Thirteen patients were admitted to the ICU. Seven required invasive ventilation, with 2 patients requiring ongoing extracorporeal membrane oxygenation (ECMO). Five patients died (mortality rate, 8%) with two deaths occurring after the study period. Patients with pandemic (H1N1) 2009 influenza were younger and less likely to be immunocompromised than patients with seasonal influenza. However, the clinical features of pandemic (H1N1) 2009 influenza and seasonal influenza were similar. CONCLUSIONS Our findings show that the clinical course and outcomes of pandemic (H1N1) 2009 influenza virus are comparable to those of the current circulating seasonal influenza in Sydney. The high number of hospital admissions reflects a high incidence of disease in the community rather than an enhanced virulence of the novel pandemic influenza virus.
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Affiliation(s)
- Ya-Shu Chang
- Department of Respiratory Medicine, Liverpool Hospital, Sydney, NSW, Australia
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van Hal SJ, Foo H, Blyth CC, McPhie K, Armstrong P, Sintchenko V, Dwyer DE. Influenza outbreak during Sydney World Youth Day 2008: the utility of laboratory testing and case definitions on mass gathering outbreak containment. PLoS One 2009; 4:e6620. [PMID: 19727401 PMCID: PMC2731881 DOI: 10.1371/journal.pone.0006620] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 07/11/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Influenza causes annual epidemics and often results in extensive outbreaks in closed communities. To minimize transmission, a range of interventions have been suggested. For these to be effective, an accurate and timely diagnosis of influenza is required. This is confirmed by a positive laboratory test result in an individual whose symptoms are consistent with a predefined clinical case definition. However, the utility of these clinical case definitions and laboratory testing in mass gathering outbreaks remains unknown. METHODS AND RESULTS An influenza outbreak was identified during World Youth Day 2008 in Sydney. From the data collected on pilgrims presenting to a single clinic, a Markov model was developed and validated against the actual epidemic curve. Simulations were performed to examine the utility of different clinical case definitions and laboratory testing strategies for containment of influenza outbreaks. Clinical case definitions were found to have the greatest impact on averting further cases with no added benefit when combined with any laboratory test. Although nucleic acid testing (NAT) demonstrated higher utility than indirect immunofluorescence antigen or on-site point-of-care testing, this effect was lost when laboratory NAT turnaround times was included. The main benefit of laboratory confirmation was limited to identification of true influenza cases amenable to interventions such as antiviral therapy. CONCLUSIONS Continuous re-evaluation of case definitions and laboratory testing strategies are essential for effective management of influenza outbreaks during mass gatherings.
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Affiliation(s)
- Sebastiaan J van Hal
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, Sydney, New South Wales, Australia.
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van Hal SJ, Herring B, Deris Z, Wang B, Saksena NK, Dwyer DE. HIV-1 integrase polymorphisms are associated with prior antiretroviral drug exposure. Retrovirology 2009; 6:12. [PMID: 19203393 PMCID: PMC2649883 DOI: 10.1186/1742-4690-6-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 02/09/2009] [Indexed: 11/30/2022] Open
Abstract
In a recent summary of integrase sequences, primary integrase inhibitor mutations were rare. In a review of integrase inhibitor-naïve Australian HIV-1 sequences, primary mutations were not identified, although the accessory mutation G140S was detected. A link with previous antiretroviral therapy, intra-subtype B divergence across the integrase gene and transmission of integrase polymorphisms were also noted. Based on these findings, we would recommend ongoing surveillance of integrase mutations, and integrase region sequencing for patients prior to commencement of integrase inhibitors.
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Affiliation(s)
- Sebastiaan J van Hal
- Centre for Infectious Diseases and Microbiology, ICPMR Westmead Hospital, University of Sydney, Westmead 2145, NSW, Australia.
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Miyakis S, van Hal SJ, Barratt J, Stark D, Marriott D, Harkness J. Absence of human Bocavirus in bronchoalveolar lavage fluid of lung transplant patients. J Clin Virol 2008; 44:179-80. [PMID: 19083266 DOI: 10.1016/j.jcv.2008.10.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 10/24/2008] [Indexed: 11/25/2022]
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van Hal SJ, Hillman R, Stark DJ, Harkness JL, Marriott D. Lymphogranuloma venereum: an emerging anorectal disease in Australia. Med J Aust 2007; 187:309-10. [PMID: 17767440 DOI: 10.5694/j.1326-5377.2007.tb01251.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 05/30/2007] [Indexed: 11/17/2022]
Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, St Vincent's Hospital, and Sexually Transmitted Infections Research Centre, University of Sydney, NSW, Australia.
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