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McLure A, Smith JJ, Firestone SM, Kirk MD, French N, Fearnley E, Wallace R, Valcanis M, Bulach D, Moffatt CRM, Selvey LA, Jennison A, Cribb DM, Glass K. Source attribution of campylobacteriosis in Australia, 2017-2019. Risk Anal 2023; 43:2527-2548. [PMID: 37032319 PMCID: PMC10947381 DOI: 10.1111/risa.14138] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Campylobacter jejuni and Campylobacter coli infections are the leading cause of foodborne gastroenteritis in high-income countries. Campylobacter colonizes a variety of warm-blooded hosts that are reservoirs for human campylobacteriosis. The proportions of Australian cases attributable to different animal reservoirs are unknown but can be estimated by comparing the frequency of different sequence types in cases and reservoirs. Campylobacter isolates were obtained from notified human cases and raw meat and offal from the major livestock in Australia between 2017 and 2019. Isolates were typed using multi-locus sequence genotyping. We used Bayesian source attribution models including the asymmetric island model, the modified Hald model, and their generalizations. Some models included an "unsampled" source to estimate the proportion of cases attributable to wild, feral, or domestic animal reservoirs not sampled in our study. Model fits were compared using the Watanabe-Akaike information criterion. We included 612 food and 710 human case isolates. The best fitting models attributed >80% of Campylobacter cases to chickens, with a greater proportion of C. coli (>84%) than C. jejuni (>77%). The best fitting model that included an unsampled source attributed 14% (95% credible interval [CrI]: 0.3%-32%) to the unsampled source and only 2% to ruminants (95% CrI: 0.3%-12%) and 2% to pigs (95% CrI: 0.2%-11%) The best fitting model that did not include an unsampled source attributed 12% to ruminants (95% CrI: 1.3%-33%) and 6% to pigs (95% CrI: 1.1%-19%). Chickens were the leading source of human Campylobacter infections in Australia in 2017-2019 and should remain the focus of interventions to reduce burden.
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Affiliation(s)
- Angus McLure
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - James J. Smith
- Food Safety Standards and Regulation, Health Protection BranchQueensland HealthBrisbaneAustralia
- School of Biology and Environmental Science, Faculty of ScienceQueensland University of TechnologyBrisbaneAustralia
| | - Simon Matthew Firestone
- Melbourne Veterinary School, Faculty of ScienceThe University of MelbourneMelbourneAustralia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Nigel French
- Infectious Disease Research Centre, Hopkirk Research InstituteMassey UniversityPalmerston NorthNew Zealand
- New Zealand Food Safety Science and Research Centre, Hopkirk Research InstituteMassey UniversityPalmerston NorthNew Zealand
| | - Emily Fearnley
- Department for Health and WellbeingGovernment of South AustraliaAdelaideAustralia
| | - Rhiannon Wallace
- Agassiz Research and Development Centre, Agriculture and Agri‐Food CanadaAgassizCanada
| | - Mary Valcanis
- The Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health LaboratoryThe University of MelbourneMelbourneAustralia
| | - Dieter Bulach
- The Doherty Institute for Infection and ImmunityMelbourneAustralia
- Melbourne BioinformaticsThe University of MelbourneMelbourneAustralia
| | - Cameron R. M. Moffatt
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Linda A. Selvey
- School of Public Health, Faculty of MedicineThe University of QueenslandBrisbaneAustralia
| | - Amy Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland HealthBrisbaneAustralia
| | - Danielle M. Cribb
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Kathryn Glass
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
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Alcorn K, Gerrard J, Cochrane T, Graham R, Jennison A, Irwin PJ, Barbosa AD. First Report of Candidatus Mycoplasma haemohominis Infection in Australia Causing Persistent Fever in an Animal Carer. Clin Infect Dis 2021; 72:634-640. [PMID: 32006025 DOI: 10.1093/cid/ciaa089] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 09/24/2019] [Accepted: 01/30/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hemotropic mycoplasmas (hemoplasmas) infect animals and humans and can lead to clinical syndromes mainly characterized by hemolytic anemia. A novel pathogen, Candidatus Mycoplasma haemohominis, was recently associated with a case of human hemoplasmosis in Europe. Here we report the first detection of this pathogen in an Australian patient exhibiting persistent fever, hemolytic anemia, and pancytopenia over a 10-month period. METHODS After exhaustive negative testing for human infectious diseases, whole genome sequencing (WGS) was performed on the patient's bone marrow aspirate, using an Illumina NextSeq500 platform. Conventional polymerase chain reaction (PCR), followed by Sanger sequencing, was then performed on blood samples using novel Mycoplasma-specific primers targeting the 16S ribosomal RNA gene. In addition, a Mycoplasma-specific fluorescence in situ hybridization (FISH) assay was developed to differentiate Mycoplasma cells from other erythrocyte inclusions (eg, Pappenheimer and Howell-Jolly bodies) which are morphologically similar to bacterial cocci by light microscopy. RESULTS WGS analysis revealed that approximately 0.04% of the total number of unmapped reads to human genome corresponded to Mycoplasma species. A 1-kb Mycoplasma 16S fragment was successfully amplified by conventional PCR, and sequence analyses revealed 100% identity with Candidatus Mycoplasma haemohominis. FISH confirmed that several (approximately 2%) epierythrocytic inclusions initially observed by light microscopy corresponded to Mycoplasma cells. CONCLUSIONS This represents the second report of hemolytic anemia associated with hemoplasma infection in a human, and the first report of human hemoplasmosis in Australia. This study highlights the importance of new and emerging diagnostic approaches and need for further investigations on the epidemiology of Candidatus Mycoplasma haemohominis in Australia.
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Affiliation(s)
- Kylie Alcorn
- Department of Immunology and Infectious Diseases, Gold Coast Health Service, Gold Coast, Australia
| | - John Gerrard
- Department of Immunology and Infectious Diseases, Gold Coast Health Service, Gold Coast, Australia
| | - Tara Cochrane
- Department of Haematology, Gold Coast University Hospital and Griffiths University, Gold Coast, Australia
| | - Rikki Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Australia
| | - Amy Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Australia
| | - Peter J Irwin
- Vector- and Water-Borne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Amanda D Barbosa
- Vector- and Water-Borne Pathogens Research Group, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
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3
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Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, Sintchenko V, Wang Q, Rockett RJ, Timms VJ, Martinez E, Ballard S, Tomita T, Isles N, Horan KA, Pitchers W, Stinear TP, Williamson DA, Howden BP, Seemann T. Complete microbial genomes for public health in Australia and the Southwest Pacific. Microb Genom 2020; 6:mgen000471. [PMID: 33180013 PMCID: PMC8116684 DOI: 10.1099/mgen.0.000471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Irani Rathnayake
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Rikki M. Graham
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Verlaine J. Timms
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Kristy A. Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - William Pitchers
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Communicable Diseases Genomics Network (CDGN)
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
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Pintara A, Jennison A, Rathnayake IU, Mellor G, Huygens F. Core and Accessory Genome Comparison of Australian and International Strains of O157 Shiga Toxin-Producing Escherichia coli. Front Microbiol 2020; 11:566415. [PMID: 33013798 PMCID: PMC7498637 DOI: 10.3389/fmicb.2020.566415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/27/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australian STEC epidemiology differs from many other countries, as severe outbreaks and HUS cases appear to be more often associated with non-O157 serogroups. It is not known why Australian strains of O157 STEC might differ in virulence to international strains. Here we investigate the reduced virulence of Australian strains. Multiple genetic analyses were performed, including SNP-typing, to compare the core genomes of the Australian to the international isolates, and accessory genome analysis to determine any significant differences in gene presence/absence that could be associated with their phenotypic differences in virulence. The most distinct difference between the isolates was the absence of the stx2a gene in all Australian isolates, with few other notable differences observed in the core and accessory genomes of the O157 STEC isolates analyzed in this study. The presence of stx1a in most Australian isolates was another notable observation. Acquisition of stx2a seems to coincide with the emergence of highly pathogenic STEC. Due to the lack of other notable genotypic differences observed between Australian and international isolates characterized as highly pathogenic, this may be further evidence that the absence of stx2a in Australian O157 STEC could be a significant characteristic defining its mild virulence. Further work investigating the driving force(s) behind Stx prophage loss and acquisition is needed to determine if this potential exists in Australian O157 isolates.
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Affiliation(s)
- Alexander Pintara
- Centre for Immunology and Infection Control, Queensland University of Technology, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Amy Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, QLD, Australia
| | - Irani U. Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, QLD, Australia
| | - Glen Mellor
- CSIRO Animal, Food and Health Sciences, Archerfield, QLD, Australia
| | - Flavia Huygens
- Centre for Immunology and Infection Control, Queensland University of Technology, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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5
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Aye AMM, Bai X, Borrow R, Bory S, Carlos J, Caugant DA, Chiou CS, Dai VTT, Dinleyici EC, Ghimire P, Handryastuti S, Heo JY, Jennison A, Kamiya H, Tonnii Sia L, Lucidarme J, Marshall H, Putri ND, Saha S, Shao Z, Sim JHC, Smith V, Taha MK, Van Thanh P, Thisyakorn U, Tshering K, Vázquez J, Veeraraghavan B, Yezli S, Zhu B. Meningococcal disease surveillance in the Asia-Pacific region (2020): The global meningococcal initiative. J Infect 2020; 81:698-711. [PMID: 32730999 DOI: 10.1016/j.jinf.2020.07.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022]
Abstract
The degree of surveillance data and control strategies for invasive meningococcal disease (IMD) varies across the Asia-Pacific region. IMD cases are often reported throughout the region, but the disease is not notifiable in some countries, including Myanmar, Bangladesh and Malaysia. Although there remains a paucity of data from many countries, specific nations have introduced additional surveillance measures. The incidence of IMD is low and similar across the represented countries (<0.2 cases per 100,000 persons per year), with the predominant serogroups of Neisseria meningitidis being B, W and Y, although serogroups A and X are present in some areas. Resistance to ciprofloxacin is also of concern, with the close monitoring of antibiotic-resistant clonal complexes (e.g., cc4821) being a priority. Meningococcal vaccination is only included in a few National Immunization Programs, but is recommended for high-risk groups, including travellers (such as pilgrims) and people with complement deficiencies or human immunodeficiency virus (HIV). Both polysaccharide and conjugate vaccines form part of recommendations. However, cost and misconceptions remain limiting factors in vaccine uptake, despite conjugate vaccines preventing the acquisition of carriage.
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Affiliation(s)
| | - Xilian Bai
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester M13 9WZ, UK.
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester M13 9WZ, UK.
| | | | - Josefina Carlos
- University of the East Ramon Magsaysay Memorial Medical Center, Quezon City, Philippines
| | | | | | - Vo Thi Trang Dai
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | | | | | | | - Jung Yeon Heo
- Department of Infectious Diseases, Ajou University School of Medicine, Suwon, South Korea.
| | | | - Hajime Kamiya
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester M13 9WZ, UK.
| | - Helen Marshall
- Robinson Research Institute and department of Paediatrics, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.
| | - Nina Dwi Putri
- Dr Cipto Mangunkusumo National Central Hospital, Jakarta, Indonesia
| | - Senjuti Saha
- Child Health Research Foundation, Mohammadpur, Dhaka1207, Bangladesh.
| | - Zhujun Shao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | | | - Vinny Smith
- Meningitis Research Foundation, Bristol, UK.
| | | | - Phan Van Thanh
- Department of Microbiology and Immunology, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Usa Thisyakorn
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Kinley Tshering
- Jigme Dorji Wangchuck National Referral Hospital, Thimpu, Bhutan
| | - Julio Vázquez
- National Reference Laboratory for Meningococci, Institute of Health Carlos III, Spain.
| | | | - Saber Yezli
- Global Center for Mass Gatherings Medicine, Saudi Arabia
| | - Bingqing Zhu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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6
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Grigg S, Hogan D, Hosein FS, Johns D, Jennison A, Subedi S. A case of toxigenic, pharyngeal diphtheria in Australia. Med J Aust 2020; 213:64-65.e1. [PMID: 32227479 DOI: 10.5694/mja2.50566] [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: 11/17/2022]
Affiliation(s)
- Sarah Grigg
- Sunshine Coast Hospital and Health Service, Sunshine Coast, QLD
| | - David Hogan
- Sunshine Coast Hospital and Health Service, Sunshine Coast, QLD
| | | | - Dean Johns
- Forensic and Scientific Services, Brisbane, QLD
| | | | - Shradha Subedi
- Sunshine Coast Hospital and Health Service, Sunshine Coast, QLD
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7
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Hume A, Nimmo G, Ranasinghe A, Jennison A, Graham R. Characterisation of Staphylococcus capitis Bloodstream isolates from south-east Queensland neonatal units. Pathology 2020. [DOI: 10.1016/j.pathol.2020.01.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Huang B, Jennison A, Whiley D, McMahon J, Hewitson G, Graham R, De Jong A, Warrilow D. Illumina sequencing of clinical samples for virus detection in a public health laboratory. Sci Rep 2019; 9:5409. [PMID: 30931974 PMCID: PMC6443674 DOI: 10.1038/s41598-019-41830-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 08/08/2018] [Accepted: 01/31/2019] [Indexed: 11/29/2022] Open
Abstract
High-throughput sequencing (HTS) provides the opportunity, once a diagnostic result is obtained, to extract additional information from a virus-containing sample. Hence, it offers advantages over established quantitative amplification technology, such as quantitative PCR, particularly in a public health environment. At this early stage of its clinical application, there have been limited studies comparing HTS performance to that of the more established quantitative PCR technology for direct detection of viruses. In this pilot-scale study, we tested HTS with a range of viruses and sample types routinely encountered in a public health virology laboratory. In comparison with quantitative PCR, our HTS method was able to sensitively (92%) detect all viruses in any sample type with the exception of certain tissues. Moreover, sufficient nucleotide sequence information was obtained to enable genotyping of strains detected, thus providing additional useful epidemiological information. While HTS sensitivity may not yet match that of PCR, the added value through enhanced epidemiological data has considerable potential to enable real-time surveillance of circulating strains so as to facilitate rapid and appropriate response to outbreaks and virus zoonotic spillover events.
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Affiliation(s)
- Bixing Huang
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Amy Jennison
- Public Health Microbiology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - David Whiley
- Microbiology Division, Pathology Queensland Central Laboratory, Brisbane, Queensland, 4029, Australia.,Faculty of Medicine, University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, 4029, Australia
| | - Jamie McMahon
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Glen Hewitson
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Rikki Graham
- Public Health Microbiology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Amanda De Jong
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - David Warrilow
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia.
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Vesey D, Chapman P, Forde B, Roberts L, Bergh H, Jennison A, Beatson S, Harris P. Managing an outbreak of extended spectrum beta-lactamase (ESBL)-producing Klebsiella oxytoca in a special care nursery (SCN). Infect Dis Health 2018. [DOI: 10.1016/j.idh.2018.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Hurst T, Doidge M, Hajkowicz K, Harris P, Forde B, Bergh H, Jennison A, Roberts L, Allworth T, Nimmo G, Beatson S, Paterson D. Mastering resistant bacteria using whole genome sequencing. Infect Dis Health 2018. [DOI: 10.1016/j.idh.2018.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Whiley DM, Jennison A, Pearson J, Lahra MM. Genetic characterisation of Neisseria gonorrhoeae resistant to both ceftriaxone and azithromycin. The Lancet Infectious Diseases 2018; 18:717-718. [DOI: 10.1016/s1473-3099(18)30340-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/16/2018] [Indexed: 10/28/2022]
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12
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Shaban R, Maloney S, Gerrard J, Collignon P, Macbeth D, Cruickshank M, Hume A, Jennison A, Graham R, Bergh H, Wilson H, Derrington P. Outbreak of healthcare-associated Burkholderia cenocepacia bacteraemia and infection attributed to contaminated ‘sterile’ gel used for central line insertion under ultrasound guidance and other procedures. Infect Dis Health 2017. [DOI: 10.1016/j.idh.2017.09.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Trembizki E, Doyle C, Buckley C, Jennison A, Smith H, Bates J, Sloots T, Nissen M, Lahra MM, Whiley D. Estimating the prevalence of mixed-type gonococcal infections in Queensland, Australia. Sex Health 2015; 12:439-44. [PMID: 26145099 DOI: 10.1071/sh15009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/07/2015] [Indexed: 11/23/2022]
Abstract
UNLABELLED Background Mixed gonococcal infections within the one anatomical site have been recognised but questions remain over how often they occur. In this study, the aim was to estimate the prevalence of mixed gonococcal infections using novel real-time polymerase chain reaction (PCR) methods that were developed and validated, targeting the gonococcal porB gene. METHODS Neisseria gonorrhoeae strains were categorised into three different porB groups, based on sequence data derived from N. gonorrhoeae multi-antigen sequence typing (NG-MAST) analyses of local isolates. Specific PCR methods for each group were then developed and these PCR methods were used to test clinical samples (n=350) that were positive for gonorrhoea as determined by nucleic acid amplification test (NAAT) diagnostic screening. RESULTS Initial validation using isolates showed the group PCR methods proved 100% sensitive and 100% specific for their respective porB groups. When applied to the clinical specimens, 298/350 (85%) provided positive results by the group PCR methods. Of these, four specimens showed evidence of mixed infections, supported by subsequent DNA sequencing of the PCR products. CONCLUSIONS The data provide further evidence of mixed gonococcal infections at the same anatomical site, but show that such infections may be relatively infrequent (1.3%; 95% confidence interval 0.01-2.6%) in a general screening population.
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Affiliation(s)
- Ella Trembizki
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Block 28, Royal Children's Hospital, Herston Road, Herston, Qld 4029, Australia
| | - Christine Doyle
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Qld 4108, Australia
| | - Cameron Buckley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Block 28, Royal Children's Hospital, Herston Road, Herston, Qld 4029, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Qld 4108, Australia
| | - Helen Smith
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Qld 4108, Australia
| | - John Bates
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Qld 4108, Australia
| | - Theo Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Block 28, Royal Children's Hospital, Herston Road, Herston, Qld 4029, Australia
| | - Michael Nissen
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Block 28, Royal Children's Hospital, Herston Road, Herston, Qld 4029, Australia
| | - Monica M Lahra
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - David Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Block 28, Royal Children's Hospital, Herston Road, Herston, Qld 4029, Australia
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14
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Trembizki E, Doyle C, Jennison A, Smith H, Bates J, Lahra M, Whiley D. A Neisseria gonorrhoeae strain with a meningococcal mtrR sequence. J Med Microbiol 2014; 63:1113-1115. [DOI: 10.1099/jmm.0.074286-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ella Trembizki
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - Christine Doyle
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - Helen Smith
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - John Bates
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - Monica Lahra
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - David Whiley
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
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15
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Rosewell A, Dagina R, Murhekar M, Ropa B, Posanai E, Dutta SR, Jennison A, Smith H, Mola G, Zwi A, MacIntyre CR. Vibrio cholerae O1 in 2 coastal villages, Papua New Guinea. Emerg Infect Dis 2011; 17:154-6. [PMID: 21192890 PMCID: PMC3204642 DOI: 10.3201/eid1701.100993] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Hanna JN, Humphreys JL, Jennison A, Penny M, Smith HV. Serotype 6C invasive pneumococcal disease in indigenous people in north Queensland. Commun Dis Intell Q Rep 2010; 34:122-123. [PMID: 20677422] [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] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Jeffrey N Hanna
- Cairns Public Health Unit, Tropical Regional Services, Division of the Chief Health Officer, Queensland Health, Cairns Queensland.
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