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O'Brien A, Hart J, Higgins A, Arthur I, Lee GH, Leung M, Kennedy K, Bradbury S, Foster S, Warren S, Korman TM, Abbott IJ, Heney C, Bletchley C, Warner M, Wells N, Wilson D, Varadhan H, Stevens R, Lahra M, Newton P, Maley M, van Hal S, Ingram PR. Nocardia species distribution and antimicrobial susceptibility within Australia. Intern Med J 2024; 54:613-619. [PMID: 37929813 DOI: 10.1111/imj.16234] [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: 03/15/2023] [Accepted: 08/29/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation. AIMS To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program. METHODS Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022. RESULTS Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation. CONCLUSIONS We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.
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Affiliation(s)
- Aine O'Brien
- Department of Infectious Diseases, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Julie Hart
- Department of Infectious Diseases, Sir Charles Gardiner Hospital, Perth, Western Australia, Australia
| | - Ammie Higgins
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Ian Arthur
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Gar-Hing Lee
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Michael Leung
- PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Karina Kennedy
- ACT Health, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Susan Bradbury
- ACT Health, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Sarah Foster
- Launceston General Hospital, Tasmanian Health Service (THS), Hobart, Tasmania, Australia
| | - Sanchia Warren
- Royal Hobart Hospital, Department of Microbiology and Infectious Diseases, Hobart, Tasmania, Australia
| | - Tony M Korman
- Monash Health, Monash Infectious Diseases, Melbourne, Victoria, Australia
| | | | - Claire Heney
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | | | - Morgyn Warner
- Infectious Diseases and Microbiology Department, Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - Nicholas Wells
- South Australia Pathology, Adelaide, South Australia, Australia
| | - Desley Wilson
- South Australia Pathology, Adelaide, South Australia, Australia
| | - Hemalatha Varadhan
- Hunter New England, NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Robert Stevens
- South Eastern Sydney, NSW Health Pathology, Sydney, New South Wales, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Monica Lahra
- NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Peter Newton
- Illawarra-Shoalhaven, NSW Health Pathology, Wollongong, New South Wales, Australia
| | - Michael Maley
- South Western Sydney, NSW Health Pathology, Sydney, New South Wales, Australia
- Microbiology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Sebastian van Hal
- NSW Health Pathology, Newcastle, New South Wales, Australia
- Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Paul R Ingram
- Department of Infectious Diseases, Fiona Stanley Hospital, Perth, Western Australia, Australia
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Butler TA, Story C, Green E, Williamson KM, Newton P, Jenkins F, Varadhan H, van Hal S. Insights gained from sequencing Australian non-invasive and invasive Streptococcus pyogenes isolates. Microb Genom 2024; 10:001152. [PMID: 38197886 PMCID: PMC10868607 DOI: 10.1099/mgen.0.001152] [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: 08/10/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024] Open
Abstract
Epidemiological data have indicated that invasive infections caused by the Gram-positive cocci Streptococcus pyogenes (group A streptococcus, GAS) have increased in many Australian states over the past two decades. In July 2022, invasive GAS (iGAS) infections became nationally notifiable in Australia via public-health agencies. Surveillance for S. pyogenes infections has been sporadic within the state of New South Wales (NSW). This has led to a lack of genetic data on GAS strains in circulation, particularly for non-invasive infections, which are the leading cause of GAS's burden on the Australian healthcare system. To address this gap, we used whole-genome sequencing to analyse the genomes of 318 S. pyogenes isolates collected within two geographical regions of NSW. Invasive isolates were collected in 2007-2017, whilst non-invasive isolates were collected in 2019-2021. We found that at least 66 different emm-types were associated with clinical disease within NSW. There was no evidence of any Australian-specific clones in circulation. The M1UK variant of the emm1 global pandemic clone (M1global) has been detected in our isolates from 2013 onwards. We detected antimicrobial-resistance genes (mainly tetM, ermA or ermB genes) in less than 10 % of our 318 isolates, which were more commonly associated with non-invasive infections. Superantigen virulence gene carriage was reasonably proportionate between non-invasive and invasive infection isolates. Our study adds rich data on the genetic makeup of historical S. pyogenes infections within Australia. Ongoing surveillance of invasive and non-invasive GAS infections within NSW by whole-genome sequencing is warranted to inform on outbreaks, antimicrobial resistance and vaccine coverage.
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Affiliation(s)
- Trent A.J. Butler
- Microbiology, NSW Health Pathology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Chloe Story
- Microbiology, NSW Health Pathology, Wollongong Hospital, Wollongong, New South Wales, Australia
| | - Emily Green
- Microbiology, NSW Health Pathology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Kirsten M. Williamson
- Hunter New England Population Health, Hunter New England Local Health District, Newcastle, New South Wales, Australia
| | - Peter Newton
- Microbiology, NSW Health Pathology, Wollongong Hospital, Wollongong, New South Wales, Australia
| | - Frances Jenkins
- Department of Infectious Diseases and Microbiology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia
| | - Hemalatha Varadhan
- Microbiology, NSW Health Pathology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Sebastiaan van Hal
- Department of Infectious Diseases and Microbiology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia
- Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
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3
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Williamson KM, Varadhan H, Taylor K, Crooks K, Brett K, Law C, Butler M, Butler T, Green E, Davis JS, Wilson P, Housen T, Merritt T, Durrheim DN. Epidemiology of Group A Streptococcal bacteraemia in Hunter New England Local Health District, 2008 to 2019. Commun Dis Intell (2018) 2023; 47. [PMID: 37817312 DOI: 10.33321/cdi.2023.47.49] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Indexed: 10/12/2023]
Abstract
Invasive Group A Streptococcal infection (iGAS) is an uncommon but serious infection with Streptococcus pyogenes in a normally sterile body site. Manifestations include bacteraemia, necrotising fasciitis and toxic shock syndrome with attendant serious morbidity and mortality. An increasing incidence of iGAS has been observed in some regions of Australia. iGAS became a nationally notifiable condition from 1 July 2021. To determine if regional incidence has increased, and to identify priority populations, we undertook a retrospective data analysis of Group A Streptococcal (GAS) bacteraemia cases in Hunter New England Local Health District (HNELHD), New South Wales, Australia, from 1 January 2008 to 31 December 2019, as identified by NSW Health Pathology, John Hunter Hospital. A total of 486 cases were identified (age-standardised rate: 4.05 cases per 100,000 population per year). Incidence in HNELHD gradually increased over the study period (adjusted incidence rate ratio: 1.04; 95% confidence interval: 1.01-1.07) and was significantly higher in children under 5 years of age; in adults over 70 years of age; in males; and in First Nations peoples. A significant peak occurred in 2017 (9.00 cases per 100,000 population), the cause of which remains unclear. GAS bacteraemia is uncommon but severe, and incidence in HNELHD has slowly increased. Public health and clinical guidelines must address the needs of priority populations, which include young children, older adults and First Nations peoples. Routine surveillance and genomic analysis will help improve our understanding of iGAS and inform best public health management.
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Affiliation(s)
- Kirsten M Williamson
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia; National Centre for Epidemiology and Population Health, Australian National University, Acton, ACT, Australia.
| | | | - Kylie Taylor
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia
| | - Kristy Crooks
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia;Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Katie Brett
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia
| | - Charlee Law
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia
| | - Michelle Butler
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia
| | - Trent Butler
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Emily Green
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Joshua S Davis
- Infectious Diseases, John Hunter Hospital, Newcastle, NSW, Australia; School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - Paul Wilson
- Calvary Mater Hospital, Newcastle, NSW, Australia
| | - Tambri Housen
- National Centre for Epidemiology and Population Health, Australian National University, Acton, ACT, Australia; School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - Tony Merritt
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia
| | - David N Durrheim
- Hunter New England Population Health, Hunter New England Local Health District, NSW, Australia; School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia
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Elias A, Tilbrook L, Gray T, Varadhan H, George CRR. Gauge against the machine: revisiting quality for multi-targeted serology platforms. Pathology 2023; 55:123-126. [PMID: 36496262 DOI: 10.1016/j.pathol.2022.10.001] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022]
Abstract
Diagnosis of infections of public health significance, such as leptospirosis, often present challenges for laboratories. To counter common challenges and ensure quality driven health responses, rigorous validation and verification processes are required. Despite such rigor, however, can one be certain laboratory reports are truly reflective of infection, given the risk of rare, but potentially very significant quality oversights? Here we present a real-world scenario where diagnosis of leptospirosis cases was compromised over a 6-year period despite quality measures suggesting a well performing serological assay. A subsequent investigation revealed this was attributed to the programming of an automated microtitration plate analyser, evading detection by both quality control and external quality assurance processes. The quality oversight provides insight into potential limitations in quality processes in multi-targeted serological platforms.
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Affiliation(s)
- Anthony Elias
- Department of Microbiology, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia.
| | - Lynelle Tilbrook
- Department of Microbiology, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Timothy Gray
- Department of Microbiology and Infectious Diseases, Concord Repatriation General Hospital, Sydney, NSW, Australia; Department of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Hemalatha Varadhan
- Department of Microbiology, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - C R Robert George
- Department of Microbiology, NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
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Gulholm T, Yeang M, Nguyen I, Andrews PI, Balgahom R, Beresford R, Branley J, Briest R, Britton P, Burrell R, Gehrig N, Kesson A, Kok J, Maley M, Newcombe J, Samarasekara H, Van Hal S, Varadhan H, Thapa K, Jones S, Newton P, Naing Z, Stelzer-Braid S, Rawlinson W. Molecular typing of enteroviruses: comparing 5'UTR, VP1 and whole genome sequencing methods. Pathology 2022; 54:779-783. [PMID: 35738943 DOI: 10.1016/j.pathol.2022.03.013] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
Enteroviruses (EV) commonly cause hand, foot and mouth disease (HFMD), and can also cause potentially fatal neurological and systemic complications. In our laboratory, sequencing 5' untranslated region (UTR) of the viral genome has been the routine method of genotyping EVs. During a recent localised outbreak of aseptic meningitis, sequencing the 5'UTR identified the causative virus as EV-A71, which did not fit with the clinical syndrome or illness severity. When genotyped using a different target gene, VP1, the result was different. This led us to evaluate the accuracy of the two different target genome regions and compare them against whole genome sequencing (WGS). We aimed to optimise the algorithm for detection and characterisation of EVs in the diagnostic laboratory. We hypothesised that VP1 and WGS genotyping would provide different results than 5'UTR in a subset of samples. Clinical samples from around New South Wales which were positive for EV by commercial polymerase chain reaction (PCR) assays were genotyped by targeting three different viral genome regions: the 5'UTR, VP1 and WGS. Sequencing was performed by Sanger and next generation sequencing. The subtyping results were compared. Of the 74/118 (63%) samples that were successfully typed using both the 5'UTR and the VP1 method, the EV typing result was identical for 46/74 (62%) samples compared to WGS as the gold standard. The same EV group but different EV types were found in 22/74 (30%) samples, and 6/74 (8%) samples belonged to different EV groups depending on typing method used. Genotyping with WGS and VP1 is more accurate than 5'UTR. Genotyping by the 5'UTR method is very sensitive, but less specific.
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Affiliation(s)
- T Gulholm
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; UNSW Clinical School, Faculty of Medicine UNSW, Kensington, NSW, Australia.
| | - M Yeang
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia
| | - I Nguyen
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - P I Andrews
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - R Balgahom
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - R Beresford
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Branley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - R Briest
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - P Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; University of Sydney Children's Hospital Westmead Clinical School, NSW, Australia
| | - R Burrell
- Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - N Gehrig
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - A Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - M Maley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Newcombe
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - H Samarasekara
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - S Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - H Varadhan
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - K Thapa
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Jones
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - P Newton
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - Z Naing
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - W Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Varadhan H, Ahuja V, Pitman C, Dwyer DE. Weak positive SARS-CoV-2 N2 gene results using the Xpress Xpert assay: the need for an alternate interpretative criteria in a low prevalence setting. Pathology 2021; 54:116-120. [PMID: 34916069 PMCID: PMC8608624 DOI: 10.1016/j.pathol.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022]
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Lennon D, George R, Varadhan H. Impact of a diagnostic stewardship initiative of bacterial 16s rRNA sequencing referrals from a regional laboratory. Pathology 2021. [DOI: 10.1016/j.pathol.2021.06.110] [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: 10/21/2022]
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Wilson PA, Varadhan H. Severe community-acquired pneumonia due to Streptococcus pyogenes in the Newcastle area. ACTA ACUST UNITED AC 2020; 44. [PMID: 33081654 DOI: 10.33321/cdi.2020.44.82] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background An apparent increase in the incidence of severe community-acquired pneumonia (CAP) caused by Streptococcus pyogenes (group A Streptococcus - GAS) was observed during 2017 in the Newcastle area. The study was undertaken to establish whether there was a true increase in severe S. pyogenes pneumonia and to explore its epidemiology and clinical features. Methods The study was a retrospective descriptive study of S. pyogenes pneumonia set in two tertiary referral hospitals in Newcastle, a large regional city, during the period 2007 to 2018. Subjects were adults identified as having S. pyogenes pneumonia by searching a database of severe CAP (defined as requiring intensive care unit [ICU] admission) for the period 2007-2018. Laboratory records were also searched for sterile site isolates of S. pyogenes to identify patients not requiring ICU admission. Results There were 13 cases of S. pyogenes CAP identified during the study period, of whom 12 (92%) required ICU admission. S. pyogenes accounted for 12/728 (1.6%) cases of severe CAP during the study period. The severity of S. pyogenes pneumonia was high despite a mean patient age of 48 years and 7/13 (54%) having no significant past medical history. The mortality rate was 2/13 (15%). Viral co-infection was found in 6/12 (50%) of patients tested. Overall 7/12 (58%) of the patients with severe S. pyogenes CAP during the study period presented in the winter or spring of 2017. Conclusions Streptococcus pyogenes is a rare cause of severe CAP in the Newcastle area, but there was a marked increase in frequency observed during the 2017 influenza season. Further study of the epidemiology of invasive GAS (iGAS) disease in Newcastle is warranted to identify emerging trends in this severe infection.
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Affiliation(s)
- Paul A Wilson
- Staff specialist physician, Calvary Mater Newcastle, Waratah, New South Wales, Australia
| | - Hemalatha Varadhan
- Clinical microbiologist, Pathology North - Hunter, NSW Pathology, New South Wales, Australia
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9
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Naqvi S, Varadhan H, Givney R. Is prolonged incubation required for optimal recovery of Burkholderia cepacia complex in sputum from cystic fibrosis patients? Data versus dogma. Pathology 2020; 52:366-369. [PMID: 32113671 DOI: 10.1016/j.pathol.2019.11.011] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 10/19/2019] [Accepted: 11/27/2019] [Indexed: 11/27/2022]
Abstract
Cystic fibrosis (CF) expert groups globally recommend using selective medium for isolation of Burkholderia cepacia complex (BCC) from respiratory specimens of CF patients. However, there is no consensus available for optimal duration of incubation and recommendations are variable. The purpose of our study was to compare the difference in recovery of BCC in CF samples at 48 hours versus 7 days when inoculated on Burkholderia cepacia selective agar. A total of 307 consecutive clinical respiratory specimens from our local CF unit were studied prospectively (August 2017 to December 2017). All specimens were inoculated on Burkholderia cepacia medium, containing polymyxin B, gentamicin and ticarcillin. In our laboratory, these plates are routinely incubated for 48 hours as per the manufacturer's recommendation. However, for this study all plates with no growth at 48 hours were further incubated for total of 7 days at 35°C in O2. Plates were read daily to look for any growth. Microbial identification was performed using MALDI-TOF Vitek MS (database V3.0). Of the 307 CF respiratory specimens cultured, 177 (58%) were from paediatric and 130 (42%) were from adult patients; 155 (50%) specimens were sputum, 148 (48%) were cough swabs and four (1%) were bronchoalveolar lavage (BAL). All specimens from adults were sputum except one BAL. Thirteen (4%) cultures from eight adult and five paediatric specimens grew BCC. The majority (294, 96%) of specimens had no growth when incubated for 7 days. All 13 positive isolates recovered within 48 hours and there were no additional positive isolates found beyond 48 hours of incubation. We conclude from our analysis that prolonged incubation is not warranted for recovery of BCC in CF specimens if selective medium containing gentamicin and polymyxin is used. By adopting this approach of non-extended incubation, the burden of work on laboratory personnel can be significantly reduced and much faster turnaround time for CF cultures achieved. Our study confirms the results of recently published data on this point and challenges the prevailing dogma of utility of extended incubation for BCC isolation. For devising consensus statements for microbiology laboratories on this issue, CF societies and expert groups should consider reviewing data from the recent studies.
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Affiliation(s)
- Syeda Naqvi
- NSW Health Pathology, John Hunter Laboratory, Newcastle, NSW, Australia.
| | | | - Rodney Givney
- NSW Health Pathology, John Hunter Laboratory, Newcastle, NSW, Australia
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10
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Stelzer-Braid S, Wynn M, Chatoor R, Scotch M, Ramachandran V, Teoh HL, Farrar MA, Sampaio H, Andrews PI, Craig ME, MacIntyre CR, Varadhan H, Kesson A, Britton PN, Newcombe J, Rawlinson WD. Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations. J Clin Virol 2019; 122:104216. [PMID: 31790967 DOI: 10.1016/j.jcv.2019.104216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 04/24/2019] [Revised: 10/08/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND The most recent documented Australian outbreak of enterovirus A71 (EV-A71) occurred in Sydney from 2012 to 2013. Over a four-month period more than 100 children presented to four paediatric hospitals with encephalitic presentations including fever and myoclonic jerks. The heterogeneous presentations included typical encephalomyelitis, and cardiopulmonary complications. OBJECTIVES To characterise the genomes of enterovirus strains circulating during the 2013 Sydney EV-A71 outbreak and determine their phylogeny, phylogeography and association between genome and clinical phenotype. STUDY DESIGN We performed an analysis of enterovirus (EV) positive specimens from children presenting to hospitals in the greater Sydney region of Australia during the 2013 outbreak. We amplified near full-length genomes of EV, and used next generation sequencing technology to sequence the virus. We used phylogenetic/phylogeographic analysis to characterize the outbreak viruses. RESULTS We amplified and sequenced 23/63 (37 %) genomes, and identified the majority (61 %) as EV-A71. The EV-A71 sequences showed high level sequence homology to C4a genogroups of EV-A71 circulating in China and Vietnam during 2012-13. Phylogenetic analysis showed EV-A71 strains associated with more severe symptoms, including encephalitis or cardiopulmonary failure, grouped together more closely than those from patients with hand, foot and mouth disease. Amongst the non-EV-A71 sequences were five other EV subtypes (representing enterovirus subtypes A and B), reflecting the diversity of EV co-circulation within the community. CONCLUSIONS This is the first Australian study investigating the near full-length genome of EV strains identified during a known outbreak of EV-A71. EV-A71 sequences were very similar to strains circulating in Asia during the same time period. Whole genome sequencing offers additional information over routine diagnostic testing such as characterisation of emerging recombinant strains and inform vaccine design.
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Affiliation(s)
- Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Matthew Wynn
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Richard Chatoor
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Matthew Scotch
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW 2033, Australia
| | - Vidiya Ramachandran
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Hooi-Ling Teoh
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Michelle A Farrar
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Hugo Sampaio
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Peter Ian Andrews
- Department of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - Maria E Craig
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
| | - C Raina MacIntyre
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia; Watts College of Public Service and Community Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | | | - Alison Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia
| | - Philip N Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia; Marie Bashir Institute, University of Sydney, Australia
| | - James Newcombe
- Pathology North, Royal North Shore Hospital, St Leonards, Sydney, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia
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Munnoch S, Deane J, Varadhan H, Givney R, Iredell J, Ben Zakour N, McIntosh J, Ferguson J. An outbreak of Carbapenemase-producing Enterobactericeae in a neonatal intensive care unit, NSW, Australia. Infect Dis Health 2018. [DOI: 10.1016/j.idh.2018.09.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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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