Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/33390
Title: Population structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in Victoria, Australia.
Austin Authors: Higgs, Charlie;Kumar, Lamali Sadeesh;Stevens, Kerrie;Strachan, Janet;Sherry, Norelle L ;Horan, Kristy;Zhang, Josh;Stinear, Timothy P;Howden, Benjamin P ;Gorrie, Claire L
Affiliation: Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Department of Health, Victoria, Australia.
Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.;Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.;Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.
Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.;Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia.
Infectious Diseases
​Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
Issue Date: Jul-2023
Publication information: Microbial Genomics 2023-07; 9(7)
Abstract: Streptococcus pneumoniae is a major human pathogen and can cause a range of conditions from asymptomatic colonization to invasive pneumococcal disease (IPD). The epidemiology and distribution of IPD-causing serotypes in Australia has undergone large changes following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV) in 2005 and the 13-valent PCV in 2011. In this study, to provide a contemporary understanding of the IPD causing population in Victoria, Australia, we aimed to examine the population structure and prevalence of antimicrobial resistance using whole-genome sequencing and comprehensive antimicrobial susceptibility data of 1288 isolates collected between 2018 and 2022. We observed high diversity among the isolates with 52 serotypes, 203 sequence types (STs) and 70 Global Pneumococcal Sequencing Project Clusters (GPSCs) identified. Serotypes contained in the 13v-PCV represented 35.3 % (n=405) of isolates. Antimicrobial resistance (AMR) to at least one antibiotic was identified in 23.8 % (n=358) of isolates with penicillin resistance the most prevalent (20.3 %, n=261 using meningitis breakpoints and 5.1 % n=65 using oral breakpoints). Of the AMR isolates, 28 % (n=101) were multidrug resistant (MDR) (resistant to three or more drug classes). Vaccination status of cases was determined for a subset of isolates with 34 cases classified as vaccine failure events (fully vaccinated IPD cases of vaccine serotype). However, no phylogenetic association with failure events was observed. Within the highly diverse IPD population, we identified six high-risk sub-populations of public health concern characterized by high prevalence, high rates of AMR and MDR, or serotype inclusion in vaccines. High-risk serotypes included serotypes 3, 19F, 19A, 14, 11A, 15A and serofamily 23. In addition, we present our data validating seroBA for in silico serotyping to facilitate ISO-accreditation of this test in routine use in a public health reference laboratory and have made this data set available. This study provides insights into the population dynamics, highlights non-vaccine serotypes of concern that are highly resistant, and provides a genomic framework for the ongoing surveillance of IPD in Australia which can inform next-generation IPD prevention strategies.
URI: https://ahro.austin.org.au/austinjspui/handle/1/33390
DOI: 10.1099/mgen.0.001070
ORCID: 
Journal: Microbial Genomics
PubMed URL: 37471116
ISSN: 2057-5858
Type: Journal Article
Subjects: Streptococcus pneumonaie
population genomics
Victoria/epidemiology
Pneumococcal Infections/epidemiology
Pneumococcal Infections/prevention & control
Anti-Bacterial Agents/pharmacology
Appears in Collections:Journal articles

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