Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis

Lijuan Luo; Michael Payne; Qinning Wang; Sandeep Kaur; Irani U. Rathnayake; Rikki Graham; Mailie Gall; Jenny Draper; Elena Martinez; Sophie Octavia; Mark M. Tanaka; Amy V. Jennison; Vitali Sintchenko; Ruiting Lan

doi:10.1128/spectrum.03014-22

Microbiology Spectrum (Feb 2023)

Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis

Lijuan Luo,
Michael Payne,
Qinning Wang,
Sandeep Kaur,
Irani U. Rathnayake,
Rikki Graham,
Mailie Gall,
Jenny Draper,
Elena Martinez,
Sophie Octavia,
Mark M. Tanaka,
Amy V. Jennison,
Vitali Sintchenko,
Ruiting Lan

Affiliations

Lijuan Luo: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
Michael Payne: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
Qinning Wang: Centre for Infectious Diseases and Microbiology–Public Health, Institute of Clinical Pathology and Medical Research–NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
Sandeep Kaur: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
Irani U. Rathnayake: Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
Rikki Graham: Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
Mailie Gall: Centre for Infectious Diseases and Microbiology–Public Health, Institute of Clinical Pathology and Medical Research–NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
Jenny Draper: Centre for Infectious Diseases and Microbiology–Public Health, Institute of Clinical Pathology and Medical Research–NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
Elena Martinez: Centre for Infectious Diseases and Microbiology–Public Health, Institute of Clinical Pathology and Medical Research–NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
Sophie Octavia: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
Mark M. Tanaka: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
Amy V. Jennison: Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Coopers Plains, Queensland, Australia
Vitali Sintchenko: Centre for Infectious Diseases and Microbiology–Public Health, Institute of Clinical Pathology and Medical Research–NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
Ruiting Lan: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia

DOI: https://doi.org/10.1128/spectrum.03014-22
Journal volume & issue: Vol. 11, no. 1

Abstract

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ABSTRACT Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 S. Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to international strains, using the S. Enteritidis multilevel genome typing (MGT) database, which contained 40,390 publicly available genomes from 99 countries. The Australian S. Enteritidis isolates were divided into three phylogenetic clades (A, B, and C). Clades A and C represented 16.4% and 3.5% of the total isolates, respectively, and were of local origin. Clade B accounted for 80.1% of the isolates which belonged to seven previously defined lineages but was dominated by the global epidemic lineage. At the MGT5 level, three out of five top sequence types (STs) in Australia were also top STs in Asia, suggesting that a fair proportion of Australian S. Enteritidis cases may be epidemiologically linked with Asian strains. In 2018, a large egg-associated local outbreak was caused by a recently defined clade B lineage prevalent in Europe and was closely related, but not directly linked, to three European isolates. Additionally, over half (54.8%) of predicted multidrug resistance (MDR) isolates belonged to 10 MDR-associated MGT-STs, which were also frequent in Asian S. Enteritidis . Overall, this study investigated the genomic epidemiology of S. Enteritidis in Australia, including the first large local outbreak, using MGT. The open MGT platform enables a standardized and sharable nomenclature that can be effectively applied to public health for unified surveillance of S. Enteritidis nationally and globally. IMPORTANCE Salmonella enterica serovar Enteritidis is a leading cause of foodborne infections. We previously developed a genomic typing database (MGTdb) for S. Enteritidis to facilitate global surveillance of this pathogen. In this study, we examined the genomic features of Australian S. Enteritidis using the MGTdb and found that Australian S. Enteritidis is mainly epidemiologically linked with Asian strains (especially strains carrying antimicrobial resistance genes), followed by European strains. The first large-scale egg-associated local outbreak in Australia was caused by a recently defined lineage prevalent in Europe, and three European isolates in the MGTdb were closely related but not directly linked to this outbreak. In summary, the S. Enteritidis MGTdb open platform is shown to be a potentially powerful tool for national and global public health surveillance of this pathogen.

Published in Microbiology Spectrum

ISSN: 2165-0497 (Online)
Publisher: American Society for Microbiology
Country of publisher: United States
LCC subjects: Science: Microbiology
Website: https://journals.asm.org/journal/spectrum

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