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Williamson DA, Baines SL, Carter GP, da Silva AG, Ren X, Sherwood J, Dufour M, Schultz MB, French NP, Seemann T, Stinear TP, Howden BP. Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis. Genome Biol Evol 2018; 8:3806-3814. [PMID: 28173076 PMCID: PMC5521734 DOI: 10.1093/gbe/evw285] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2016] [Indexed: 12/26/2022] Open
Abstract
In 2014, a sustained outbreak of yersiniosis due to Yersinia pseudotuberculosis occurred across all major cities in New Zealand (NZ), with a total of 220 laboratory-confirmed cases, representing one of the largest ever reported outbreaks of Y. pseudotuberculosis. Here, we performed whole genome sequencing of outbreak-associated isolates to produce the largest population analysis to date of Y. pseudotuberculosis, giving us unprecedented capacity to understand the emergence and evolution of the outbreak clone. Multivariate analysis incorporating our genomic and clinical epidemiological data strongly suggested a single point-source contamination of the food chain, with subsequent nationwide distribution of contaminated produce. We additionally uncovered significant diversity in key determinants of virulence, which we speculate may help explain the high morbidity linked to this outbreak.
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Affiliation(s)
- Deborah A Williamson
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen P Carter
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anders Gonçalves da Silva
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Jill Sherwood
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Muriel Dufour
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Mark B Schultz
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nigel P French
- Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
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Eppinger M, Rosovitz MJ, Fricke WF, Rasko DA, Kokorina G, Fayolle C, Lindler LE, Carniel E, Ravel J. The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever. PLoS Genet 2007; 3:e142. [PMID: 17784789 PMCID: PMC1959361 DOI: 10.1371/journal.pgen.0030142] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 07/10/2007] [Indexed: 12/25/2022] Open
Abstract
The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation, exanthema, hyperhemic tongue, and a toxic shock syndrome. The term FESLF was coined for the infection because it shares clinical presentations with scarlet fever caused by group A streptococci. The causative agent was later identified as Yersinia pseudotuberculosis, although the range of morbidities was vastly different from classical pseudotuberculosis symptoms. To understand the origin and emergence of the peculiar clinical features of FESLF, we have sequenced the genome of the FESLF-causing strain Y. pseudotuberculosis IP31758 and compared it with that of another Y. pseudotuberculosis strain, IP32953, which causes classical gastrointestinal symptoms. The unique gene pool of Y pseudotuberculosis IP31758 accounts for more than 260 strain-specific genes and introduces individual physiological capabilities and virulence determinants, with a significant proportion horizontally acquired that likely originated from Enterobacteriaceae and other soil-dwelling bacteria that persist in the same ecological niche. The mobile genome pool includes two novel plasmids phylogenetically unrelated to all currently reported Yersinia plasmids. An icm/dot type IVB secretion system, shared only with the intracellular persisting pathogens of the order Legionellales, was found on the larger plasmid and could contribute to scarlatinoid fever symptoms in patients due to the introduction of immunomodulatory and immunosuppressive capabilities. We determined the common and unique traits resulting from genome evolution and speciation within the genus Yersinia and drew a more accurate species border between Y. pseudotuberculosis and Y. pestis. In contrast to the lack of genetic diversity observed in the evolutionary young descending Y. pestis lineage, the population genetics of Y. pseudotuberculosis is more heterogenous. Both Y. pseudotuberculosis strains IP31758 and the previously sequenced Y. pseudotuberculosis strain IP32953 have evolved by the acquisition of specific plasmids and by the horizontal acquisition and incorporation of different genetic information into the chromosome, which all together or independently seems to potentially impact the phenotypic adaptation of these two strains.
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Affiliation(s)
- Mark Eppinger
- J. Craig Venter Institute/The Institute for Genomic Research, Microbial Genomics, Rockville, Maryland, United States of America
| | - M. J Rosovitz
- J. Craig Venter Institute/The Institute for Genomic Research, Microbial Genomics, Rockville, Maryland, United States of America
| | - Wolfgang Florian Fricke
- J. Craig Venter Institute/The Institute for Genomic Research, Microbial Genomics, Rockville, Maryland, United States of America
| | - David A Rasko
- J. Craig Venter Institute/The Institute for Genomic Research, Microbial Genomics, Rockville, Maryland, United States of America
| | | | | | - Luther E Lindler
- Department of Defense, Global Emerging Infections Surveillance and Response System, Silver Spring, Maryland, United States of America
| | | | - Jacques Ravel
- J. Craig Venter Institute/The Institute for Genomic Research, Microbial Genomics, Rockville, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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