Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing

We aim to provide insight and guidance on the utility of whole genome sequencing (WGS) data for investigating food-borne outbreaks of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in England between 2013 and 2017. Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with multilocus variable number tandem repeat analysis. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured. There was evidence that phylogeny derived from WGS data can be used to trace the geographical origin of an isolate. Further analysis of the phylogenetic data provided insight on the evolutionary context of emerging pathogenic strains. Publically available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain has improved trace back investigations during outbreaks. Expanding the use of WGS-based typing analysis globally will ensure the rapid implementation of interventions to protect public health, inform risk assessment and facilitate the management of national and international food-borne outbreaks of STEC O157:H7.

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Whole Genome Sequencing for the Retrospective Investigation of an Outbreak of Salmonella Typhimurium DT 8

PLoS Currents ◽

10.1371/currents.outbreaks.2c05a47d292f376afc5a6fcdd8a7a3b6 ◽

2015 ◽

Cited By ~ 18

Author(s):

Philip M Ashton ◽

Tansy Peters ◽

Linda Ameh ◽

Ralph McAleer ◽

Stewart Petrie ◽

...

Keyword(s):

Salmonella Typhimurium ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Retrospective Investigation

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Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

BMC Microbiology ◽

10.1186/s12866-016-0831-3 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 16

Author(s):

Anastasia Phillips ◽

Cristina Sotomayor ◽

Qinning Wang ◽

Nadine Holmes ◽

Catriona Furlong ◽

...

Keyword(s):

Salmonella Typhimurium ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Whole Genome ◽

Repeat Analysis

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Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak

BMC Research Notes ◽

10.1186/s13104-015-1687-6 ◽

2015 ◽

Vol 8 (1) ◽

Cited By ~ 8

Author(s):

Manal Mohammed ◽

Martin Cormican

Keyword(s):

Salmonella Typhimurium ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Foodborne Outbreak ◽

Phage Types ◽

The Difference

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Cross-border outbreak of Yersinia enterocolitica O3 associated with imported fresh spinach, Sweden and Denmark, March 2019

Eurosurveillance ◽

10.2807/1560-7917.es.2019.24.24.1900368 ◽

2019 ◽

Vol 24 (24) ◽

Cited By ~ 6

Author(s):

Laura Espenhain ◽

Maximilian Riess ◽

Luise Müller ◽

Soledad Colombe ◽

Steen Ethelberg ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Yersinia Enterocolitica ◽

Whole Genome ◽

Cross Border ◽

Trace Back

In April 2019, a cross-border outbreak of Yersinia entercolitica O3 was identified in Sweden and Denmark and confirmed using whole genome sequencing. Close cross-border collaboration with representatives from human and food authorities helped direct resources and investigations. Combined epidemiological and trace-back investigations pointed to imported fresh spinach as the outbreak vehicle and highlight that other vehicles of Y. enterocolitica outbreaks than pork should be considered.

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Investigation using whole genome sequencing of a prolonged restaurant outbreak of Salmonella Typhimurium linked to the building drainage system, England, February 2015 to March 2016

Eurosurveillance ◽

10.2807/1560-7917.es.2017.22.49.17-00037 ◽

2017 ◽

Vol 22 (49) ◽

Cited By ~ 11

Author(s):

John Mair-Jenkins ◽

Roberta Borges-Stewart ◽

Caroline Harbour ◽

Judith Cox-Rogers ◽

Tim Dallman ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Drainage System ◽

Control Analysis ◽

Whole Genome ◽

Single Nucleotide ◽

Water Testing ◽

Trace Back ◽

Serovar Typhimurium ◽

Case Control Analysis

Following notification of a Salmonella enterica serovar Typhimurium gastroenteritis outbreak, we identified 82 cases linked to a restaurant with symptom onset from 12 February 2015 to 8 March 2016. Seventy-two cases had an isolate matching the nationally unique whole genome sequencing profile (single nucleotide polymorphism (SNP) address: 1.1.1.124.395.395). Interviews established exposure to the restaurant and subsequent case–control analysis identified an association with eating carvery buffet food (adjusted odds ratios (AOR): 20.9; 95% confidence interval (CI): 2.2 – ∞). Environmental inspections, food/water testing, and a food trace-back investigation were inconclusive. Repeated cycles of cleaning were undertaken, including hydrogen peroxide fogging, however, transmission continued. After 7 months of investigation, environmental swabbing identified 106 isolates from kitchen surfaces and restaurant drains matching the outbreak profile. We found structural faults with the drainage system and hypothesised that a reservoir of bacteria in drain biofilm and underfloor flooded areas may have sustained this outbreak. Ineffective drain water-traps (U-bends) may have also contributed by allowing transmission of contaminated aerosols into the kitchen environment. These findings suggest that routine swabbing of sink drain points and inspection of drainage systems should be considered in future outbreak scenarios.

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Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing

PLoS ONE ◽

10.1371/journal.pone.0201882 ◽

2018 ◽

Vol 13 (8) ◽

pp. e0201882 ◽

Cited By ~ 18

Author(s):

Fernanda Almeida ◽

Amanda Aparecida Seribelli ◽

Marta Inês Cazentini Medeiros ◽

Dália dos Prazeres Rodrigues ◽

Alessandro de MelloVarani ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Salmonella Typhimurium ◽

Whole Genome Sequencing ◽

Resistance Gene ◽

Genome Sequencing ◽

Gene Analysis ◽

Whole Genome ◽

Antimicrobial Resistance Gene

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Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia

Foodborne Pathogens and Disease ◽

10.1089/fpd.2017.2352 ◽

2018 ◽

Vol 15 (3) ◽

pp. 161-167 ◽

Cited By ~ 13

Author(s):

Laura Ford ◽

Glen P. Carter ◽

Qinning Wang ◽

Torsten Seemann ◽

Vitali Sintchenko ◽

...

Keyword(s):

Public Health ◽

Salmonella Typhimurium ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Public Health Surveillance ◽

Health Surveillance ◽

Whole Genome

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Caracterización molecular y fenotípica de aislamientos clínicos de Salmonella Typhimurium variante monofásica (1,4,[5],12:i:-) recuperados en Colombia

Biomédica ◽

10.7705/biomedica.5417 ◽

2020 ◽

Vol 40 (4) ◽

pp. 722-733

Author(s):

Paloma Cuenca-Arias ◽

Lucy Angeline Montaño ◽

José Miguel Villarreal ◽

Magdalena Wiesner

Keyword(s):

Salmonella Typhimurium ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Whole Genome

Introducción. La variante monofásica (1,4,[5],12:i:-) de Salmonella Typhimurium ocupa los primeros lugares en los programas de vigilancia de Salmonella a nivel mundial. En Colombia, Salmonella enterica variante monofásica alcanza el cuarto lugar en cuanto a los aislamientos clínicos recuperados por medio de la vigilancia por laboratorio del Grupo de Microbiología del Instituto Nacional de Salud, pero se desconoce si dichos aislamientos están relacionados con la variante monofásica de Typhimurium que circula a nivel global, y con sus características genéticas y fenotípicas.Objetivo. Caracterizar los aislamientos de Salmonella monofásica recuperados en Colombia entre el 2015 y el 2018 por el Grupo de Microbiología del Instituto Nacional de Salud.Materiales y métodos. Se analizaron 286 aislamientos clínicos de Salmonella enterica variante monofásica mediante PCR o secuenciación del genoma completo (Whole Genome Sequencing, WGS) para confirmar si correspondían a Salmonella Typhimurium variante monofásica, en tanto que, en 54 aislamientos, se determinó la estructura genética del operón que codifica la segunda fase flagelar y, en 23, se evaluó la motilidad, el crecimiento y la expresión de las proteínas de membrana externa.Resultados. El 61 % (n=174) de los aislamientos de Salmonella monofásica correspondió a Salmonella Typhimurium serovar monofásico. El 64,8 % (n=35/54) se relacionó con el clon europeo-español y, el 13 % (n=7/54), con el estadounidense. En dos aislamientos de orina se encontró una diferencia significativa en la motilidad y el crecimiento, así como ausencia de la porina OmpD en medio mínimo M9.Conclusiones. En el periodo de estudio, circuló en Colombia la variante monofásica de Salmonella Typhimurium relacionada con el clon europeo-español, y se registró ausencia total del operón fljAB. Los resultados evidenciaron cambios fenotípicos en los aislamientos provenientes de muestras de orina que sugieren adaptación en procesos invasivos.

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