How routine public health genomic surveillance helped solve an S. Enteritidis outbreak investigation

Posted on August 2, 2023   by Dr Irani Rathnayake

Dr Irani Rathnayake takes us behind the scenes of their latest publication, 'Implementation of routine genomic surveillance provided insights into a locally acquired outbreak caused by a rare clade of Salmonella enterica serovar Enteritidis in Queensland, Australia' published in Microbial Genomics. 

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Molecular Epidemiology team at Public Health Microbiology


My name is Irani Udeshika Rathnayake, and I am a Senior Scientist at Public Health Microbiology and Queensland Public Health and Infectious Diseases Reference Genomics (Q-PHIRE Genomics), Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia. Over the course of the last decade, we have implemented Whole Genome Sequencing (WGS) in routine genomic surveillance - especially in outbreak investigation. We found that WGS is an “all-in-one molecular tool for the real world” which has a superpower: to provide unparalleled clarity of associations between clinical isolates and suspected sources. The article “Implementation of routine genomic surveillance provided insights into a locally acquired outbreak caused by a rare clade of Salmonella enterica serovar Enteritidis in Queensland, Australia”, published in Microbial Genomics, describes one of the S. Enteritidis outbreaks that we have investigated with the aid of routine genomic surveillance.

Being the public health reference laboratory for Queensland (QLD), our lab receives all Salmonella that are isolated by private and public pathology laboratories in QLD. Our group: Molecular Epidemiology (Mol Epi) performs WGS of all S. Enteritidis received and routinely releases genomics surveillance reports. One of the main objectives of this surveillance is to assess the genetic relatedness of S. Enteritidis and identify potential clusters that could be responsible for outbreaks. In an outbreak situation this information will assist public health officials in their investigation. This manuscript describes a S. Enteritidis outbreak from a rare, but endemic clade; “An Australian clade”. This is one of the many situations where our WGS surveillance findings assist in S. Enteritidis outbreak investigation.

In December 2018, public health officials identified an outbreak in a remote Far North Queensland Region and the causative agent was S. Enteritidis. In parallel to this outbreak, there was an ongoing S. Enteritidis outbreak occurring in an adjacent Australian state, associated with poultry farms, causing cases in a number of Australian jurisdictions. Therefore, it was important to determine whether these QLD cases were related to the interstate outbreak. To investigate this, we included representative sequences from the interstate outbreak in our routine genomic analysis of all Queensland S. Enteritidis cases. The sequence analysis allowed the Queensland outbreak response team to rapidly determine that the QLD outbreak was not related to the interstate outbreak and that it was from a totally different clade, clade C, which is one of the endemic Australian clades. Bioinformatic analysis showed that this new cluster emerging in clade C was a type not previously seen, harbouring a novel hisD gene allele. In total, seven patients belonging to this new cluster were identified - one of which had no known epidemiological link to the region prior to the genomics linking the case. Public health officials interviewed the patients and carried out an in-depth investigation to find out the source of infection. Our laboratory received a number of possible food types from commercial sources that patients had consumed in the region with Salmonella not detected in any samples suggesting that the source of the outbreak was not foodborne. Analysis of bore water used by a local store during food preparation found S. Enteritidis in the water samples. Subsequent sequence analysis confirmed that this S. Enteritidis genomically clustered with the outbreak cases. Further public health follow-up identified issues with the bore water treatment which meant that the water had not been treated sufficiently. As mentioned in the manuscript, WGS enabled timely outbreak detection, case attribution, and guidance for public health interventions, which prevented the further dissemination of the causative agent. Another interesting finding during source tracking was an overseas resident travelling through the area was identified as being part of the outbreak cluster. Subsequent public health follow-up confirmed that the case had visited the affected region regularly at the time of the outbreak. This connection would have been missed if we did not employ routine genomic surveillance on all cases of S. Enteritidis in the state.

This timely outbreak investigation was not possible without the great teamwork of our Mol epi team at Public Health Microbiology who perform routine genomic surveillance on all S. Enteritidis cases. We always aim for a rapid turnaround time for our analysis so that it can be used to inform the public health response in any outbreak situation. We have a well-established workflow, which includes DNA extraction from isolates, library preparation using robotics and genome sequencing utilising cutting-edge sequencing platforms. Downstream sequencing analysis is facilitated by well curated pipelines and cloud computing platforms. These advanced technologies and techniques enable us to provide timely solutions for real-world questions. This publication is an example of one such situation. Furthermore, the impeccable support of Public Health Microbiology staff, members of all Public Health Units and the Communicable Diseases Branch Brisbane who were involved in this outbreak investigation is greatly appreciated.

At the end of this outbreak investigation, we decided to publish our findings to highlight the advantages that expansive genomic surveillance of pathogens brings to outbreak cluster discovery and public health inclusion of cases. It is for these reasons the molecular landscape in outbreak investigations is moving from traditional molecular subtyping to WGS methods; “All-in-one molecular tool for the real world”.