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.

Salmonellosis is a significant public health problem globally. In Australia, Salmonella enterica serovar Enteritidis is one of the main causes of salmonellosis. This study reports how the implementation of routine genetic surveillance of isolates from human S. Enteritidis cases enabled identification of the likely source of an outbreak that occurred in a remote town in Far North Queensland, Australia. This study included patient, food and water samples collected during an outbreak investigation. S. Enteritidis of the novel sequence type 5438 was isolated from all seven patient samples and one bore water sample but not any of the food samples. Both whole-genome single nucleotide polymorphism (SNP) and core-genome multilocus sequence typing analysis revealed that S. Enteritidis isolated from outbreak-related patient samples and the bore water isolates clustered together with fewer than five SNP differences and ten allelic differences. This genetic relatedness informed the outbreak response team around public health interventions and no further cases were identified post-treatment of the bore water. This disease cluster was identified through the routine sequencing of S. Enteritidis performed by the state public health laboratory in an actionable time frame. Additionally, genomic surveillance captured a case with unknown epidemiological links to the affected community, ruled out a simultaneous outbreak in an adjacent state as the source and provided evidence for the likely source preventing further transmission. Therefore, this report provides compelling support for the implementation of whole-genome sequencing based genotyping methods in public health microbiology laboratories for better outbreak detection and management.

Queensland typhoid cluster linked to twelve-year carriage of Salmonella Typhi.

In September 2021, a household cluster of three typhoid cases was investigated by Queensland public health authorities. Through case interviews and molecular typing, the investigation revealed chronic carriage of Salmonella Typhi persisting at least 12 years in the index case. This case report summarises the investigation and highlights the complexity of chronic pathogen carriage in the control and management of typhoid disease. Our findings raise considerations for prevention and treatment guidelines in Australia and demonstrate the beneficial role of molecular typing for complex case investigations.

Distribution of Gifsy-3 and of variants of ST64B and Gifsy-1 prophages amongst Salmonella enterica Serovar Typhimurium isolates: evidence that combinations of prophages promote clonality.

Salmonella isolates harbour a range of resident prophages which can influence their virulence and ability to compete and survive in their environment. Phage gene profiling of a range of phage types of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) indicates a significant level of correlation of phage gene profile with phage type as well as correlation with genotypes determined by a combination of multi-locus variable-number tandem repeat (VNTR) typing and clustered regularly interspaced short palindromic repeats (CRISPR) typing. Variation in phage gene profiles appears to be partly linked to differences in composition of variants of known prophages. We therefore conducted a study of the distribution of variants of ST64B and Gifsy-1 prophages and coincidently the presence of Gifsy-3 prophage in a range of S. Typhimurium phage types and genotypes. We have discovered two variants of the DT104 variant of ST64B and at least two new variants of Gifsy-1 as well as variants of related phage genes. While there is definite correlation between phage type and the prophage profile based on ST64B and Gifsy-1 variants we find stronger correlation between the VNTR/CRISPR genotype and prophage profile. Further differentiation of some genotypes is obtained by addition of the distribution of Gifsy-3 and a sequence variant of the substituted SB26 gene from the DT104 variant of ST64B. To explain the correlation between genotype and prophage profile we propose that suites of resident prophages promote clonality possibly through superinfection exclusion systems.

ß-Lactamases in Salmonella enterica isolated in Australia.

Understanding the antibiotic susceptibility of Salmonella enterica is important both from a clinical treatment and a public health perspective. The emergence of extended spectrum ß-lactamases (ESßLs) and AmpC ß-lactamases in S. enterica is important, as this will limit treatment options and could provide a strain with a significant selective advantage. The aim of the study was to screen isolates of S. enterica, including isolates that had previously shown antibiotic resistance, to gauge the extent of ß-lactamase activity in S. enterica in Australia. Phenotypic detection involved screening in accordance with Clinical and Laboratory Standards Institute double disk synergy test guidelines and assessing susceptibility to cefoxitin. Presumptive positives were then screened using a MAST® AmpC and ESßL detection set. S. enterica isolates that were consecutively received in the laboratory (n=624), or had previously exhibited some antibiotic resistance (n=351), were screened for ß-lactamase activity. None of the isolates in the second group were included in the first. ß-lactamase activity was detected in nine of the consecutively received isolates; one with demonstrated ESßL activity and eight others with demonstrated AmpC ß-lactamase. ß-lactamase activity was detected in 16 of the isolates that had previously demonstrated some antibiotic resistance; three with demonstrated ESßL activity and 13 others with demonstrated AmpC ß-lactamase activity. S. enterica serovar Stanley is a serovar that is frequently acquired overseas and this serovar had the highest proportion of isolates that demonstrated ß-Lactamase activity in consecutively sampled isolates (4.95%), reflecting the emergence of an epidemic clone within South East Asia. While antibiotic resistance is being detected in Salmonella isolates, the data indicates that there is limited awareness of, or screening for, ß-lactamases in S. enterica. This study will help to overcome these deficiencies and provide some baseline surveillance data against which future trends can be measured.

A statewide outbreak of Salmonella bovismorbificans phage type 32 infection in Queensland.

Between 30 May and 1 June 2001, 10 cases of Salmonella Bovismorbificans infection were reported to Public Health Services, Queensland Health. Investigations included enhanced surveillance, case interviews, a matched case control study, environmental audit and microbiological testing of faecal isolates (phage typing) and implicated food products. Forty-one cases of S. Bovismorbificans infection were detected, 36 cases were phage type 32. A matched case control study identified that illness was associated with consumption of food from 15 outlets of a fast food chain, Company A (matched odds ratio [MOR] 17.5, 95% CI 2.0-657.3, p = 0.004) and consumption of a particular product, Product X (MOR undefined, p < 0.001) in the week before onset of illness. Manufacturers of Product X ingredients were audited. Deficiencies were identified in equipment cleansing at the salad mixture processing plant (Manufacturer M). A swab of food residue behind the cutting wheel rim of the lettuce shredder was positive for S. Bovismorbificans phage type 32. This appears to be the first reported Australian outbreak of salmonellosis associated with a lettuce product. The investigations suggest that inadequate maintenance of cutting equipment to prepare lettuce ingredients for Product X by Manufacturer M was a key factor in this statewide outbreak. The statewide nature of this outbreak demonstrates the role of timely serovar identification of Salmonella isolates by a reference laboratory as an aid to outbreak identification, and the importance of adherence to appropriate food safety procedures in the manufacture and preparation of mass produced food items for the public.