Carbapenemase-producing Enterobacterales (CPE) are among the most concerning antibiotic-resistant organisms. In South Australia, colonisation or infection with CPE has been a notifiable condition under the South Australian Public Health Act, 2011 from April 2020, since which all CPE-positive isolates have been referred to the SA Pathology Public Health Laboratory (PHL) for Whole Genome Sequencing (WGS).

Between 2020 and February 2025, SA Pathology PHL sequenced 277 CPE isolates, with year-on-year increases in the number of CPE isolates sequenced. Carbapenem-producing genes were predominately detected in Klebsiella pneumoniae and Escherichia coli species, with genomically linked isolates associated with healthcare transmission more common among K. pneumoniae sequence types (STs). High-risk E. coli STs considered a risk to community spread, including ST410, ST131, ST361 and ST648, were also detected with increasing frequency. The most frequently acquired carbapenemase genes were NDM metallo-beta-lactamases, detected in over 60% of sequenced isolates. These genes were predominately blaNDM-5 and blaNDM-4, both associated with local plasmid-mediated and clonal transmission. Extended-spectrum beta-lactamases (ESBLs) genes were also found on over half of the sequenced CPE isolates. Concerningly, 20 isolates had acquired two carbapenem-producing genes, increasing from two isolates in 2020 to seven in 2024.

Consistent with recent data describing the deteriorating CPE situation in the European Union, the epidemiological changes observed in South Australia are concerning and likely an indication of the growing problem in Australia. These trends underscore the critical need for adequate laboratory capacity and the value of genomic surveillance in identifying emerging threats, distinct outbreaks, and community transmission, essential for tailoring effective infection control responses. Beyond surveillance, WGS can help interpret phenotypic data and optimise drug therapy by detecting the presence of multiple genes (e.g. carbapenemase, ESBL and AmpC genes) whose combined effect on susceptibility to beta-lactam antibiotics is different from that predicted by carbapenemase gene carriage alone.

Campylobacter is the leading cause of bacterial gastroenteritis globally and is an established food-borne and animal pathogen. It is part of the normal flora of avian species, and poultry is a major reservoir and transmission source to humans. Campylobacter infections are typically self-limiting, but vulnerable populations can develop severe illness. In New South Wales, approximately 13,000 laboratory confirmed Campylobacter cases are reported annually, with a notification rate approaching 150 per 100,000 people. Despite the high incidence of human infections, there are no surveillance strategies to inform rapid detection, genotype distribution or infection prevention.

This cross-sectional study aimed to determine the epidemiological and genomic characteristics of human and poultry Campylobacter isolates from urban and regional NSW. Using whole genome sequencing, we performed in silico speciation, genotyping and identification of antimicrobial resistance markers among poultry and human isolates collected in 2023-2024. Genomic analysis identified two Campylobacter species from poultry sources – C. jejuni and C. coli, and three Campylobacter species from human sources – C. jejuni, C. coli and C. lari. Notably, C. coli was over-represented in poultry sources compared with the human cohort. In all cases, the in silico predicted species was consistent with phenotypic speciation performed with PCR and MALDI-TOF. Genomic markers of resistance were detected for quinolones, macrolides and aminoglycosides in the human and poultry cohorts.

This research has enhanced the understanding of Campylobacter diversity across clinical and poultry isolates, and between urban and regional communities in NSW. The high incidence of Campylobacter infections in NSW highlights the need for more targeted control strategies with genomic characterisation offering a foundation for improving surveillance, molecular typing, source attribution and intervention approaches in Australia. The identified antimicrobial resistance markers underlines the need for an integrated One Health approach to surveillance and management across Australia, particularly in remote and regional communities.

Background:
Typhoid fever, caused by Salmonella Typhi, is a nationally notifiable disease in Australia. The incubation period is typically cited as 6 to 30 days, with approximately 90% of cases developing symptoms within 14 days of exposure. In Australia, cases with onset within 28 days of returning are classified as overseas acquired. The proportion of cases with longer incubation periods (than 28 days) is poorly documented, complicating case classification and understanding of public risk. This study aims to better characterize incubation periods beyond 28 days in typhoid cases in NSW to inform more effective public health surveillance.
Methods:
We conducted a retrospective analysis of notification and travel history data for typhoid cases in NSW between 2019 and 2024. For cases likely acquired overseas, we calculated the time between last potential overseas exposure and symptom onset to estimate incubation periods. Statistical analysis included percentile distributions of incubation period, stratified by demographic details. Whole genome sequencing (WGS) was used to compare genomic relatedness and support source attribution.
Results:
Among 312 typhoid cases notified from 2019-2024, 287 (92.0%) were classified as overseas acquired, and 3 (1.0%) were suspected long-term carriers. Among acute overseas-acquired cases, 4.9% (n=14) had an incubation period exceeding 28 days, with the longest period 65 days. In cases with unclear acquisition sources, WGS successfully linked the infection to a probable overseas exposure location in in all but one case which lacked associated contextual data.
Conclusions:
This study highlights the variability in typhoid incubation periods, with approximately 1 in 20 cases exceeding the traditionally accepted 28-day limit. Public health staff should be cognisant of the variability in incubation periods for typhoid fever and prepared to employ thorough risk assessments that go beyond the typical 28-day period. WGS can play a critical role in supporting risk assessment and source attribution investigations.

Background
Foodborne outbreaks of listeriosis occur occasionally in Australia and can lead to severe outcomes for at risk populations. We identified invasive listeriosis outbreaks investigated in Australia from 2012 to 2022. We summarised the key features of these outbreaks and assessed the implications for food safety and future outbreak investigations.
Methods
Outbreak data was extracted from the national OzFoodNet Outbreak Register and described by year reported, size, severity, type of evidence, food implicated, setting the food was prepared and eaten, and likely cause of contamination.
Results
Twelve listeriosis outbreaks were identified. These outbreaks involved a total of 94 cases, with 20 deaths reported (an overall case fatality rate of 21.3%). The median number of cases per outbreak was three (range 2 – 34) and the median number of deaths was one (range 0 – 7). The median age per outbreak ranged from 62 – 92 years, except for one outbreak with a median age of 32 years. The most common food type implicated was pre-prepared composite foods (25%), including frozen meals and sandwiches. Emerging laboratory methods, such as whole genome sequencing, were used to investigate the relatedness of isolates from cases and suspected food vehicles, with ten outbreak investigations (83.3%) identifying the same aetiological agent in the cases and suspected food vehicle. Most outbreaks (ten outbreaks, 83.3%) were caused by contamination of the product in the production environment, with one outbreak associated with extreme weather events.
Conclusion
Use of novel microbiologic techniques has increased listeriosis outbreak detection and improved the ability to identify sources of outbreaks. It is important that public health communication emphasises the risks of consuming high-risk ingredients in composite foods, not just as standalone products. Food safety protocols should undergo ongoing review to ensure they are responsive to a changing climate.

Background
Genomic surveillance of HEV is currently limited to single gene sequencing (ORF2), which provides limited differentiation and geographical resolution between highly diverse HEV genotypes. We investigated the utility of WGS to characterise a recent multi-state surge of locally-acquired HEV infections in Australia.

Methods
Whole genome sequencing (WGS) was performed using target-enrichment and compared with ORF2 sequencing using samples collected from two study cohorts. Cohort A consisted of recent clinical specimens collected from patients with acute HEV (n=30, Oct 2022-Dec 2023) and Cohort B comprised of archived clinical specimens (n=21, Jan 2013 to Sep 2022) with robust epidemiological data. We analysed HEV relatedness (phylogeny, mutual nearest-neighbour clustering), subtyping and vaccine amino acid mapping, to explore the concordance between partial ORF2-490bp, full-length ORF2 and whole-genome analyses. Additionally, we assessed the HEV-3 SNP distance threshold appropriate for cluster assignment.

Findings
Fifty-one samples (14 HEV-1, 35 HEV-3, 2 HEV-4) were subjected to WGS and ORF2 sequencing, with whole-genomes obtained from 78% (n=40) of samples. WGS and ORF2-490bp demonstrated high genotyping agreement, although 97% (34/35) of HEV-3 samples were not able to be classified into a known subgenotype using either method. Global co-phylogenetic analysis demonstrated high level of congruence between ORF-490bp, full-length ORF2 and whole-genome sequences. Australian HEV-3 sequences analysed using phylogenetic and mutual nearest-neighbour approaches support the presence of unique subgenotypes with different common ancestries. An outbreak cluster demonstrated a median SNP distance of 10 (IQR 6-11) compared with 1304 (IQR 1281-1313) for an overseas acquired case. High amino acid variability was seen between Australian HEV-3 sequences and two vaccine targets.

Findings of our study suggest the recent increase in Australian cases of HEV genotype 3 is geographically distinct, with plausibility of either endemic circulation or from consumption of contaminated imported product. WGS of HEV is useful for global contextualization of HEV-3 outbreaks.

Climate change and rising ambient temperatures with heatwaves have been associated with increased risk of food borne infections. Existing literature has demonstrated associations between climate variables and bacterial gastroenteritis but not serious manifestations like bacteraemia. We conducted a time series analysis in Queensland, Australia to estimate the risk of bacteraemia from Salmonella and Campylobacter from 2010 to 2020. Using Quasi-Poisson regression and a Distributed Lag Non-Linear Model, we analysed weekly cases of bacteraemia, controlling for seasonal trends and precipitation. There were a total of 1034 cases of Salmonella and 234 Campylobacter bacteraemia cases. Compared to reference values, the risk of salmonellosis increased to 2.13 (95% CI: 1.62, 2.79) at the 95th mean temperature percentile (26.7C) and to 2.71 (95% CI :1.90, 3.55) at the 95th maximum temperature percentile (34.4C). Significant association was found for weekly maximum temperature and Campylobacteriosis at the 99% quantile,37.7 0 C, with RR of 9.34(1.08,8.03e+). Heat waves were also significantly associated with Salmonella bacteraemia. In Southeast-QLD, the rise in cases was within a week of exposure and in Tropical North QLD, another rise was noted after 4 weeks. This study confirms the risk of bacteraemia from these two pathogens from rising ambient temperatures and heat waves.
 

A novel outbreak of Brucella suis in a veterinary practice: a One Health investigation
In January 2025, an outbreak of brucellosis was identified by the Hunter New England Public Health Unit (HNEPHU) at a veterinary practice following notification of three cases amongst staff, the first known outbreak of this nature in Australia. Active case finding revealed an additional five cases. Typing confirmed B. suis in 2 cases.
In Australia, B. suis affects feral pigs (after being eradicated from the Australian domestic pig population), pig-hunting dogs, and uncommonly humans (usually involved in pig hunting). In humans, the clinical presentation is variable, but may include a flu-like illness, including fever, headache, weakness, and generalised body aches, however there is a risk of severe complications and undulating illness.
A comprehensive One Health approach was taken to this investigation; HNEPHU worked with counterparts in animal health, clinical infectious diseases, and veterinary and human health laboratories.
An expert panel included these partners, and colleagues with specific national brucella experts provided guidance to the investigation and interpretation of findings. A site visit was conducted by HNEPHU and LLS, with a detailed inspection of the clinic – including environmental sampling, a serosurvey and a questionnaire for all staff (n=34). Cases were reviewed by the John Hunter Infectious Diseases Team. Laboratory investigations included serology and cultures for staff willing to be tested, followed by whole genome sequencing (WGS) for positive cultures. Environmental samples from the clinic were tested by EMAI and revealed multiple positive PCR brucella results.
To explore the source of the outbreak, high-risk procedures in pig-hunting dogs were cross matched with staff rosters. This process was complicated by data quality issues, and dogs identified for testing having been euthanised and disposed of. Investigations are ongoing, and our presentation will outline findings and learnings from this novel outbreak.