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.

A multi-jurisdictional outbreak of Salmonella Typhimurium infections linked to backyard poultry-Australia, 2020.

Zoonotic salmonellosis can occur either through direct contact with an infected animal or through indirect contact, such as exposure to an infected animal's contaminated environment. Between May and August 2020, a multi-jurisdictional outbreak of Salmonella Typhimurium (STm) infection due to zoonotic transmission was investigated in Australia. In total, 38 outbreak cases of STm with a median age of 5 years were reported. Epidemiological investigation showed contact with live poultry to be a common risk factor with most cases recently purchasing one-week old chicks from produce/pet stores. Traceback investigation of cases identified 25 product/pet stores of which 18 were linked to a single poultry breeder farm. On farm environmental sampling identified the same STm genotype as identified in cases. Whole genome sequencing of both environmental and human outbreak isolates found them to be highly related by phylogenetic analysis. This investigation describes the first documented widespread zoonotic salmonellosis outbreak in Australia attributed to backyard poultry exposure and identified potential risk factors and prevention and control measures for future outbreaks. Prevention of future outbreaks will require an integrated One Health approach involving the poultry industry, produce/pet store owners, animal healthcare providers, public health and veterinary health agencies and the public.

Risk factors for campylobacteriosis in Australia: outcomes of a 2018-2019 case-control study.

BACKGROUND: We aimed to identify risk factors for sporadic campylobacteriosis in Australia, and to compare these for Campylobacter jejuni and Campylobacter coli infections. METHODS: In a multi-jurisdictional case-control study, we recruited culture-confirmed cases of campylobacteriosis reported to state and territory health departments from February 2018 through October 2019. We recruited controls from notified influenza cases in the previous 12 months that were frequency matched to cases by age group, sex, and location. Campylobacter isolates were confirmed to species level by public health laboratories using molecular methods. We conducted backward stepwise multivariable logistic regression to identify significant risk factors. RESULTS: We recruited 571 cases of campylobacteriosis (422 C. jejuni and 84 C. coli) and 586 controls. Important risk factors for campylobacteriosis included eating undercooked chicken (adjusted odds ratio [aOR] 70, 95% CI 13-1296) or cooked chicken (aOR 1.7, 95% CI 1.1-2.8), owning a pet dog aged < 6 months (aOR 6.4, 95% CI 3.4-12), and the regular use of proton-pump inhibitors in the 4 weeks prior to illness (aOR 2.8, 95% CI 1.9-4.3). Risk factors remained similar when analysed specifically for C. jejuni infection. Unique risks for C. coli infection included eating chicken pâté (aOR 6.1, 95% CI 1.5-25) and delicatessen meats (aOR 1.8, 95% CI 1.0-3.3). Eating any chicken carried a high population attributable fraction for campylobacteriosis of 42% (95% CI 13-68), while the attributable fraction for proton-pump inhibitors was 13% (95% CI 8.3-18) and owning a pet dog aged < 6 months was 9.6% (95% CI 6.5-13). The population attributable fractions for these variables were similar when analysed by campylobacter species. Eating delicatessen meats was attributed to 31% (95% CI 0.0-54) of cases for C. coli and eating chicken pâté was attributed to 6.0% (95% CI 0.0-11). CONCLUSIONS: The main risk factor for campylobacteriosis in Australia is consumption of chicken meat. However, contact with young pet dogs may also be an important source of infection. Proton-pump inhibitors are likely to increase vulnerability to infection.

Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia.

Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistance-associated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but ten-fold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.

Prevalence of Campylobacter coli and Campylobacter jejuni in Retail Chicken, Beef, Lamb, and Pork Products in Three Australian States.

The aim of this study was to investigate the prevalence and distribution of Campylobacter species in a variety of fresh and frozen meat and offal products collected from retail outlets in New South Wales (NSW), Queensland (Qld), and Victoria (Vic). A total of 1,490 chicken, beef, lamb, and pork samples were collected from Australian supermarkets and butcher shops over a 2-year sampling period (October 2016 to October 2018). Campylobacter spp. were detected in 90% of chicken meat and 73% of chicken offal products (giblet and liver), with significantly lower prevalence in lamb (38%), pork (31%), and beef (14%) offal (kidney and liver). Although retail chicken meat was frequently contaminated with Campylobacter, the level of contamination was generally low. Where quantitative analysis was conducted, 98% of chicken meat samples, on average, had <10,000 CFU Campylobacter per carcass, with 10% <21 CFU per carcass. Campylobacter coli was the most frequently recovered species in chicken meat collected in NSW (53%) and Vic (56%) and in chicken offal collected in NSW (77%), Qld (59%), and Vic (58%). In beef, lamb, and pork offal, C. jejuni was generally the most common species (50 to 86%), with the exception of pork offal collected in NSW, where C. coli was more prevalent (69%). Campylobacter prevalence was significantly higher in fresh lamb (46%) and pork (31%) offal than in frozen offal (17 and 11%, respectively). For chicken, beef, and pork offal, the prevalence of Campylobacter spp. was significantly higher on delicatessen products compared with prepackaged products. This study demonstrated that meat and offal products are frequently contaminated with Campylobacter. However, the prevalence is markedly different in different meats, and the level of chicken meat portion contamination is generally low. By identifying the types of meat and offal products types that pose the greatest risk of Campylobacter infection to consumers, targeted control strategies can be developed.

Analysis of the Listeria monocytogenes Population Structure among Isolates from 1931 to 2015 in Australia.

Listeriosis remains among the most important bacterial illnesses, with a high associated mortality rate. Efforts to control listeriosis require detailed knowledge of the epidemiology of the disease itself, and its etiological bacterium, Listeria monocytogenes. In this study we provide an in-depth analysis of the epidemiology of 224 L. monocytogenes isolates from Australian clinical and non-clinical sources. Non-human sources included meat, dairy, seafood, fruit, and vegetables, along with animal and environmental isolates. Serotyping, Multi-Locus Sequence Typing, and analysis of inlA gene sequence were performed. Serogroups IIA, IIB, and IVB comprised 94% of all isolates, with IVB over-represented among clinical isolates. Serogroup IIA was the most common among dairy and meat isolates. Lineage I isolates were most common among clinical isolates, and 52% of clinical isolates belonged to ST1. Overall 39 STs were identified in this study, with ST1 and ST3 containing the largest numbers of L. monocytogenes isolates. These STs comprised 40% of the total isolates (n = 90), and both harbored isolates from clinical and non-clinical sources. ST204 was the third most common ST. The high prevalence of this group among L. monocytogenes populations has not been reported outside Australia. Twenty-seven percent of the STs in this study contained exclusively clinical isolates. Analysis of the virulence protein InlA among isolates in this study identified a truncated form of the protein among isolates from ST121 and ST325. The ST325 group contained a previously unreported novel mutation leading to production of a 93 amino acid protein. This study provides insights in the population structure of L. monocytogenes isolated in Australia, which will contribute to public health knowledge relating to this important human pathogen.

Identification of an optimized panel of variable number tandem-repeat (VNTR) loci for Listeria monocytogenes typing.

Listeria monocytogenes is an important worldwide foodborne pathogen. For listeriosis outbreak investigations, an optimal multiple-locus variable-number-tandem-repeat analysis typing panel was identified from 4 previously reported schemes. The optimal combination of loci consisted of 9 loci (LMV6, LMV1, LMV2, Lm11, Lm10, LMV7, Lm32, LM-TR6, and Lm23), which produced the same level of differentiation ability Simpson index of 0.9914 as that of all 14 loci combined in the previous 4 reports. This panel provided higher differentiation ability than the individual of the 4 previously reported schemes, suggesting it would be useful for future surveillance and outbreak investigations.

Comparison of multiplex PCR with conventional biochemical methods for the identification of Listeria spp. isolates from food and clinical samples in Queensland, Australia.

Listeria monocytogenes is an important foodborne pathogen with high mortality. L. monocytogenes and five other Listeria species can frequently be found in the same sample. To identify Listeria isolates found in foods to the species level, two multiplex PCRs were designed. The PCR and conventional biochemical methods were compared for the identification of 456 Listeria isolates collected from routine food quality monitoring schemes between June 2004 and February 2006 and for 62 L. monocytogenes isolates from patients between 1999 and 2005. The results showed that the PCR and biochemical methods had 100% agreement in Listeria identification. The distribution of Listeria species from foods was as follows: L. monocytogenes, 50.4%; L. innocua, 33.8%; L. welshimeri, 14.9%; L. seeligeri, 0.7%; L. grayi, 0.2%; and L. ivanovii, 0.0%. Additional analyses were performed to identify the major serotypes (1/2a, 1/2b, 1/2c, and 4b) and the three lineages of L. monocytogenes isolates from foods and patients, with 1/2a (69.6%) and 1/2b (21.7%) dominating the food isolates and 1/2b (54.8%) and 4b (30.7%) dominating the patient isolates. The lineage results showed that isolates of 1/2a and 1/2c belonged to lineage II and that isolates of 1/2b and 4b belonged to lineage I. The multiplex PCRs for Listeria identification that have been established provide an accurate and rapid method for food quality control. This study has provided the basic knowledge of distribution of Listeria species and L. monocytogenes serotypes in Queensland, Australia, which is useful for epidemiological investigations of listeriosis.