Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments.

After a limited first wave of community transmission in March 2020 and until 2022, Western Australia was largely free of COVID-19, with cases restricted to hotel quarantine, commercial vessels, and small, infrequent community clusters. Despite the low case load setting, sequencing of wastewater samples from large municipal treatment plants produced SARS-CoV-2 genomes with coverage up to 99.7 % and depth to 4000×, which was sufficient to link wastewater sequences to those of active cases in the catchment at the time. This study demonstrates that ≤5 positive individuals can be enough to produce high genomic coverage (>90 %) assemblies even in catchments of up to a quarter of a million people. Genomic analysis of wastewater contemporaneous with clinical cases can also be used to rule out transmission between cases in different catchments, when their SARS-CoV-2 genomes have distinguishing nucleotide polymorphisms. These findings reveal a greater potential of wastewater WGS to inform outbreak management and disease surveillance than previously recognized.

Legionnaires' Disease Outbreak on a Merchant Vessel, Indian Ocean, Australia, 2015.

Two cases of Legionnaires' disease and 1 of Pontiac fever occurred among the crew of a merchant ship operating off the shores of Australia. PCR assays identified potential sources in the ship's cabins. Modification of maritime regulations for Legionnaires' disease prevention in commercial vessels is needed for nonpassenger merchant ships.

Diagnosis of pertussis using nasopharyngeal IgA and polymerase chain reaction in specimens from outpatients in Australia.

We assessed IgA antibodies and polymerase chain reaction (PCR) for diagnosis of pertussis in nasopharyngeal aspiration (NPA) samples from outpatients in Australia. A total of 1700 patients (849 adults, 851 children) from Western Australia and the Northern Territory fulfilled the laboratory case definition for pertussis between 2004 and 2013: 732 specimens were positive by NPA IgA alone, 559 by PCR alone, and 409 by both tests. Overall, 968 cases (56.8%) were positive by PCR and 1141 cases (67.2%) by IgA [p < 0.00025]. Among pediatric patients, PCR was positive in 524 (61.3%) and IgA in 569 (67%). In 849 adult cases, the respective proportions were 52.3% and 67.4% [p < 0.00025]. The duration of cough in 507 patients was shorter in 262 pediatric cases (mean, 2.51 weeks; standard deviation [SD], 2.25) than 245 adult patients (3.27 weeks; SD, 2.79) [p = 0.0009]. PCR positivity showed a season-dependent variance (range, 5.6 to 85.9%) and peaked in the second week (71.7%) of illness. IgA antibodies peaked in the fifth week (89.5%) postinfection, and the positivity rate for NPA IgA was less variable (range, 38.3-97.2%). Nasopharyngeal Bordetella pertussis-specific IgA antibodies are valuable in diagnosis of pertussis in Australia. Reliance on PCR alone misses a significant proportion of pertussis cases, especially those with a delayed presentation.

Intussusception is associated with the detection of adenovirus C, enterovirus B and rotavirus in a rotavirus vaccinated population.

BACKGROUND: Intussusception, a condition where one segment of intestine invaginates into another, occurs predominantly in infants and young children. A number of potential causes have been identified including infectious agents and rotavirus vaccination. Following the introduction of rotavirus vaccination of infants in Western Australia, a laboratory surveillance programme testing notified intussusception cases for infectious agents was commenced. This led to a PCR-based study of the association between gastrointestinal viruses and intussusception. OBJECTIVES: Conduct viral testing on stool samples from intussusception patients to determine viruses that may have an association with intussusception. STUDY DESIGN: A retrospective case-control study was conducted using stool samples collected from children with intussusception (n=74) and matched controls (n=289) between 2008 and 2011. Samples were tested for rotavirus, norovirus, adenovirus, enterovirus, rhinovirus, astrovirus, parechovirus and bocavirus. Adenovirus, enterovirus and rhinovirus species were determined by DNA sequencing. RESULTS: Human adenovirus C was detected in significantly more cases than controls with 31/74 (41.9%) cases testing positive compared to 39/289 (13.49%) controls (OR=4.38, p<0.001). A significant difference was seen in Enterovirus B detections with 11/74 (14.9%) cases testing positive compared to 21/289 (7.3%) controls (OR=2.24, p=0.04). Rotavirus was detected in 7/74 (9.46%) cases and 11/289 (3.81%) controls, which was also a significant difference (OR=2.88, p=0.045). CONCLUSIONS: Our results show that intussusception is associated with non-enteric adenovirus infections, and Enterovirus B infections. While a statistical association was seen with rotavirus and intussusception, we were not able to determine if this was related to vaccine strain or wild type rotavirus.

Real-time PCR assay for detection of blaZ genes in Staphylococcus aureus clinical isolates.

The Clinical and Laboratory Standards Institute recommends consideration of blaZ gene testing for cases of serious Staphylococcus aureus infection. Conventional PCR methods have demonstrated superior sensitivity and specificity to phenotypic tests. To our knowledge, this is the first description of real-time PCR detection of the blaZ gene.

A prolonged mumps outbreak among highly vaccinated Aboriginal people in the Kimberley region of Western Australia.

OBJECTIVE: To describe a prolonged outbreak of mumps in the Kimberley region of Western Australia in 2007-2008. DESIGN: Descriptive analysis of all mumps cases notified to the WA Notifiable Infectious Diseases Database for the period 1 July 2007 to 30 June 2008. MAIN OUTCOME MEASURES: Notified cases of mumps by patients' place of residence, age, Indigenous or non-Indigenous ethnicity, vaccination status and method of diagnosis. RESULTS: 84% (153/183) of mumps notifications in WA over the study period occurred in the Kimberley region or were directly linked to Kimberley cases. Median age of patients was 18 years (range, 2-63 years), and 54% of patients were aged less than 20 years. Almost all (92%) were Australian Aboriginal people; 67% (102/153) had received at least one dose of mumps vaccine, and 52% had received two doses. The highest notification rate (1816 cases per 100,000 population) was in the Aboriginal 15-19-years age group, and 92% of these patients had received at least one dose of mumps vaccine. Almost all outbreak cases (94%) were laboratory confirmed. Genotyping was performed on 20 mumps virus isolates: all were genotype J. CONCLUSION: A prolonged outbreak of mumps occurred in a well defined, highly vaccinated, predominantly young Aboriginal population in the remote Kimberley region of WA. This outbreak raises questions about the effectiveness and scheduling of the current vaccine (which is genotype A-derived), especially for Aboriginal people. Surveillance of circulating mumps virus genotypes and neutralisation studies will help in evaluating the protection provided by the current vaccine against genotypically different strains.

Melioidosis risk in a tropical industrial environment.

An investigation into the risk of occupationally acquired melioidosis at a mine site in northern Australia found that 45 (13%) of 345 staff had serologic evidence of exposure and 14 (4%) had recent exposure to Burkholderia pseudomallei or closely related bacteria. There was only one culture-confirmed case of melioidosis in mine staff during the study period. The lack of overt infection directly attributable to work activities despite detectable B. pseudomallei on site, the absence of an association between positive serology and occupational activity on site, or duration of employment in the mining industry stand against a significant occupationally acquired infection risk on this industrial site. Workplace exposure to a dust-generating tropical environment in the melioidosis-endemic north of Australia did not appear to pose a measurable increase in infection risk. The effect of long-term climatic trends on this potential biologic threat requires further study.

Expanded range of Burkholderia species in Australia.

This study describes the isolation and characterization of several Burkholderia species from soil in northern Australia. Phenotypic and molecular tests indicate that these isolates belong to the species Burkholderia thailandensis and Burkholderia ubonensis. These observations significantly extend our knowledge of the geographic distribution of these 2 species. Evidence of these species in Australia has implications for bacterial identification in clinical laboratories, diagnostic serology tests, and environmental biodiversity studies.

A hospital-wide study of the impact of introducing a personal data assistant-augmented blood culture round.

Blood culture is the cornerstone of an established aetiological diagnosis of septicaemia. The automated blood culture systems used for this purpose have changed little in the last decade, and the clinical value of results depends on a variety of factors, including pre- and post-analytical variables. Growing scepticism over the value of blood culture results and pressure for the introduction of molecular detection systems have prompted a critical path analysis of pre-, peri- and post-analytical stages in the generation of positive blood culture results. The impact of a positive blood culture was studied in a teaching hospital for 12 months before and 12 months after the introduction of a microbiologist's blood culture round. Active culture reporting via a blood culture ward round was supported by a personal data assistant database of contemporaneous laboratory and clinical data. Hospital occupancy and death register records were subsequently obtained through the State Government data linkage project. There was no evidence that faster laboratory generation of positive blood culture results, faster reporting of results or direct clinical interaction with the patient's primary medical team reduced the risk of death in hospital. However, there was a threefold increase in the rate of death in hospital following a 1 day delay in collection of blood cultures after hospital admission (P=0.0010). The overall duration of hospital stay for patients with a positive blood culture fell by 2.5 days compared with the previous 12 month period (P=0.0003). The interval between the initial positive culture result and patient discharge fell by 2 days (P=0.0010). This difference was attributed to shorter overall admissions and shorter intervals between positive cultures containing Gram-positive cocci and subsequent patient discharge (P=0.0018). An increased mortality rate from community-acquired bacteraemic infections was associated with delayed culture collection, but not with a prolonged laboratory processing interval. Thus, the speed of conventional blood culture analysis and the form of clinical reporting have little direct effect on the clinical outcome of bacteraemia, but may contribute to a reduction in the length of hospital admission. Introduction of molecular identification tests, such as multiplex PCR methods, at the Gram-stain stage of blood culture is unlikely to affect the rate of death in hospital, but may reduce the length of hospital admission.