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.

A protracted mumps outbreak in Western Australia despite high vaccine coverage: a population-based surveillance study.

BACKGROUND: In 2007-08, a genotype J mumps outbreak occurred among Aboriginal people in northern Western Australia, despite high vaccine coverage. In March, 2015, a second protracted mumps outbreak occurred in northern Western Australia and spread widely across rural areas of the state. This time the outbreak was caused by a genotype G virus and again primarily affected Aboriginal people. We aimed to describe the epidemiology of this outbreak. METHODS: In this population-based surveillance study, we analysed statutory notifications and public health case follow-up data from the Western Australia Notifiable Infectious Diseases Database and vaccination information from the Australian Childhood Immunisation Register. An outbreak case of mumps was notified if the affected person was living in or visiting a community in Western Australia where there was active mumps transmission, and if mumps infection was confirmed by laboratory diagnosis or by an epidemiological link. We analysed case demographics, vaccination status, and age-standardised attack rates in Aboriginal and non-Aboriginal people by region of notification. Laboratory diagnoses were made by real-time RT-PCR, serology, or both, and carried out by the sole public pathology provider in Western Australia. FINDINGS: Between March 1, 2015, and December 31, 2016, 893 outbreak cases were notified. 798 (89%) of 893 outbreak cases were reported in Aboriginal people. 40 (4%) of 893 people were admitted to hospital, and 33 (7%) of 462 men reported orchitis. Mumps attack rates increased sharply with age, peaking in the 15-19 age group. 371 (89%) of 419 people aged 1-19 years were fully vaccinated and 29 (7%) were partly vaccinated. Of the 240 people who tested positive by real-time RT-PCR and had also been tested for mumps-specific IgG and IgM, 165 (69%) were positive for IgG but negative for IgM, indicating the importance of RT-PCR testing for diagnosis in vaccinated populations. None of the cases from the 2007-08 genotype J outbreak were re-notified. INTERPRETATION: The number of mumps outbreaks reported in recent years among highly vaccinated populations, including Indigenous populations, has been growing. More widespread and pre-emptive use of the third dose of measles, mumps, and rubella vaccine might be required to control and prevent future outbreaks in high-risk populations. Research should explore the benefit of increasing the intervals between vaccine doses to strengthen the durability of vaccine protection. FUNDING: None.

Re-emergence of thiamine deficiency disease in the Pacific islands (2014-15): A case-control study.

BACKGROUND: From late 2014 multiple atolls in Kiribati reported an unusual and sometimes fatal illness. We conducted an investigation to identify the etiology of the outbreak on the most severely affected atoll, Kuria, and identified thiamine deficiency disease as the cause. Thiamine deficiency disease has not been reported in the Pacific islands for >5 decades. We present the epidemiological, clinical, and laboratory findings of the investigation. METHODOLOGY/PRINCIPAL FINDINGS: We initially conducted detailed interviews and examinations on previously identified cases to characterize the unknown illness and develop a case definition. Active and passive surveillance was then conducted to identify additional cases. A questionnaire to identify potential risk factors and blood samples to assay biochemical indices were collected from cases and asymptomatic controls. Thiamine hydrochloride treatment was implemented and the response to treatment was systematically monitored using a five-point visual analogue scale and by assessing resolution of previously abnormal neurological examination findings. Risk factors and biochemical results were assessed by univariate and multivariate analyses. 69 cases were identified on Kuria (7% attack rate) including 34 confirmed and 35 unconfirmed. Most were adults (median age 28 years [range 0-62]) and 83% were male. Seven adult males and two infants died (13% case fatality rate). Resolution of objective clinical signs (78%) or symptoms (94%) were identified within one week of starting treatment. Risk factors included having a friend with thiamine deficiency disease and drinking kava; drinking yeast alcohol reduced the risk of disease. Higher chromium (p<0·001) but not thiamine deficiency (p = 0·66) or other biochemical indices were associated with disease by univariate analyses. Chromium (p<0·001) and thiamine deficiency (p = 0·02) were associated with disease by multivariate analysis. CONCLUSIONS/SIGNIFICANCE: An outbreak of thiamine deficiency disease (beriberi) in Kiribati signals the re-emergence of a classic nutritional disease in the Pacific islands after five decades. Although treatment is safe and effective, the underlying reason for the re-emergence remains unknown. Chromium was highly and positively correlated with disease in this study raising questions about the potential role of factors other than thiamine in the biochemistry and pathophysiology of clinical disease.

Hepatitis A outbreak associated with kava drinking.

Hepatitis A is caused by the hepatitis A virus (HAV), with transmission occurring through the faecal-oral route. In May 2013, a case of hepatitis A infection was reported to a Western Australian regional public health unit, with infection acquired in Fiji. Following this, 2 further cases were linked to the index case by kava drinking and 1 further case was a household contact of a secondary case. This outbreak highlights that the preparation of kava drink and/or the use of a common drinking vessel could be a vehicle for the transmission of HAV.

Should there be a standardised approach to the diagnostic workup of suspected adult encephalitis? A case series from Australia.

BACKGROUND: The clinical diagnosis of encephalitis is often difficult and identification of a causative organism is infrequent. The encephalitis syndrome may herald the emergence of novel pathogens with outbreak potential. Individual treatment and an effective public health response rely on identifying a specific pathogen. In Australia there have been no studies to try to improve the identification rate of encephalitis pathogens. This study aims to review the diagnostic assessment of adult suspected encephalitis cases. METHODS: A retrospective clinical audit was performed, of all adult encephalitis presentations between July 1998 and December 2007 to the three hospitals with adult neurological services in the Hunter New England area, northern New South Wales, Australia. Case notes were examined for evidence of relevant history taking, clinical features, physical examination, laboratory and neuroradiology investigations, and outcomes. RESULTS: A total of 74 cases were included in the case series. Amongst suspected encephalitis cases, presenting symptoms and signs included fever (77.0%), headache (62.1%), altered consciousness (63.5%), lethargy (32.4%), seizures (25.7%), focal neurological deficits (31.1%) and photophobia (17.6%). The most common diagnostic laboratory test performed was cerebrospinal fluid (CSF) analysis (n = 67, 91%). Herpes virus polymerase chain reaction (n = 53, 71.6%) and cryptococcal antigen (n = 46, 62.2%) were the antigenic tests most regularly performed on CSF. Neuroradiological procedures employed were computerized tomographic brain scanning (n = 68, 91.9%) and magnetic resonance imaging of the brain (n = 35, 47.3%). Thirty-five patients (47.3%) had electroencephalograms. The treating clinicians suspected a specific causative organism in 14/74 cases (18.9%), of which nine (12.1%) were confirmed by laboratory testing. CONCLUSIONS: The diagnostic assessment of patients with suspected encephalitis was not standardised. Appropriate assessment is necessary to exclude treatable agents and identify pathogens warranting public health interventions, such as those transmitted by mosquitoes and those that are vaccine preventable. An algorithm and guidelines for the diagnostic workup of encephalitis cases would assist in optimising laboratory testing so that clinical management can be best tailored to the pathogen, and appropriate public health measures implemented.

Field exercises are useful for improving public health emergency responses.

PROBLEM: Emergencies resulting from disease outbreaks and extreme environmental events present significant challenges for health services. CONTEXT: Preparing to effectively manage emergencies is a core activity in public health units. Field exercises support consolidation of biopreparedness by testing plans, identifying weaknesses, providing training opportunities and developing surge capacity. ACTION: An extended field exercise to test response to a novel influenza strain was conducted in New South Wales, Australia in September 2008, eight months before the influenza A(H1N1) 2009 pandemic emerged. Lasting four days and involving over 300 participants, the exercise was set in the early response phase with the staggered presentation of 41 cases to 36 emergency departments in the health area. An additional 150 contacts were written into a complex scenario to test the public health response. OUTCOME: The subsequent pandemic emergence in mid-2009 offered a unique opportunity to assess the field exercise format for disaster preparedness. Most roles were adequately tested with recognized benefit during the actual pandemic response. However, the exercise did not adequately challenge the public health planning team that synthesizes surveillance data and forecasts risk, nor did it identify planning issues that became evident during the subsequent pandemic. DISCUSSION: Field exercises offer the opportunity to rigorously test public health emergency preparedness but can be expensive and labour-intensive. Our exercise provided effective and timely preparation for the influenza A(H1N1) 2009 pandemic but showed that more emphasis needs to be placed on the role and training of the public health planning team.

Encephalitis in Australia, 1979-2006: trends and aetiologies.

The acute encephalitis syndrome has heralded the emergence of multiple virulent pathogens, including Murray Valley encephalitis, Hendra virus and Australian bat lyssavirus, which may result in severe morbidity and mortality. In Australia, encephalitis is not notifiable and there has been no analysis of trends in encephalitis death rates or causation. Australian Bureau of Statistics mortality and population data for the period 1979-2006 were obtained and cause of death data were extracted using ICD-9 (1979-1998) and ICD-10 (1999-2006) codes that included all relevant encephalitis related diagnoses. Encephalitis-associated deaths were analysed by cause, year, age and gender. Between 1979 and 2006 there were 1,118 encephalitis-associated deaths in Australia. The average annual death rate was 2.3 per 1 million population (range 1.3-3.6). There was a significant decline in encephalitis-associated deaths, particularly due to 'known' pathogens (4.3% decline per year, 95% CI 3.1-5.4%, P<0.0001). The aetiology of 576 deaths were unknown and the proportion of deaths due to 'unknown' encephalitis increased from 47.0% between 1979 and 1992, to 57.2% from 1993 to 2006. Downward trends in encephalitis deaths due to 'known' causes can largely be explained by changes in treatment and prevention methods, particularly for herpes encephalitis (use of acyclovir), and measles encephalitis and subacute sclerosing panencephalitis (measles vaccination). The high proportion of encephalitis deaths from 'unknown' pathogens in Australia highlights the importance of monitoring encephalitis morbidity and mortality with a view to improving pathogen diagnosis and identifying emerging infectious diseases.

Etiology of encephalitis in Australia, 1990-2007.

Encephalitis is a clinical syndrome commonly caused by emerging pathogens, which are not under surveillance in Australia. We reviewed rates of hospitalization for patients with encephalitis in Australia's most populous state, New South Wales, from January 1990 through December 2007. Encephalitis was the primary discharge diagnosis for 5,926 hospital admissions; average annual hospitalization rate was 5.2/100,000 population. The most commonly identified pathogen was herpes simplex virus (n = 763, 12.9%). Toxoplasma encephalitis and subacute sclerosing panencephalitis showed notable declines. The average annual encephalitis case-fatality rate (4.6%) and the proportion of patients hospitalized with encephalitis with no identified pathogen (69.8%, range 61.5%-78.7%) were stable during the study period. The nonnotifiable status of encephalitis in Australia and the high proportion of this disease with no known etiology may conceal emergence of novel pathogens. Unexplained encephalitis should be investigated, and encephalitis hospitalizations should be subject to statutory notification in Australia.

Lessons from the Pacific programme to eliminate lymphatic filariasis: a case study of 5 countries.

BACKGROUND: Lymphatic Filariasis (LF) is an important Neglected Tropical Disease, being a major cause of disability worldwide. The Global Programme to Eliminate Lymphatic Filariasis aims to eliminate LF as a public health problem by the year 2020, primarily through repeated Mass Drug Administration (MDA). The Pacific region programme commenced in 1999. By June 2007, five of the eleven countries classified as endemic had completed five MDA campaigns and post-MDA prevalence surveys to assess their progress. We review available programme data and discuss their implications for other LF elimination programs in developing countries. METHODS: Reported MDA coverage and results from initial surveys and post-MDA surveys of LF using the immunochromatographic test (ICT) from these five Pacific Island countries (Tonga, Niue, Vanuatu, Samoa and Cook Islands) were analysed to provide an understanding of their quality and programme progress towards LF elimination. Denominator data reported by each country programme for 2001 was compared to official sources to assess the accuracy of MDA coverage data. RESULTS: Initial survey results from these five countries revealed an ICT prevalence of between 2.7 and 8.6 percent in individuals tested prior to commencement of the programme. Country MDA coverage results varied depending on the source of denominator data. Of the five countries in this case study, three countries (Tonga, Niue and Vanuatu) reached the target prevalence of <1% antigenaemia following five rounds of MDA. However, endpoint data could not be reliably compared to baseline data as survey methodology varied. CONCLUSION: Accurate and representative baseline and post-campaign prevalence data is crucial for determining program effectiveness and the factors contributing to effectiveness. This is emphasised by the findings of this case study. While three of the five Pacific countries reported achieving the target prevalence of <1% antigenaemia, limitations in the data preclude identification of key determinants of this achievement.

A norovirus outbreak associated with consumption of NSW oysters: implications for quality assurance systems.

Norovirus is a common cause of gastroenteritis outbreaks associated with raw shellfish consumption. In Australia there have been several reports of norovirus outbreaks associated with oysters despite the application of regulatory measures recommended by Food Standards Australia New Zealand. This study describes an outbreak of norovirus gastroenteritis following the consumption of New South Wales oysters. In September 2007, OzFoodNet conducted a cohort study of a gastroenteritis outbreak amongst people that had dined at a Port Macquarie restaurant. Illness was strongly associated with oyster consumption, with all cases having eaten oysters from the same lease (RR undefined, p < 0.0001). Norovirus was detected in a faecal specimen. Although no pathogen was identified during the environmental investigation, the source oyster lease had been closed just prior to harvesting due to sewage contamination. Australian quality assurance programs do not routinely test oysters for viral contamination that pose a risk to human health. It is recommended that the feasibility of testing oysters for norovirus, particularly after known faecal contamination of oyster leases, be assessed.