Clinical and public health utility of Mycobacterium tuberculosis whole genome sequencing.

The World Health Organization (WHO) estimates that around 10 million people develop tuberculosis (TB) every year, with 1.5 million deaths attributed to TB in 2019 (World Health Organization, 2020). The majority of the disease burden occurs in low-income countries, where access to diagnostics and tailored treatment remains problematic. The current COVID-19 pandemic further threatens to impact global TB control by diverting resources, reducing notifications and hence significantly increasing deaths attributable to TB (World Health Organization, 2020). Whole genome sequencing (WGS) is becoming increasingly accessible, and has particular value in the diagnosis and management of TB disease (Cabibbe et al., 2018; Meehan et al., 2019). Not only does it have the potential to give more rapid and complete information on drug-resistance, but the high discriminatory power it offers allows detection of clusters and transmission pathways, as well as likely contamination events, mixed infections and to differentiate between re-infection and relapse with much greater confidence than previous typing methods.

Clinical characteristics and outcomes of COVID-19 in a low-prevalence, well resourced setting, Sydney, Australia.

BACKGROUND: The Northern Sydney Local Health District was one of the first health regions to be affected by COVID-19 in Australia. AIMS: To describe the clinical characteristics, risk factors and outcomes in our low-prevalence Australian population. METHODS: This is a retrospective analysis of 517 laboratory-confirmed COVID-19 cases between January and June 2020. Patient information was collected as part of routine care within the COVID-19 Virtual Hospital system. Outcomes examined were death, recovery at 30 days and intensive care unit (ICU) admission. RESULTS: The case fatality rate was 1.8%. Multivariate analysis showed factors independently associated with death, composite outcome of death/ICU admission or incomplete recovery at 30 days were age >80 years and presence of two or more comorbidities. Most cases acquired COVID-19 through international (50.9%) or cruise ship travel (9.1%). Healthcare workers comprised 12.8% of the cohort and represented a disproportionately high percentage of the 'unknown' source group (27.6%). The median incubation period was 5 days (interquartile range 3-8); one patient had an incubation period of 15 days. Hospitalisation was required in 11.8%, ICU admission in 2.1% and ventilation in 1.4%. A Radiographic Assessment of Lung Oedema score on chest X-ray of >10 was independently associated with death. CONCLUSIONS: In this low prevalence, well resourced Australian setting, we report an overall low mortality. Factors associated with adverse patient outcomes on multivariate analysis were age greater than 80 and the presence of two or more comorbidities. These data can assist in early risk stratification of COVID-19 patients, and in surge capacity planning for hospitals.