Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.

Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.

Risk Stratification of Nursing Homes to Plan COVID-19 Responses: A Case Study of Victoria, Australia.

OBJECTIVE: Emergency management responses to coronavirus disease 2019 (COVID-19) in nursing homes lacked preparation and nuance; moving forward, responses must recognize nursing homes are not generic organizations or services, and individually appreciate each's unique nature, strengths, and limitations. The objective of this study was to describe an approach to stratifying nursing homes according to risk for COVID-19 outbreak. METHODS: Population-based cross-sectional study of all accredited nursing homes in Victoria (n = 766), accommodating 48,824 permanent residents. We examined each home's facility structure, governance history, socio-economic status, proximity to high-risk industry, and proximity and size of local acute public hospital, stratified by location, size, and organizational structure. RESULTS: Privately owned nursing homes tend to be larger and metropolitan-based, and publicly owned homes regionally based and smaller in size. The details reveal additional nuance, eg, privately owned metropolitan-based medium- to large-sized facilities tended to have more regulatory noncompliance, no board of governance, and fewer Chief Executive Officers with clinical background. In contrast, the smaller, publicly owned, remote facilities perform better on those same metrics. CONCLUSIONS: Nursing homes should not be regarded as generic entities, and there is significant underlying heterogeneity. Stratification of nursing homes according to risk level is a viable approach to informing more nuanced policy direction and resource allocation for emergency management responses.

Characteristics of nursing homes associated with COVID-19 outbreaks and mortality among residents in Victoria, Australia.

OBJECTIVE: To determine nursing home characteristics associated with COVID-19 outbreak, outbreak size and mortality, during the second wave in Victoria, Australia. METHOD: Population-based cross-sectional study of all nursing homes in Victoria between 7 July and 13 November 2020. RESULTS: There were one or more resident cases of COVID-19 in 9.7% of nursing homes (74/766). COVID-19 intrusion was more likely in larger metropolitan facilities, privately owned by large chains, with a past history of regulatory non-compliance, located close to high-risk industry. Larger outbreaks were associated with homes in metropolitan areas, accommodating 91 or more residents, with shared rooms, owned by private providers operating many (11 or more) facilities. The highest case-fatality rates were observed in homes owned by not-for-profit providers operating many facilities, located close to high-risk industry. CONCLUSION: Stratifying nursing homes according to characteristics associated with morbidity and mortality can inform risk management, prioritising emergency responses and optimising future nursing home operations.