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Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals – the time between symptom onset in an infector and infectee – are fundamental, and help to define rates of transmission, estimates of reproductive numbers, and vaccination levels needed to prevent transmission. However, estimating the serial interval requires knowledge of individuals’ contacts and exposures (who infected whom), which is typically obtained through resource-intensive contact tracing efforts. We develop an alternate framework that uses virus sequences to inform who infected whom and thereby estimate serial intervals. The advantages are many-fold: virus sequences are often routinely collected to support epidemiological investigations and to monitor viral evolution. The genomic approach offers high resolution and cluster-specific estimates of the serial interval that are comparable with those obtained from contact tracing data. Our approach does not require contact tracing data, and can be used in large populations and over a range of time periods. We apply our techniques to SARS-CoV-2 sequence data from the first two waves of COVID-19 in Victoria, Australia. We find that serial interval estimates vary between clusters, supporting the need to monitor this key parameter and use updated estimates in onward applications. Compared to an early published serial interval estimate, using cluster-specific serial intervals can cause estimates of the effective reproduction number Rt to vary by a factor of up to 2–3. We also find that serial intervals estimated in settings such as schools and meat processing/packing plants tend to be shorter than those estimated in healthcare facilities.

Deroceras reticulatum also known as the Grey Field Slug is a serious agricultural and horticultural pest. Integrated pest management of D. reticulatum and other pest molluscs includes the use of ch...

Tetrahymena rostrata is a free-living ciliated protozoan and is a facultative parasite of some species of terrestrial mollusks. It is a potential biopesticide of pest slugs, such as the grey field slug, which cause considerable damage to crops. T. rostrata has several developmental forms. Homogeneous preparations of the feeding stage cells (trophonts) and excysted stage cells (theronts) were compared for their ability to infect and kill Deroceras reticulatum slugs. Theronts were more effective and remained viable and infective, even after prolonged starvation.

BackgroundCOVID-19 has resulted in many infections in healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks.MethodsGenome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire Victorian dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links.FindingsBetween March and October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of individual patients including super-spreading events. Key limitations at the HCF level were identified.InterpretationGenomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics.FundingThe Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.

Tetrahymena rostrata is a ciliated protist which can parasitize the gray field slug, Deroceras reticulatum. Here, we report the sequence of the mitochondrial genome (mt genome) of a strain of T. rostrata that was isolated from the egg of D. reticulatum. Whole cell genomic DNA was sequenced using Illumina® MiSeq and the mitochondrial DNA sequence reads were extracted and assembled. The resulting 47,235 bp assembly contained rRNAs, tRNAs, and 45 protein coding DNA sequences of which 21 encoded proteins of unknown function. Phylogenetic analysis showed T. rostrata clustered with Tetrahymena thermophila, Tetrahymena pigmentosa, Tetrahymena pyriformis, Tetrahymena paravorax, and Tetrahymena malaccensis.

Respiratory infections caused by Actinobacillus pleuropneumoniae have a large impact on commercial pig farms globally. As current vaccines have limited efficacy, animal care and air hygiene are critical for disease control. Here we used a Coriolis μ cyclonic air sampler and an A. pleuropneumoniae-specific apxIV gene qPCR assay to detect the organism. Air samples were collected into a liquid medium by the Coriolis μ sampler for A. pleuropneumoniae detection by plate culture and qPCR assay. The method was validated by comparing the Coriolis μ sampler and a plate impactor (Millipore Air-T) in a specially designed aerosolization chamber. Two commercial farms, housing pigs between 3 and 21 weeks of age, were tested. On one farm, A. pleuropneumoniae was detected in low numbers (1000 organisms/m3 air) by qPCR, but not by culture, from sheds containing 8, 12, 16, and 18 weeks-old pigs. To our knowledge this is the first successful detection of naturally aerosolised A. pleuropneumoniae in commercial farms with the Coriolis μ air sampler, potentially allowing the identification of sub-clinically infected populations of pigs in the field.

An unknown member of the family Pasteurellaceae was repeatedly isolated from 20- to 24-week-old pigs with severe pulmonary lesions reared on the same farm in Victoria, Australia. The etiological diagnosis of the disease was inconclusive. The complete genome sequence analysis of one strain, 15-184, revealed some phylogenic proximity to Glaesserella ( Haemophilus ) parasuis , the cause of Glasser's disease. However, the sequences of the 16S rRNA and housekeeping genes, as well as the average nucleotide identity scores, differed from those of all other known species in the family Pasteurellaceae . The protein content of 15-184 was composite, with 60% of coding sequences matching known G. parasuis products, while more than 20% had a closer relative in the genera Actinobacillus , Mannheimia , Pasteurella , and Bibersteinia . Several putative virulence genes absent from G. parasuis but present in other Pasteurellaceae were also found, including the apxIII RTX toxin gene from Actinobacillus pleuropneumoniae , ABC transporters from Actinobacillus minor , and iron transporters from various species. Three prophages and one integrative conjugative element were present in the isolate. Horizontal gene transfers might explain the mosaic genomic structure and atypical metabolic and virulence characteristics of 15-184. This organism has not been assigned a taxonomic position in the family, but this study underlines the need for a large-scale epidemiological and clinical characterization of this novel pathogen in swine populations, as a genomic analysis suggests it could have a severe impact on pig health. IMPORTANCE Several species of Pasteurellaceae cause a range of significant diseases in pigs. A novel member of this family was recently isolated from Australian pigs suffering from severe respiratory infections. Comparative whole-genome analyses suggest that this bacterium represents a new species, which possesses a number of virulence genes horizontally acquired from a diverse range of other Pasteurellaceae . While the possible contribution of other coinfecting noncultivable agents to the disease has not been ruled out in this study, the repertoire of virulence genes found in this organism may nevertheless explain some aspects of the associated pathology observed on the farm. The prevalence of this novel pathogen within pig populations is currently unknown. This finding is of particular importance for the pig industry, as this organism can have a serious impact on the health of these animals.