Publications by authors named "Anne Watt"

Genomics is a cornerstone of modern pathogen epidemiology yet demonstrating transmission in a One Health context is challenging, as strains circulate and evolve within and between diverse hosts and environments. To identify phylogenetic linkages and better define relevant measures of genomic relatedness in a One Health context, we collated 5471 Escherichia coli genome sequences from Australia originating from humans (n = 2996), wild animals (n = 870), livestock (n = 649), companion animals (n = 375), environmental sources (n = 292) and food (n = 289) spanning over 36 years. Of the 827 multi-locus sequence types (STs) identified, 10 STs were commonly associated with cross-source genomic clusters, including the highly clonal ST131, pandemic zoonotic lineages such as ST95, and emerging human ExPEC ST1193.

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Article Synopsis
  • - The Australian Pathogen Genomics Program (AusPathoGen) was launched in January 2021 as a national partnership aimed at enhancing public health through pathogen genomics surveillance.
  • - Successful implementation of this program relies on collaboration among academia, public health labs, and agencies, while prioritizing public health needs and building national genomics capacity.
  • - Key components for success include data integration tools like AusTrakka, standardized bioinformatics procedures, ethics agreements, and training for public health officials to effectively use genomic data.
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In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new 'phylepic' visualization that combines a phylogenomic tree with an epidemic curve.

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Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations.

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Serial intervals - the time between symptom onset in infector and infectee - are a fundamental quantity in infectious disease control. However, their estimation requires knowledge of individuals' exposures, typically obtained through resource-intensive contact tracing efforts. We introduce an alternate framework using virus sequences to inform who infected whom and thereby estimate serial intervals.

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Article Synopsis
  • The coronavirus pandemic has underscored the importance of using pathogen genomics in public health, though the ability to analyze genomic data varies globally, particularly in countries like Papua New Guinea (PNG) with limited resources.
  • PNG has faced significant COVID-19 outbreaks, with initial genomic analyses showing many cases from unclassified lineages, prompting collaboration between local health agencies and Australian laboratories to improve genomic monitoring.
  • An analysis of 1,797 SARS-CoV-2 sequences from PNG revealed the rapid spread of the B.1.466.2 lineage, pointing to multiple virus introductions and emphasizing the challenges posed by unclear lineage classifications in managing outbreaks.
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Background: COVID-19 has affected many 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.

Methods: Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia.

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Infection with Mycoplasma bovis has been identified as a growing threat in dairy industries worldwide and there is an urgent need for an inexpensive and accurate herd-level screening tool to identify herds that have been exposed to M. bovis. This study aimed to evaluate the use of the MilA ELISA for testing bulk tank milk (BTM) samples for antibodies against M.

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Two distinct isolates of the facultative parasite, were compared, identifying and utilising markers that are useful for studying clonal variation within the species were identified and utilised. The sequences of mitochondrial genomes and several nuclear genes were determined using Illumina short read sequencing. The two isolates had similar morphology.

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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. has several developmental forms.

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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.

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An unknown member of the family 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 () , the cause of Glasser's disease.

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