Alexandersen, S. | Search bioRxiv

bioRxiv2020

A preliminary investigation of major bacterial antibiotic resistance genes present in Australian fecal samples using shotgun metagenomics and targeted sequencing.

The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs); however, in Australia the profile of the gut resistome, or ensemble of ARGs, has not been investigated. This study provides a first preliminary mapping of the major bacterial ARGs present in human, domestic dog and wild duck fecal samples collected from south-eastern Victoria, Australia; and evaluates the use of shotgun metagenomics sequencing (SMS) and targeted amplification of ARGs. We analysed SMS data using an in-house method and web-based bioinformatics tools: ResFinder and KmerResistance. We examined targeted sequences using One Codex or the PanBacterialAnalysis Torrent Suite plugin. All methods detected ARGs in all samples, with resistance to up to 13 classes of antibiotics detected overall. ARGs were more abundant in the human and dog samples than the duck samples. They mostly conferred resistance to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, {beta}-lactams and MLSB (macrolide, lincosamide, streptogramin B). Targeted sequencing significantly improved sensitivity for detection of ARGs included in the panel; however, SMS provided quantitative information and allowed tentative identification of the host bacteria. For SMS, web-based and in-house methods gave comparable results, with discrepancies mostly due to different reference databases. The in-house method allowed manually checking results and potential errors, while web-based methods were user-friendlier and less time-consuming. More samples need to be investigated to fully describe the resistome in humans and animals in Australia.

genomics↗

bioRxiv2018

Descriptive analysis in time and space of recorded data for Buruli Ulcer occurrence in Victoria over 22 years

BackgroundBuruli ulcer (BU) is a subcutaneous necrotic infection of the skin caused by Mycobacterium ulcerans. There has been increasing BU incidence in Victoria, Australia. The aim of this study to provide an epidemiological update of BU cases in Victoria to understand the pattern of distribution over time and space and attempt to identify local risk factors.\n\nMethodsA comprehensive descriptive epidemiological analyses were performed on BU notification data from 1994 to 2016. In addition, retrospective temporal, spatial and spatio-temporal analyses were conducted to understand the distribution of cases. Quantum GIS was used to generate maps. Demographic, new housing settlements and historical rainfall data were analysed to assess their effects on BU incidence in Victoria.\n\nFindingsThere were a total of 902 patients notified from 1994-2016. The incidence rate was 0.8/100,000 persons in Victoria. Space and time analyses showed that the most likely disease cluster was the Bellarine and Mornington Peninsulas with incidence rate 50 times higher than the State of Victoria rate. Gender was not a risk factor, but age was, with increased susceptibility among the over 60 year old group. There was an unusual high risk in the 15-24 age group in Point Lonsdale. Correlation analyses indicated that increase in population and construction of new settlements might be some of the reasons contributing to the rise in cases in Victoria.\n\nInterpretationThe findings agreed with published works in Australia of the increase in BU cases in Victoria. However, our findings also highlights the endemic nature of cases. The identified spatial disease clusters could be relevant for future environmental sampling studies or screening tests for M. ulcerans exposure.\n\nAuthor SummaryBuruli ulcer (BU) has been reported in 33 countries, mainly from the Tropics and Sub-tropics. Tropical cases are mainly within the West African region. Australia is the only country outside Africa in the top six highest incidence countries for BU. The exact mode of transmission remains unclear. Disease cases are rising in Australia, especially in Victoria for reasons that remains unclear. We have provided a descriptive epidemiological analyses in space and time of 22 years of recorded data on BU cases in Victoria from 1994 to 2016. We have also discussed demographic and new settlement dynamics over the study period. There were a total of 902 PCR-confirmed BU cases from 245 suburbs. Five suburbs on the Bellarine and Mornington Peninsulas were identified as the most endemic locations in Victoria. Spatial analyses detected a wider disease cluster area on the Peninsulas. We propose environmental sampling for risk factors analyses should focus on the endemic regions and some secondary clusters.

epidemiology↗