Biology subjects

Katouli, M.

Publications and source records attributed to Katouli, M..

3 recordsLinked to original sources

bioRxiv2021

Simple and cost-effective SNP genotyping method for discriminating subpopulations of the fish pathogen, Nocardia seriolae

Nocardia seriolae has caused significant fish losses in Asia and the Americas in recent decades, including in Vietnam, which has witnessed devastating economic and social impacts due to this bacterial pathogen. Surveillance strategies are urgently needed to mitigate N. seriolae dissemination in Vietnamese aquaculture and mariculture industries. Whole-genome sequencing (WGS) offers the highest level of resolution to discriminate closely related strains and to determine their putative origin and transmission routes. However, WGS is impractical for epidemiological investigations and pathogen surveillance due to its time-consuming and costly nature, putting this technology out-of-reach for many industry end-users. To overcome this issue, we targeted two previously characterised, phylogenetically informative single-nucleotide polymorphisms (SNPs) in N. seriolae that accurately distinguish: i) Vietnamese from non-Vietnamese strains, and ii) the two Vietnamese subclades. Using the mismatch amplification mutation assay (MAMA) format, we developed assays that genotype strains based on differences in amplicon melting temperature (melt-MAMA) and size (agarose-MAMA). Our MAMA assays accurately genotyped strains both from culture and fish tissues at low cost, using either real-time (~AUD$1/per sample) or conventional (~AUD$0.50/per sample) PCR instrumentation. Our novel assays provide a rapid, reproducible, and cost-effective tool for routine genotyping of this pathogen, allowing faster identification and treatment of nocardiosis-effected permit fish within Vietnamese aquaculture/mariculture facilities, an essential step in mitigating N. seriolae-associated losses.

microbiology↗

bioRxiv2021

Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in South Central Coast, Vietnam

Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin, and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South-Central Coast of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. Pulsed-field gel electrophoresis identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and single-nucleotide polymorphism (SNP) genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0-2 SNPs). There was no association between geographic origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 217 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55-7.96 Mbp in size, have an average G+C content of 68.2%, and encode 7,602-7,958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into N. seriolae epidemiology and pathogenicity and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.

genomics↗

bioRxiv2018

Acinetobacter baumannii detected on mCCDA medium in a waste stabilisation pond

Acinetobacter baumannii survives for prolonged periods under a wide range of environmental conditions. In a larger study investigating the efficacy of pathogen removal in a waste stabilization ponds (WSP), we cultivated microbes from wastewater samples on mCCDA agar containing selective and recommended supplements for the growth of Campylobacter. This bacterium is a recommended reference pathogen for the verification and validation of water recycling schemes in Australia and other parts of the world. A high number of colonies characteristic of Campylobacter grew on the selective media but this did not correlate with qPCR data. Using primers targeting the16S rRNA gene, and additional confirmatory tests such as detection of VS1, ompA, blaOXA-51-like, blaOXA-23-like genes, we tested eight random colonies from eight samples (64 colonies in total) and identified them as A. baumannii. Wastewater grab samples taken three times over 6 months throughout the WSP system showed removal of A. baumannii in the WSP atrates similar to E. coli. In contrast, further intensive sampling from the inlet and the outlet of the WSP using a refrigerated auto-sampler showed that the number of A. baumannii in most sampling rounds did not differ significantly between the inlet and outlet of the WSP and that there was high variation between replicates at the outlet only. Resistance genes were detected in most A. baumannii isolated from the waste stabilisation pond and may potentially be a source of antibiotic resistance for environmental strains.

microbiology↗