Biology subjects

Sintchenko, V.

Publications and source records attributed to Sintchenko, V..

24 records · Page 2Linked to original sources

bioRxiv2020

REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING

Community transmission of the new coronavirus SARS-CoV-2 is a major public health concern that remains difficult to assess. We present a genomic survey of SARS-CoV-2 from a during the first 10 weeks of COVID-19 activity in New South Wales, Australia. Transmission events were monitored prospectively during the critical period of implementation of national control measures. SARS-CoV-2 genomes were sequenced from 209 patients diagnosed with COVID-19 infection between January and March 2020. Only a quarter of cases appeared to be locally acquired and genomic-based estimates of local transmission rates were concordant with predictions from a computational agent-based model. This convergent assessment indicates that genome sequencing provides key information to inform public health action and has improved our understanding of the COVID-19 evolution from outbreak to epidemic.

microbiology↗

bioRxiv2020

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

microbiology↗

bioRxiv2020

Genomic surveillance enables suitability assessment of Salmonella gene targets used for culture-independent diagnostic testing

Salmonella is a highly diverse genus consisting of over 2600 serovars responsible for high-burden food- and water-borne gastroenteritis worldwide. Sensitivity and specificity of PCR-based culture-independent diagnostic testing (CIDT) systems for Salmonella, which depend on a highly conserved gene target, can be affected by single nucleotide polymorphisms (SNPs), indels and genomic rearrangements within primer and probe sequences. This report demonstrates the value of prospectively collected genomic data for verifying CIDT targets. We utilised the genomes of 3165 Salmonella isolates prospectively collected and sequenced in Australia. The sequence of Salmonella CIDT PCR gene targets (ttrA, spaO and invA) were systematically interrogated to measure nucleotide dissimilarity. Analysis of 52 different serovars and 79 MLST types demonstrated dissimilarity within and between PCR gene targets ranging between 0 - 81.3 SNP/Kbp (0 and 141 SNPs). Lowest average dissimilarity was observed in the ttrA target gene used by the Roche LightMix at 2.0 SNP/Kbp [range 0 - 46.7]), however entropy across the gene demonstrates it may not be the most stable CIDT target. While debate continues over the benefits and pitfalls of replacing bacterial culture with molecular assays, the growing volumes of genomic surveillance data enable periodic regional reassessment and validation of CIDT targets against both prevalent and emerging serovars. If PCR systems are to become the primary screening and diagnostic tool for laboratory diagnosis of salmonellosis, ongoing monitoring of the genomic diversity in PCR target regions is warranted as is the potential inclusion of two Salmonella PCR targets into frontline diagnostic systems.

microbiology↗

bioRxiv2019

Complete microbial genomes for public health in Australia and Southwest Pacific

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia. These enrich the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health labs.\n\nAnnouncementWhole-genome sequence (WGS) data is increasingly important in public health microbiology (1-4). The data can be used to replicate many of the basic bacterial sub-typing approaches, as well as support epidemiological investigations, such as surveillance and outbreak investigation (5-7). The appeal of WGS data comes from the promise of a single workflow to process all microbial pathogens that can provide easily portable data that promotes deeper integration of surveillance and investigation efforts across jurisdictions. This promise is leading to a concerted effort to move microbial public health to a primarily genome-based workflow at numerous jurisdictions (8-10), including Australia (11).

genomics↗

bioRxiv2017

Genome Sequencing Links Persistent Outbreak Of Legionellosis In Sydney To An Emerging Clone Of Legionella pneumophila ST211

The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and bring the outbreak to a close we examined the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks. A total of 48 isolates from patients and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (March and May) and Suburb 1. These isolates were designated \"Main cluster\" and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from Suburb 1 and isolates from two cooling towers and three patients from the CDB May outbreak. All main cluster isolates were sequence type ST211 which has only ever been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique T4ASS that was specific to the main cluster and co-circulating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing was key in deciphering the environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in this highly populated urban setting. Further, the discovery of a unique T4ASS emphasises the potential contribution of genome recombination in the emergence of successful Lp1 clones.

genomics↗

bioRxiv2017

Genome-Wide Comparison Of Toxigenic And Non-Toxigenic Corynebacterium diphtheriae Isolates Identifies Differences In The Pan Genomes Between Respiratory And Cutaneous Strains

ObjectivesCorynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C. diphtheriae strains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species.\n\nMethodsThis study examined genomic diversity among 47 C. diphtheriae isolates collected in Australia over a 10-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis.\n\nResultsC. diphtheriae sequence type (ST) 32, a non-toxigenic ST with evidence of enhanced virulence that is also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by toxigenic as well as non-toxigenic strains.\n\nConclusionsThe genomic diversity of toxigenic and non-toxigenic strains of C. diphtheriae in Australia suggests multiple local and overseas sources of infection and colonisation. Our findings suggest that regular genomic surveillance of co-circulating toxigenic and non-toxigenic C. diphtheriae can deliver highly nuanced data in order to inform targeted public health actions and policy for predicting the future impact of this highly successful pathogen.

microbiology↗