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Vitali Sintchenko

Shradha Subedi, Fanrong Kong, Peter Jelfs, Timothy J Gray, Meng Xiao, Vitali Sintchenko, Sharon C-A Chen
Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included...
2016: PloS One
Ulziijargal Gurjav, Alexander C Outhred, Peter Jelfs, Nadine McCallum, Qinning Wang, Grant A Hill-Cawthorne, Ben J Marais, Vitali Sintchenko
Australia has a low tuberculosis incidence rate with most cases occurring among recent immigrants. Given suboptimal cluster resolution achieved with 24-locus mycobacterium interspersed repetitive unit (MIRU-24) genotyping, the added value of whole genome sequencing was explored. MIRU-24 profiles of all Mycobacterium tuberculosis culture-confirmed tuberculosis cases diagnosed between 2009 and 2013 in New South Wales (NSW), Australia, were examined and clusters identified. The relatedness of cases within the largest MIRU-24 clusters was assessed using whole genome sequencing and phylogenetic analyses...
2016: PloS One
Carmen H S Chan, Sophie Octavia, Vitali Sintchenko, Ruiting Lan
De novo assembly of bacterial genomes from next-generation sequencing (NGS) data allows a reference-free discovery of single nucleotide polymorphisms (SNP). However, substantial rates of errors in genomes assembled by this approach remain a major barrier for the reference-free analysis of genome variations in medically important bacteria. The aim of this report was to improve the quality of SNP identification in bacterial genomes without closely related references. We developed a bioinformatics pipeline (SnpFilt) that constructs an assembly using SPAdes and then removes unreliable regions based on the quality and coverage of re-aligned reads at neighbouring regions...
September 9, 2016: Computational Biology and Chemistry
Anastasia Phillips, Cristina Sotomayor, Qinning Wang, Nadine Holmes, Catriona Furlong, Kate Ward, Peter Howard, Sophie Octavia, Ruiting Lan, Vitali Sintchenko
BACKGROUND: Salmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance. METHODS: We performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, food-borne outbreaks along with sporadic cases in New South Wales, Australia, during 2014...
2016: BMC Microbiology
Azadeh Safarchi, Sophie Octavia, Laurence Don Wai Luu, Chin Yen Tay, Vitali Sintchenko, Nicholas Wood, Helen Marshall, Peter McIntyre, Ruiting Lan
Molecular epidemiological data indicates that the resurgence of pertussis (whooping cough) in populations with high vaccine coverage is associated with genomic adaptation of Bordetella pertussis, the causative agent of the disease, to vaccine selection pressure. We have previously shown that in the period after the introduction of acellular pertussis vaccine (ACV), the majority of circulating strains in Australia switched to single nucleotide polymorphism (SNP) cluster I (carrying ptxP3/prn2), replacing SNP cluster II (carrying ptxP1/prn3)...
July 25, 2016: Vaccine
Mingfeng Yu, Gayathri Nagalingam, Samantha Ellis, Elena Martinez, Vitali Sintchenko, Malcolm Spain, Peter J Rutledge, Matthew H Todd, James A Triccas
Tuberculosis (TB) accounted for 1.5 million deaths in 2014, and new classes of anti-TB drugs are required. We report a class of functionalized 1,8-disubstituted cyclam derivatives that display low micromolar activity against pathogenic mycobacteria. These compounds inhibit intracellular growth of Mycobacterium tuberculosis, are nontoxic to human cell lines, and are active against multidrug-resistant M. tuberculosis strains, indicating a distinct mode of action. These compounds warrant further appraisal as novel agents to control TB in humans...
June 23, 2016: Journal of Medicinal Chemistry
Danesh Moradigaravand, Louis Grandjean, Elena Martinez, Hao Li, Jun Zheng, Jorge Coronel, David Moore, M Estée Török, Vitali Sintchenko, Hairong Huang, Babak Javid, Julian Parkhill, Sharon J Peacock, Claudio U Köser
No abstract text is available yet for this article.
June 2016: Antimicrobial Agents and Chemotherapy
David J Dickeson, Sharon C-A Chen, Vitali G Sintchenko
Serological tests show considerable variation in their ability to correctly diagnose Lyme borreliosis (LB). This study compared four commercially available screening enzyme immunoassays (EIA) for the detection of LB IgG using either whole cell lysate (WCL) antigens, purified proteins or recombinant antigens with the second-tier whole cell sonicate (WCS) western immunoblots or recombinant antigen line blots. A consensus between three EIA results from 222 patient sera was designated as a point of comparison for each method which gave 66 positive and 156 negative results...
April 2016: Pathology
Alexander C Outhred, Nadine Holmes, Rosemarie Sadsad, Elena Martinez, Peter Jelfs, Grant A Hill-Cawthorne, Gwendolyn L Gilbert, Ben J Marais, Vitali Sintchenko
BACKGROUND: Improved tuberculosis control and the need to contain the spread of drug-resistant strains provide a strong rationale for exploring tuberculosis transmission dynamics at the population level. Whole-genome sequencing provides optimal strain resolution, facilitating detailed mapping of potential transmission pathways. METHODS: We sequenced 22 isolates from a Mycobacterium tuberculosis cluster in New South Wales, Australia, identified during routine 24-locus mycobacterial interspersed repetitive unit typing...
2016: PloS One
Qinning Wang, Nadine Holmes, Elena Martinez, Peter Howard, Grant Hill-Cawthorne, Vitali Sintchenko
The control of food-borne outbreaks caused by Listeria monocytogenes in humans relies on the timely identification of food or environmental sources and the differentiation of outbreak-related isolates from unrelated ones. This study illustrates the utility of whole-genome sequencing for examining the link between clinical and environmental isolates of L. monocytogenes associated with an outbreak of hospital-acquired listeriosis in Sydney, Australia. Comparative genomic analysis confirmed an epidemiological link between the three clinical and two environmental isolates...
November 2015: Journal of Clinical Microbiology
Sophie Octavia, Qinning Wang, Mark M Tanaka, Vitali Sintchenko, Ruiting Lan
Salmonella enterica serovar Typhimurium is an important foodborne human pathogen that often causes self-limiting but severe gastroenteritis. Prolonged excretion of S. Typhimurium after the infection can lead to secondary transmissions. However, little is known about within-host genomic variation in bacteria associated with asymptomatic shedding. Genomes of 35 longitudinal isolates of S. Typhimurium recovered from 11 patients (children and adults) with culture-confirmed gastroenteritis were sequenced. There were three or four isolates obtained from each patient...
November 2015: Journal of Clinical Microbiology
Ulziijargal Gurjav, Peter Jelfs, Grant A Hill-Cawthorne, Ben J Marais, Vitali Sintchenko
In recent years the State of New South Wales (NSW), Australia, has maintained a low tuberculosis incidence rate with little evidence of local transmission. Nearly 90% of notified tuberculosis cases occurred in people born in tuberculosis-endemic countries. We analyzed geographic, epidemiological and genotypic data of all culture-confirmed tuberculosis cases to identify the bacterial and demographic determinants of tuberculosis hotspot areas in NSW. Standard 24-loci mycobacterium interspersed repetitive unit-variable number tandem repeat (MIRU-24) typing was performed on all isolates recovered between 2009 and 2013...
June 2016: Infection, Genetics and Evolution
Chinmay Khandkar, Zinta Harrington, Peter J Jelfs, Vitali Sintchenko, Claudia C Dobler
BACKGROUND: This study examined potential risk factors of lymph node tuberculosis (LNTB), including phylogenetic lineages of Mycobacterium tuberculosis (MTB), in comparison to pulmonary tuberculosis (PTB) in a setting with an ethnically diverse population. METHODS: We conducted a case-control study at a major tuberculosis clinic in Sydney, Australia, which included all patients with peripheral LNTB seen at the clinic between 2000 and 2012. Controls were randomly selected patients with PTB seen at the same clinic during the study period...
2015: PloS One
Jen Kok, Vitali Sintchenko, Dominic E Dwyer, Sharon C-A Chen
No abstract text is available yet for this article.
August 2015: Pathology
Nadine McCallum, Timothy J Gray, Qinning Wang, Jimmy Ng, Leanne Hicks, Trang Nguyen, Marion Yuen, Grant A Hill-Cawthorne, Vitali Sintchenko
Infant botulism is a potentially life-threatening paralytic disease that can be associated with prolonged morbidity if not rapidly diagnosed and treated. Four infants were diagnosed and treated for infant botulism in NSW, Australia, between May 2011 and August 2013. Despite the temporal relationship between the cases, there was no close geographical clustering or other epidemiological links. Clostridium botulinum isolates, three of which produced botulism neurotoxin serotype A (BoNT/A) and one BoNT serotype B (BoNT/B), were characterized using whole-genome sequencing (WGS)...
September 2015: Journal of Clinical Microbiology
Songzhe Fu, Sophie Octavia, Mark M Tanaka, Vitali Sintchenko, Ruiting Lan
Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined...
August 2015: Journal of Clinical Microbiology
Elena Martinez, Nadine Holmes, Peter Jelfs, Vitali Sintchenko
OBJECTIVES: Detection of pyrazinamide resistance in Mycobacterium tuberculosis isolates presents significant challenges in settings with no dominant clonal lineages, such as Australia. We assessed the utility of WGS versus standard PCR amplification assays for the characterization of pyrazinamide resistance in MDR-TB isolates identified in New South Wales, Australia, over an 8 year period. METHODS: PCR amplicon sequencing was used to identify molecular markers associated with antibiotic resistance in pyrazinamide-resistant MDR-TB isolates recovered by the New South Wales Mycobacterium Reference Laboratory between 2007 and 2014...
September 2015: Journal of Antimicrobial Chemotherapy
Vitali Sintchenko, Edward C Holmes
Whole genome sequencing (WGS) of pathogens enables the sources and patterns of transmission to be identified during specific disease outbreaks and promises to transform epidemiological research on communicable diseases. This review discusses new insights into disease spread and transmission that have come from the use of WGS, particularly when combined with genomic scale phylogenetic analyses. These include elucidation of the mechanisms of cross species transmission, the potential modes of pathogen transmission, and which people in the population contribute most to transmission...
2015: BMJ: British Medical Journal
Kate S Baker, Timothy J Dallman, Philip M Ashton, Martin Day, Gwenda Hughes, Paul D Crook, Victoria L Gilbart, Sandra Zittermann, Vanessa G Allen, Benjamin P Howden, Takehiro Tomita, Mary Valcanis, Simon R Harris, Thomas R Connor, Vitali Sintchenko, Peter Howard, Jeremy D Brown, Nicola K Petty, Malika Gouali, Duy Pham Thanh, Karen H Keddy, Anthony M Smith, Kaisar A Talukder, Shah M Faruque, Julian Parkhill, Stephen Baker, François-Xavier Weill, Claire Jenkins, Nicholas R Thomson
BACKGROUND: Shigellosis is an acute, severe bacterial colitis that, in high-income countries, is typically associated with travel to high-risk regions (Africa, Asia, and Latin America). Since the 1970s, shigellosis has also been reported as a sexually transmitted infection in men who have sex with men (MSM), in whom transmission is an important component of shigellosis epidemiology in high-income nations. We aimed to use sophisticated subtyping and international sampling to determine factors driving shigellosis emergence in MSM linked to an outbreak in the UK...
August 2015: Lancet Infectious Diseases
Zeina Najjar, Leena Gupta, Vitali Sintchenko, Craig Shadbolt, Qinning Wang, Narinder Bansal
No abstract text is available yet for this article.
May 4, 2015: Medical Journal of Australia
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