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Vitali Sintchenko

Ben J Marais, Timothy M Walker, Daniela M Cirillo, Mario Raviglione, Ibrahim Abubakar, Marieke J van der Werf, Catharina Boehme, Stefan Niemann, Kenneth G Castro, Alimuddin Zumla, Vitali Sintchenko, Derrick W Crook
No abstract text is available yet for this article.
October 12, 2017: Lancet Respiratory Medicine
Songzhe Fu, Lester Hiley, Sophie Octavia, Mark M Tanaka, Vitali Sintchenko, Ruiting Lan
Salmonella enterica subsp enterica serovar Typhimurium (S. Typhimurium) is a serovar with broad host range. To determine the genomic diversity of S. Typhimurium, we sequenced 39 isolates (37 Australian and 2 UK isolates) representing 14 Repeats Groups (RGs) determined primarily by clustered regularly interspaced short palindromic repeats (CRISPR). Analysis of single nucleotide polymorphisms (SNPs) among the 39 isolates yielded an average of 1,232 SNPs per isolate, ranging from 128 SNPs to 11,339 SNPs relative to the reference strain LT2...
August 29, 2017: Scientific Reports
Trinh Quynh Mai, Nguyen Thi Van Anh, Nguyen Tran Hien, Nguyen Huu Lan, Do Chau Giang, Pham Thi Thu Hang, Nguyen Thi Ngoc Lan, Ben J Marais, Vitali Sintchenko
BACKGROUND: Mycobacterium tuberculosis strain diversity and drug resistance among people living with human immunodeficiency virus (HIV) in Vietnam have not been described previously. METHODS: We examined M. tuberculosis isolates from TB/HIV co-infected patients in Ho Chi Minh City, Vietnam. Drug susceptibility testing (DST), spoligotyping and 24-locus Mycobacterial Interspersed Repetitive Unit (MIRU-24 typing) were performed, and the rpoB, katG, inhA and inhA promoter, rpsL, rrs and embB genes were sequenced in all drug resistant isolates identified...
September 2017: Journal of Global Antimicrobial Resistance
John-Sebastian Eden, Karrie Rose, Jimmy Ng, Mang Shi, Qinning Wang, Vitali Sintchenko, Edward C Holmes
The occurrence of Francisella tularensis outside of endemic areas, such as North America and Eurasia, has been enigmatic. We report the metagenomic discovery and isolation of F. tularensis ssp. holarctica biovar japonica from diseased ringtail possums in Sydney, Australia. This finding confirms the presence of F. tularensis in the Southern Hemisphere.
July 2017: Emerging Infectious Diseases
C Biswas, S C-A Chen, C Halliday, K Kennedy, E G Playford, D J Marriott, M A Slavin, T C Sorrell, V Sintchenko
OBJECTIVES: Multi-antifungal drug resistance in Candida glabrata is increasing. We examined the feasibility of next-generation sequencing (NGS) to investigate the presence of antifungal drug resistance markers in C. glabrata. METHODS: The antifungal susceptibility of 12 clinical isolates and one ATCC strain of C. glabrata was determined using the Sensititre YeastOne(®) YO10 assay. These included three isolate pairs where the second isolate of each pair had developed a rise in drug MICs...
March 23, 2017: Clinical Microbiology and Infection
Sophie Octavia, Qinning Wang, Mark M Tanaka, Vitali Sintchenko, Ruiting Lan
We sequenced the genomes of 14 sequential Salmonella enterica serovar Typhimurium isolates obtained over a five year period from a patient with persistent Salmonella bacteriuria. The isolates formed five distinct lineages; two of which co-existed over four years. We inferred that the observed within-patient variation resulted from mutation events.
March 7, 2017: Infection, Genetics and Evolution
Laurence Don Wai Luu, Sophie Octavia, Ling Zhong, Mark Raftery, Vitali Sintchenko, Ruiting Lan
Our understanding of the Bordetella pertussis secretome remains limited including the role of different growth conditions in the secretome. In this study the secretome of L1423, a clinical isolate from the 2008-2012 Australian epidemic, cultured on Stainer-Scholte (SS) and Thalen-IJssel (THIJS) media for 12h was characterised using liquid chromatography-mass spectrometry (LC-MS/MS). In the supernatant, LC-MS/MS identified 260 proteins with 143 bioinformatically predicted to be secreted. Eighty percent of proteins were identified in both media...
March 31, 2017: Journal of Proteomics
Ben J Marais, Vitali Sintchenko
No abstract text is available yet for this article.
December 2, 2016: Lancet Infectious Diseases
Ulziijargal Gurjav, Baasansuren Erkhembayar, Buyankhishig Burneebaatar, Erdenegerel Narmandakh, Oyuntuya Tumenbayar, Grant A Hill-Cawthorne, Ben J Marais, Vitali Sintchenko
BACKGROUND: Mongolia has high and rising rates of multi-drug resistant tuberculosis (MDR-TB). Spatio-temporal and programmatic evidence suggests a major contribution from MDR-TB transmission, but genotypic evidence has not been assessed. METHODS: All MDR-TB cases identified during 2012 were examined. Demographic and bacteriological data were obtained from the National Tuberculosis Reference Laboratory. Isolates of Mycobacterium tuberculosis from culture-confirmed category 1 treatment failures were genotyped using 24-loci mycobacterium interspersed repetitive unit (MIRU-24) analysis...
December 2016: Tuberculosis
Jeremy Brown, Jason Patterson, Briony Hazelton, Mitchell Brown, Peter Jelfs, Vitali Sintchenko, Sharon C-A Chen
No abstract text is available yet for this article.
February 2016: Pathology
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...
December 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...
September 15, 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
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