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Vitali Sintchenko

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https://www.readbyqxmd.com/read/29566173/relentless-spread-and-adaptation-of-non-typeable-vana-vancomycin-resistant-enterococcus-faecium-a-genome-wide-investigation
#1
Sebastiaan J van Hal, Alicia G Beukers, Verlaine J Timms, Justin A Ellem, Peter Taylor, Michael W Maley, Peter J Newton, John K Ferguson, Andie Lee, Sharon C-A Chen, Vitali Sintchenko
Background: VRE are prevalent among patients in ICUs. Non-typeable vanA VRE, due to loss of one of the genes used for MLST (pstS), have increased in Australia, suggestive of a new, hospital-acquired lineage. Objectives: To understand the significance of this lineage and its transmission using WGS of strains isolated from patients in ICUs across New South Wales, Australia. Methods: A total of 240 Enterococcus faecium isolates collected between February and May 2016, and identified by conventional PCR as vanA positive, were sequenced...
March 16, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29553318/multidrug-resistant-salmonella-enterica-4-5-12-i-sequence-type-34-new-south-wales-australia-2016-2017
#2
Alicia Arnott, Qinning Wang, Nathan Bachmann, Rosemarie Sadsad, Chayanika Biswas, Cristina Sotomayor, Peter Howard, Rebecca Rockett, Agnieszka Wiklendt, Jon R Iredell, Vitali Sintchenko
Multidrug- and colistin-resistant Salmonella enterica serotype 4,[5],12:i:- sequence type 34 is present in Europe and Asia. Using genomic surveillance, we determined that this sequence type is also endemic to Australia. Our findings highlight the public health benefits of genome sequencing-guided surveillance for monitoring the spread of multidrug-resistant mobile genes and isolates.
April 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29464899/proteomic-adaptation-of-australian-epidemic-bordetella-pertussis
#3
Laurence Don Wai Luu, Sophie Octavia, Ling Zhong, Mark Raftery, Vitali Sintchenko, Ruiting Lan
Bordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from cluster II (non-ptxP3/non-prn2). Cluster I were mostly responsible for the 2008-2012 Australian epidemic and were found to have higher fitness compared to cluster II using an in vivo mouse competition assay, regardless of host's immunisation status. This study aimed to identify proteomic differences that explain higher fitness in cluster I using iTRAQ, and high-resolution multiple reaction monitoring (MRM-hr)...
February 21, 2018: Proteomics
https://www.readbyqxmd.com/read/29455870/detection-and-incidence-of-bordetella-holmesii-in-respiratory-specimens-from-patients-with-pertussis-like-symptoms-in-new-south-wales-australia
#4
Winkie Fong, Verlaine Timms, Nadine Holmes, Vitali Sintchenko
Bordetella pertussis, the aetiological agent of whooping cough is routinely diagnosed by polymerase chain reaction (PCR) directed at IS481, an insertion sequence target also found in Bordetella holmesii. Recent reports have suggested that B. holmesii infections can be misdiagnosed as pertussis, which can have a significant impact on public health surveillance. This study investigated the presence of B. holmesii in B. pertussis positive clinical samples, in order to determine the incidence of B. holmesii. Clinical cases of pertussis diagnosed by IS481-specific PCR between October 2008 and March 2016 in New South Wales were included...
February 15, 2018: Pathology
https://www.readbyqxmd.com/read/29364212/whole-genome-sequencing-of-candida-glabrata-for-detection-of-markers-of-antifungal-drug-resistance
#5
Chayanika Biswas, Sharon C-A Chen, Catriona Halliday, Elena Martinez, Rebecca J Rockett, Qinning Wang, Verlaine J Timms, Rajat Dhakal, Rosemarie Sadsad, Karina J Kennedy, Geoffrey Playford, Deborah J Marriott, Monica A Slavin, Tania C Sorrell, Vitali Sintchenko
Candida glabrata can rapidly acquire mutations that result in drug resistance, especially to azoles and echinocandins. Identification of genetic mutations is essential, as resistance detected in vitro can often be correlated with clinical failure. We examined the feasibility of using whole genome sequencing (WGS) for genome-wide analysis of antifungal drug resistance in C. glabrata. The aim was torecognize enablers and barriers in the implementation WGS and measure its effectiveness. This paper outlines the key quality control checkpoints and essential components of WGS methodology to investigate genetic markers associated with reduced susceptibility to antifungal agents...
December 28, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29336594/incorporating-whole-genome-sequencing-into-public-health-surveillance-lessons-from-prospective-sequencing-of-salmonella-typhimurium-in-australia
#6
Laura Ford, Glen P Carter, Qinning Wang, Torsten Seemann, Vitali Sintchenko, Kathryn Glass, Deborah A Williamson, Peter Howard, Mary Valcanis, Cristina Fabiola Sotomayor Castillo, Michelle Sait, Benjamin P Howden, Martyn D Kirk
In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months. We exchanged data via a central shared virtual machine and performed comparative genomic analyses...
March 2018: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/29247056/genome-sequencing-links-persistent-outbreak-of-legionellosis-in-sydney-new-south-wales-australia-to-an-emerging-clone-of-legionella-pneumophila-sequence-type-211
#7
Verlaine J Timms, Rebecca Rockett, Nathan L Bachmann, Elena Martinez, Qinning Wang, Sharon C-A Chen, Neisha Jeoffreys, Peter J Howard, Anna Smith, Sheena Adamson, Robin Gilmour, Vicky Sheppeard, Vitali Sintchenko
The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions, the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using single-nucleotide polymorphism (SNP)-based core-genome multilocus sequencing typing (MLST) and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and those in suburb 1...
March 1, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29033268/aiming-for-zero-tuberculosis-transmission-in-low-burden-countries
#8
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
https://www.readbyqxmd.com/read/28851865/comparative-genomics-of-australian-and-international-isolates-of-salmonella-typhimurium-correlation-of-core-genome-evolution-with-crispr-and-prophage-profiles
#9
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
https://www.readbyqxmd.com/read/28743648/drug-resistance-and-mycobacterium-tuberculosis-strain-diversity-in-tb-hiv-co-infected-patients-in-ho-chi-minh-city-vietnam
#10
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
https://www.readbyqxmd.com/read/28628459/francisella-tularensis-ssp-holarctica-in-ringtail-possums-australia
#11
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
https://www.readbyqxmd.com/read/28344162/identification-of-genetic-markers-of-resistance-to-echinocandins-azoles-and-5-fluorocytosine-in-candida-glabrata-by-next-generation-sequencing-a-feasibility-study
#12
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
https://www.readbyqxmd.com/read/28279807/genomic-heterogeneity-of-salmonella-enterica-serovar-typhimurium-bacteriuria-from-chronic-infection
#13
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
https://www.readbyqxmd.com/read/28242451/characterisation-of-the-bordetella-pertussis-secretome-under-different-media
#14
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
https://www.readbyqxmd.com/read/27919642/epidemic-spread-of-multidrug-resistant-tuberculosis-in-china
#15
Ben J Marais, Vitali Sintchenko
No abstract text is available yet for this article.
December 2, 2016: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/27865397/transmission%C3%A2-of-multi-drug-resistant-tuberculosis-in-mongolia-is-driven-by-beijing-strains-of-mycobacterium-tuberculosis-resistant-to-all-first-line-drugs
#16
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
https://www.readbyqxmd.com/read/27773076/pathology-use-stewardship-pre-analytical-review-of-tissue-specimens-previously-processed-by-default-for-mycobacterial-culture-maintains-the-quality-of-laboratory-diagnosis-and-optimises-the-use-of-laboratory-resources
#17
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
https://www.readbyqxmd.com/read/27749897/16s-23s-internal-transcribed-spacer-region-pcr-and-sequencer-based-capillary-gel-electrophoresis-has-potential-as-an-alternative-to-high-performance-liquid-chromatography-for-identification-of-slowly-growing-nontuberculous-mycobacteria
#18
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
https://www.readbyqxmd.com/read/27737005/whole-genome-sequencing-demonstrates-limited-transmission-within-identified-mycobacterium-tuberculosis-clusters-in-new-south-wales-australia
#19
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
https://www.readbyqxmd.com/read/27647159/snpfilt-a-pipeline-for-reference-free-assembly-based-identification-of-snps-in-bacterial-genomes
#20
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
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