scholarly journals Application of whole genome sequencing to characterize Mycobacterium tuberculosis strains circulating in Far North Queensland, Australia and Western Province, Papua New Guinea

2018 ◽  
Author(s):  
Abwooli Bainomugisa
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Papua New Guinea ◽  
Genome Sequencing ◽  
New Guinea ◽  
Whole Genome ◽  
Far North ◽  
Western Province

scholarly journals Multi-clonal evolution of MDR/XDRM. tuberculosisin a high prevalence setting in Papua New Guinea over three decades

2017 ◽  
Author(s):  
Arnold Bainomugisa ◽  
Evelyn Lavu ◽  
Stenard Hiashiri ◽  
Suman Majumdar ◽  
Alice Honjepari ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Papua New Guinea ◽  
Genome Sequencing ◽  
Clonal Evolution ◽  
New Guinea ◽  
Molecular Dating ◽  
Whole Genome ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Public Health Response

AbstractAn outbreak of multi-drug resistant tuberculosis has been reported on Daru Island, Papua New Guinea. TheMycobacterium tuberculosisstrains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. We analyzed 100 isolates using whole genome sequencing and found 95 belonged to a single modern Beijing strain cluster. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with virulence potentially enhanced by amycP1mutation. The outbreak cluster demonstrated a high degree of co-resistance between isoniazid and ethionamide (80/95; 84.2%) attributed to aninhApromoter mutation combined withinhAandndhcoding mutations. Multidrug resistance (MDR), observed in 78/95 samples, emerged with the acquisition of a typicalrpoBmutation together with a compensatoryrpoCmutation in the 1980s. There was independent acquisition of fluoroquinolone and aminoglycoside resistance; with evidence of local transmission of extensively-drug resistant (XDR) strains from 2009. These findings underscore the importance of whole-genome sequencing in informing an effective public health response to MDR/XDRM. tuberculosis.

scholarly journals Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories forAnopheles punctulatusmosquitoes in Papua New Guinea

2015 ◽  
Vol 24 (6) ◽  
pp. 1263-1274 ◽  
Author(s):  
Kyle Logue ◽  
Scott T. Small ◽  
Ernest R. Chan ◽  
Lisa Reimer ◽  
Peter M. Siba ◽  
...  
Keyword(s):  
Gene Flow ◽  
Whole Genome Sequencing ◽  
Papua New Guinea ◽  
Genome Sequencing ◽  
New Guinea ◽  
Whole Genome ◽  
Recent Gene Flow

scholarly journals Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State

2017 ◽  
Vol 55 (6) ◽  
pp. 1871-1882 ◽  
Author(s):  
Joseph Shea ◽  
Tanya A. Halse ◽  
Pascal Lapierre ◽  
Matthew Shudt ◽  
Donna Kohlerschmidt ◽  
...  
Keyword(s):  
New York ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Predictive Value ◽  
New York State ◽  
Whole Genome ◽  
Content Type ◽  
York State

ABSTRACTWhole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterizeMycobacterium tuberculosisand otherM. tuberculosiscomplex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.

scholarly journals Genome Sequencing of Polydrug-, Multidrug-, and Extensively Drug-Resistant Mycobacterium tuberculosis Strains from South India

2019 ◽  
Vol 8 (12) ◽  
Author(s):  
Sivakumar Shanmugam ◽  
Narender Kumar ◽  
Dina Nair ◽  
Mohan Natrajan ◽  
Srikanth Prasad Tripathy ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
South India ◽  
Sequence Data ◽  
Whole Genome ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Content Type ◽  
Extensively Drug Resistant

The genomes of 16 clinical Mycobacterium tuberculosis isolates were subjected to whole-genome sequencing to identify mutations related to resistance to one or more anti-Mycobacterium drugs. The sequence data will help in understanding the genomic characteristics of M. tuberculosis isolates and their resistance mutations prevalent in South India.

scholarly journals Whole-Genome Sequencing of Drug-Resistant Mycobacterium tuberculosis Strains, Tunisia, 2012–2016

2019 ◽  
Vol 25 (3) ◽  
pp. 538-546
Author(s):  
Imen Bouzouita ◽  
Andrea Maurizio Cabibbe ◽  
Alberto Trovato ◽  
Henda Daroui ◽  
Asma Ghariani ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Drug Resistant

scholarly journals Whole genome sequencing of Mycobacterium tuberculosis

2018 ◽  
Vol 52 (5) ◽  
pp. 1801163 ◽  
Author(s):  
Andrea M. Cabibbe ◽  
Timothy M. Walker ◽  
Stefan Niemann ◽  
Daniela M. Cirillo
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome
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