Whole-Genome Sequencing Reveals Recent Transmission of Multidrug-Resistant Mycobacterium tuberculosis CAS1-Kili Strains in Lusaka, Zambia

Globally, tuberculosis (TB) is a major cause of death due to antimicrobial resistance. Mycobacterium tuberculosis CAS1-Kili strains that belong to lineage 3 (Central Asian Strain, CAS) were previously implicated in the spread of multidrug-resistant (MDR)-TB in Lusaka, Zambia. Thus, we investigated recent transmission of those strains by whole-genome sequencing (WGS) with Illumina MiSeq platform. Twelve MDR CAS1-Kili isolates clustered by traditional methods (MIRU-VNTR and spoligotyping) were used. A total of 92% (11/12) of isolates belonged to a cluster (≤12 SNPs) while 50% (6/12) were involved in recent transmission events, as they differed by ≤5 SNPs. All the isolates had KatG Ser315Thr (isoniazid resistance), EmbB Met306 substitutions (ethambutol resistance) and several kinds of rpoB mutations (rifampicin resistance). WGS also revealed compensatory mutations including a novel deletion in embA regulatory region (−35A > del). Several strains shared the same combinations of drug-resistance-associated mutations indicating transmission of MDR strains. Zambian strains belonged to the same clade as Tanzanian, Malawian and European strains, although most of those were pan-drug-susceptible. Hence, complimentary use of WGS to traditional epidemiological methods provides an in-depth insight on transmission and drug resistance patterns which can guide targeted control measures to stop the spread of MDR-TB.

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Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia

Journal of Medical Microbiology ◽

10.1099/jmm.0.001221 ◽

2020 ◽

Vol 69 (7) ◽

pp. 1013-1019

Author(s):

Tryna Tania ◽

Pratiwi Sudarmono ◽

R. Lia Kusumawati ◽

Andriansjah Rukmana ◽

Wahyu Agung Pratama ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Public Health Problem ◽

Multidrug Resistant ◽

Drug Susceptibility Testing ◽

Major Public Health Problem ◽

Whole Genome ◽

Sequencing Analysis ◽

Mdr Tb

Introduction. Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia. Aim. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant Mycobacterium tuberculosis in Java, Indonesia. Methodology. Thirty suspected MDR-TB isolates were subjected to MGIT 960 system (MGIT)-based DST and to WGS. Phylogenetic analysis was done using the WGS data. Results obtained using MGIT-based DST and WGS-based DST were compared. Results. Agreement between WGS and MGIT was 93.33 % for rifampicin, 83.33 % for isoniazid and 76.67 % for streptomycin but only 63.33 % for ethambutol. Moderate WGS–MGIT agreement was found for second-line drugs including amikacin, kanamycin and fluoroquinolone (73.33–76.67 %). MDR-TB was more common in isolates of the East Asian Lineage (63.3%). No evidence of clonal transmission of DR-TB was found among members of the tested population. Conclusion. Our study demonstrated the applicability of WGS for DST and molecular epidemiology of DR-TB in Java, Indonesia. We found no transmission of DR-TB in Indonesia.

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Transmission of multidrug-resistant tuberculosis in Shimen community in Shanghai, China: a molecular epidemiology study

BMC Infectious Diseases ◽

10.1186/s12879-021-06725-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhiying Han ◽

Jing Li ◽

Guomei Sun ◽

Kaikan Gu ◽

Yangyi Zhang ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Whole Genome ◽

Epidemiological Investigation ◽

Transmission Pattern ◽

Resistant Tuberculosis ◽

Multidrug Resistant Tuberculosis ◽

Recent Transmission ◽

Mdr Tb

Abstract Background Multidrug-resistant tuberculosis (MDR-TB) has become a major public health problem in China, with mounting evidence suggesting that recent transmission accounts for the majority of MDR-TB. Here we aimed to reveal the transmission pattern of an MDR-TB outbreak in the Jing'an District of Shanghai between 2010 and 2015. Methods We used whole-genome sequencing (WGS) to conduct genomic clustering analysis along with field epidemiological investigation to determine the transmission pattern and drug resistance profile of a cluster with ten MDR-TB patients in combining field epidemiological investigation. Results The ten MDR-TB patients with genotypically clustered Beijing lineage strains lived in a densely populated, old alley with direct or indirect contact history. The analysis of genomic data showed that the genetic distances of the ten strains (excluding drug-resistant mutations) were 0–20 single nucleotide polymorphisms (SNPs), with an average distance of 9 SNPs, suggesting that the ten MDR-TB patients were infected and developed the onset of illness by the recent transmission of M. tuberculosis. The genetic analysis confirmed definite epidemiological links between the clustered cases. Conclusions The integration of the genotyping tool in routine tuberculosis surveillance can play a substantial role in the detection of MDR-TB transmission events. The leverage of genomic analysis in combination with the epidemiological investigation could further elucidate transmission patterns. Whole-genome sequencing could be integrated into intensive case-finding strategies to identify missed cases of MDR-TB and strengthen efforts to interrupt transmission.

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Genetic Diversity of Multi- and Extensively Drug-Resistant Mycobacterium tuberculosis Isolates in the Capital of Iran, Revealed by Whole-Genome Sequencing

Journal of Clinical Microbiology ◽

10.1128/jcm.01477-18 ◽

2018 ◽

Vol 57 (1) ◽

Cited By ~ 4

Author(s):

Farzam Vaziri ◽

Thomas A. Kohl ◽

Hasan Ghajavand ◽

Mansour Kargarpour Kamakoli ◽

Matthias Merker ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Drug Resistant ◽

Content Type ◽

Extensively Drug Resistant ◽

Recent Transmission ◽

Mdr Tb ◽

Lineage 2

ABSTRACT The emergence and spread of multidrug resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains is a critical global health problem. Between 2014 and 2018, 606 MTBC strains were isolated from 13,892 suspected pulmonary tuberculosis (TB) patients in Tehran, Iran, including 16 (2.6%) MDR-TB cases. A combination of phenotypic and genotypic methods (whole-genome sequencing) was employed for the identification of additional drug resistances and strain-to-strain genetic distances as a marker for recent transmission events. MDR and extensively drug-resistant (XDR) TB cases were almost exclusively infected by lineage 2/Beijing strains (14/16, P < 0.001). We further showed that recent transmission and/or recent introduction of lineage 2/Beijing strains contribute to high XDR-TB rates among all MDR-TB cases and should be considered an emerging threat for TB control in Tehran. In addition, the extensive pre-existing drug resistance profiles of MDR/XDR strains will further challenge TB diagnostics in the region.

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Impact of Whole-Genome Sequencing of Mycobacterium Tuberculosis On Treatment Outcomes for MDR-TB/ XDR-TB: A Systematic Review Protocol

10.21203/rs.3.rs-1046897/v1 ◽

2021 ◽

Author(s):

Druti Hazra ◽

Connie Lam ◽

Vijay Shree Dhyani ◽

Bhumika T V ◽

Kiran Chawla ◽

...

Keyword(s):

Systematic Review ◽

Drug Resistance ◽

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Treatment Outcomes ◽

Genome Sequencing ◽

Meta Analysis ◽

Cochrane Library ◽

Whole Genome ◽

Mdr Tb

Abstract Background The emergence of drug-resistant tuberculosis (DR-TB) is a persistent threat to public health. The detection of DR-TB requires culture-based drug susceptibility testing (DST) or rapid molecular assays for targeted genes. The recent advances in Whole-genome sequencing (WGS) technology have offered a new capacity to identify resistance-conferring mutations in Mycobacterium tuberculosis (MTB). This study reviews and quantifies the emerging evidence on the association between genomic markers of drug resistance in MTB identified by WGS and treatment outcomes for DR-TB. Methods A literature search will be conducted in NCBI PubMed, Scopus, Cochrane Library, Web of Science, and CINAHL (Ebsco) to retrieve all the relevant original reports from 2000 onwards. Clinical trials and observational studies describing different applications of WGS to genotypic resistance testing for TB and detection of MDR-TB/ XDR-TB as well as treatment outcomes of the patients will be included. Two primary reviewers will separately screen and select papers for data extraction, risk of bias, and assess the quality. Any disagreement between the reviewers' will be clarified by a third reviewer. The I2 statistics will be used to assess the heterogeneity of the included studies and if the data are sufficiently homogenous, a meta-analysis will be performed. The Egger's test and visual representation of the funnel plot will be used to monitor for publication bias. Narrative data synthesis will be conducted for all the included studies if performing meta-analysis is not possible. Discussion This systematic review will examine the evidence on the feasibility and added value of WGS in improving treatment outcomes in DR-TB patients. The rapid detection of drug-resistance conferring mutations and selection of appropriate drug regimens is likely to improve the cure rates while minimizing adverse events and treatment costs. Hence, the outcome of this systematic review will inform policy-making and will guide clinical laboratory practice to improve drug resistance diagnostic capacity and treatment outcomes. Systematic review registration: PROSPERO CRD42020197099.

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Drug-resistance profiling and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis in Saudi Arabia revealed by whole genome sequencing

Infection and Drug Resistance ◽

10.2147/idr.s181124 ◽

2018 ◽

Vol Volume 11 ◽

pp. 2219-2229 ◽

Cited By ~ 2

Author(s):

Hawra Al-Ghafli ◽

Thomas A. Kohl ◽

Matthias Merker ◽

Bright Varghese ◽

Anason Halees ◽

...

Keyword(s):

Drug Resistance ◽

Saudi Arabia ◽

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Transmission Dynamics ◽

Whole Genome

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Genetic Variation Putatively Associated with Mycobacterium tuberculosis Resistance to Perchlozone, a New Thiosemicarbazone: Clues from Whole Genome Sequencing and Implications for Treatment of Multidrug-Resistant Tuberculosis

Antibiotics ◽

10.3390/antibiotics9100669 ◽

2020 ◽

Vol 9 (10) ◽

pp. 669

Author(s):

Igor Mokrousov ◽

Anna Vyazovaya ◽

Gulnora Akhmedova ◽

Natalia Solovieva ◽

Eugeni Turkin ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Genetic Variation ◽

Whole Genome Sequencing ◽

Treatment Regimen ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Whole Genome ◽

Resistant Tuberculosis ◽

Multidrug Resistant Tuberculosis ◽

Mdr Tb

Perchlozone ([PCZ] 4-thioureido-iminomethylpyridinium perchlorate) is a new thiosemicarbazone approved for the treatment of multidrug-resistant tuberculosis (MDR-TB) in Russia and some other countries. The ethA and hadABC mutations may confer PCZ resistance. At the same time, ethA mutations are known to mediate resistance to ethionamide (ETH) and prothionamide (PTH). We aimed to study the genetic variation underlying Mycobacterium tuberculosis resistance to PCZ through whole genome sequencing (WGS) of consecutive isolates recovered during long-term treatment. This prospective study included patients admitted in 2018–2019 to the regional tuberculosis dispensary, Kaliningrad, Russia, whose treatment regimen included PCZ. Multiple M. tuberculosis isolates were recovered during PCZ treatment, and the bacterial DNA was subjected to WGS followed by bioinformatics analysis. We identified mutations in the genes putatively associated with PCZ resistance, ethA, and hadA. The most frequent one was a frameshift ethA 106 GA > G (seven of nine patients) and most of the other mutations were also likely present before PCZ treatment. In one patient, a frameshift mutation ethA 702 CT > C emerged after six months of PCZ treatment. A frequent presence of cross-resistance mutations to PCZ and ETH/PTH should be taken into consideration when PCZ is included in the treatment regimen of MDR-TB patients.

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Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance

BMC Genomics ◽

10.1186/s12864-018-4734-6 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Xi Zeng ◽

Jamie Sui-Lam Kwok ◽

Kevin Yi Yang ◽

Kenneth Siu-Sing Leung ◽

Mai Shi ◽

...

Keyword(s):

Drug Resistance ◽

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Insertions And Deletions

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

Journal of Clinical Microbiology ◽

10.1128/jcm.00298-17 ◽

2017 ◽

Vol 55 (6) ◽

pp. 1871-1882 ◽

Cited By ~ 46

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.

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