Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania

Background: Mycobacterium yongonense is a recently described novel species belonging to Mycobacterium avium complex, which is the most prevalent aetiology of non-tuberculous mycobacteria associated with pulmonary infections, and poses tuberculosis diagnostic challenges in high-burden, resource-constrained settings. Methods: Whole genome shotgun sequencing and comparative microbial genomic analyses were used to characterize the isolate from a patient diagnosed with multidrug-resistant tuberculosis (MDR-TB) after relapse. Results: The genome sequence of the first case of M. yongonense (M. yongonense RT 955-2015) in Tanzania is presented. Sequence analysis revealed that the RT 955-2015 strain had a high similarity to M. yongonense 05-1390(T) (98.74%) and Mycobacterium chimaera DSM 44623(T) (98%). Its 16S rRNA showed similarity to Mycobacterium paraintracellulare KCTC 290849(T) (100%), Mycobacterium intracellulare ATCC 13950(T) (100%), M. chimaera DSM 44623(T) (99.9%), and M. yongonense 05-1390(T) (98%). The strain exhibited a substantially different rpoB sequence to that of M. yongonense 05-1390 (95.16%), but closely related to that of M. chimaera DSM 44623(T) (99.86%), M. intracellulare ATCC 13950(T), (99.53%), and M. paraintracellulare KCTC 290849(T) (99.53%). Conclusions: In light of the OrthoANI algorithm and phylogenetic analysis, it was concluded that the isolate was M. yongonense Type II genotype, which is an indication that the patient was misdiagnosed with TB/MDR-TB and received inappropriate treatment. (C) 2018 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.

Characterization of mutations in drug resistant tuberculosis and diagnostic challenges in referral health facilities, Tanzania

A Dissertation Submitted in Partial Fulfilment of the Requirements for the Degree of Doctor of Philosophy in Life Sciences of the Nelson Mandela African Institution of Science and TechnologyTuberculosis remains one of the world’s deadliest infectious diseases in resource-limited settings, including Tanzania. Diagnostic challenges and minimal information on resistant tuberculosis complicate building effective management strategies. The current study employed whole genome shotgun sequencing and genotyping methods to characterize genetics of drug resistant tuberculosis strains and diagnostic impedes of tuberculosis in Tanzania. A total of 134 positive sputa from collected at Central Tuberculosis Reference Laboratory from different parts of the country. Forty patients were regarded as multi-drug resistant tuberculosis (MDR-TB), of which 18 (45%) were classified as relapse cases. The remaining 94 were smear-positive culture-negative samples and treated as susceptible tuberculosis. Sequence analysis of 40 MDR-TB isolates identified a set of genetic markers (including additional variants) in the following known drug-resistant genes: katG, inhA, embCAB, ethA, inhA, rpoB, rpoC, rpsL, gyrA, eis, and pncA. Additionally, there was evidence of positive selection in other three novel genomic regions namely: ndhC, ndhI and ndhK. Sequence analysis also identified one isolate of M. yongonense, the first case to be described in Tanzania, suggesting that the patient was misdiagnosed with multi-drug resistant tuberculosis. Out of 94 smear-positive but culture negative sputa, 25 (26.60%) were GeneXpert® mycobacteria TB positive. Repeat-culture identified 11/94 (11.70) as culture positive, of which 5 were Capilia TB-Neo positive and confirmed by GenoType MTBC to be Mycobacterium tuberculosis/Mycobacterium canettii. The remaining 6 Capilia TB-Neo negative samples were typed by GenoType® CM/AS and identified 3 (3.19%) nontuberculous mycobacteria, 2 Gram positive bacteria, and 1 isolate tested negative, together, making a total of 6/94 (6.38%) confirmed false smear-positives. Overall, 28/94 (29.79%) isolates were confirmed TB cases while 60 (63.83%) remained unconfirmed tuberculosis cases. These findings on misdiagnosis and the suggestive of novel resistance-associated mutations in resistant tuberculosis emphasize the need for accurate molecular diagnostic tests for delineating the tuberculosis cases and their drug susceptibility profiles in clinical settings

Assessment of GeneXpert GxAlert platform for multi-drug resistant tuberculosis diagnosis and patients’ linkage to care in Tanzania

Abstract Objective The gap between patients diagnosed with multi-drug resistant tuberculosis (MDR-TB) and enrolment in treatment is one of the major challenges in tuberculosis control programmes. A 4-year (2013–2016) retrospective review of patients’ clinical data and subsequent in-depth interviews with health providers were conducted to assess the effectiveness of the GeneXpert GxAlert platform for MDR-TB diagnosis and its impact on linkage of patients to care in Tanzania. Results A total of 782 new rifampicin resistant cases were notified, but only 242 (32.3%) were placed in an MDR-TB regimens. The remaining 540 (67.07%) patients were not on treatment, of which 103 patients had complete records on the GxAlert database. Of the 103 patients: 39 were judged as untraceable; 27 died before treatment; 12 were treated with first-line anti-TBs; 9 repeat tests did not show rifampicin resistance; 15 were not on treatment due to communication breakdown, and 1 patient was transferred outside the country. In-depth interviews with health providers suggested that the pre-treatment loss for the MDR-TB patients was primarily attributed to health system and patients themselves. We recommend strengthening the health system by developing and implementing well-defined interventions to ensure all diagnosed MDR-TB patients are accurately reported and timely linked to treatment