Improved performance of Xpert MTB/RIF assay on sputum sediment samples obtained from presumptive pulmonary tuberculosis cases at Kibong’oto infectious diseases hospital in Tanzania

Abstract

BackgroundThe introduction of Xpert MTB/RIF assay (Xpert) has significantly improved diagnosis of Tuberculosis (TB) in resource limited human immunodeficiency virus (HIV) endemic settings. We aimed to modify the Xpert protocol to improve the detection of Mycobacterium tuberculosis (MTB).MethodsThis cross sectional study was conducted among presumptive pulmonary tuberculosis (PTB) patients at Kibong’oto Infectious Diseases Hospital between August and November 2015. Each patient consented to provide 2 samples of raw sputa. One-sputum sample was sedimented using the Petroff’s method and divided into two portions. One portion of sediment was inoculated on Lowenstein-Jensen culture media and observed for any growth for up to 8 weeks. Both, raw sputum and the portions of sediments were tested separately using Xpert with a sample reagent ratio of 1:2. Mean age of patients, prevalence of MTB, Xpert sensitivity, specificity, positive and negative predictive value were calculated. An incremental sensitivity was determined. Pearson chi-square and either an independent T or Mann-Whitney U-test were used to compared categorical and continuous variables respectively. A p- value of ≤0.05 was considered significant.ResultsOf the 270 presumptive PTB cases, 262 were eligible for analysis. Eight (3%) were excluded due to contaminated culture. Patients’ mean age was 42.9 (±SD 15.1) years of which 173 (66%) were female. The overall prevalence of PTB was 112 (43%), of which the Xpert detected 105 (40%) in sediments and 98 (37%) in raw sputa as compared to culture which detected 85 (32%) cases of PTB. Sensitivity, specificity, positive and negative predictive values of Xpert on sputum sediments were 92%, 85%, 74% and 96% respectively. Overall, the incremental sensitivity of Xpert on sediment over raw sputum was 6%. In HIV infected Presumptive PTB, the incremental sensitivity was 12%.ConclusionLowering the sample reagent to sediment dilution ratio increases sensitivity of Xpert on MTB detection among presumptive PTB cases, especially in HIV infected individuals.

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

“…Studies have shown phenotypic susceptibility tests to serve as reference standards [25], and that both Xpert assay and DST can provide information on polyresistance in pre-XDR-TB [26] despite varying sensitivities [27,28]. The current practice in diagnosing drug resistant tuberculosis is through the WHO-approved probe-based assays like Xpert® MTB/RIF (Cepheid, USA) for RIF [16] and either genotype MTBDRplus for RIF and INH or genotype MTBDRsl (Hain Lifesciences, Germany) for aminoglycosides/capreomycin and fluoroquinolones that must be confirmed with culture-based DST [29]. Unlike WGS, these assays not only have limited DST range to identify hot-spot resistant determining regions but they also cannot inform transmission dynamics [30,31].…”

“…This study involved 57 and 30 participants who harboured M. tuberculosis that were resistant and susceptible to anti-TB drugs respectively, presenting at KIDH during the study period in 2014. Participants with resistant isolates were recruited if they had laboratory results by either GeneXpert MTB/RIF or phenotypic culture and DST [16]. The drug resistance was either mono/ polyresistance-resistant or MDR-TB.…”

“…As in other TB endemic settings, Tanzania has deployed rapid molecular methods for dual detection of MTBC and susceptibility to either RIF alone or along with INH and second-line injectable and fluoroquinolones. For example, while the Xpert®MTB/Rif assay (Cepheid, USA) detects MTBC and provides information about susceptibility to RIF only [16], the genotype MTBDRplus and MTBDRsl assays (Hain Life sciences, Germany) detect mutations that are strongly associated with multiple types of MDR-TB and also XDR-TB respectively [17,18]. These assays have potential to guide implementation of the new WHO shorter regimen for treating MDR-TB [15,19].…”

Deploying a novel tuberculosis molecular bacterial load assay to assess the elimination rate ofMycobacterium tuberculosisin patients with multidrug-resistant tuberculosis in Tanzania

“…From August 2018 to December 2019, longitudinal cohort study was conducted among patients with RR/MDR-and DS-TB confirmed using Xpert® MTB /Rif [9] . The study was approved by the National Institute for Medical Research (NIMR) in Tanzania (NIMR/HQ/R.8a/Vol.…”

“…Patients were recruited at KIDH, national centre of excellence for clinical management of drug resistant (DR)-TB located in the Siha district of Kilimanjaro region in Tanzania [9] . TB-MBLA testing was performed at the National Institute for Medical Research, Mbeya Medical Research Centre branch, given that laboratory's prior experience with the assay.…”