Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country.
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ABSTRACT:
SUBMITTER: Vogel M
PROVIDER: S-EPMC8319420 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundIncreasing incidence of multidrug-resistant Mycobacterium tuberculosis infections is hampering global tuberculosis control efforts. Kuwait is a low-tuberculosis-incidence country, and ~ 1% of M. tuberculosis strains are resistant to rifampicin and isoniazid (MDR-TB). This study detected mutations in seven genes predicting resistance to rifampicin, isoniazid, pyrazinamide, ethambutol and streptomycin in MDR-TB strains. Sequence data were combined with spoligotypes for detecting local transmission of MDR-TB in Kuwait.MethodsNinety-three MDR-TB strains isolated from 12 Kuwaiti and 81 expatriate patients and 50 pansusceptible strains were used. Phenotypic drug susceptibility was determined by MGIT 460 TB/960 system. Mutations conferring resistance to rifampicin, isoniazid, pyrazinamide, ethambutol and streptomycin were detected by genotype MTBDRplus assay and/or PCR sequencing of three rpoB regions, katG codon 315 (katG315) + inhA regulatory region, pncA, three embB regions and rpsL + rrs-500-900 regions. Spoligotyping kit was used, spoligotypes were identified by SITVIT2, and phylogenetic tree was constructed by using MIRU-VNTRplus software. Phylogenetic tree was also constructed from concatenated sequences by MEGA7 software. Additional PCR sequencing of gidB and rpsA was performed for cluster isolates.ResultsPansusceptible isolates contained wild-type sequences. Mutations in rpoB and katG and/or inhA were detected in 93/93 and 92/93 MDR-TB strains, respectively. Mutations were also detected for pyrazinamide resistance, ethambutol resistance and streptomycin resistance in MDR-TB isolates in pncA, embB and rpsL + rrs, respectively. Spoligotyping identified 35 patterns with 18 isolates exhibiting unique patterns while 75 isolates grouped in 17 patterns. Beijing genotype was most common (32/93), and 11 isolates showed nine orphan patterns. Phylogenetic analysis of concatenated sequences showed unique patterns for 51 isolates while 42 isolates grouped in 16 clusters. Interestingly, 22 isolates in eight clusters by both methods were isolated from TB patients typically within a span of 2 years. Five of eight clusters were confirmed by additional gidB and rpsA sequence data.ConclusionsOur study provides the first insight into molecular epidemiology of MDR-TB in Kuwait and identified several potential clusters of local transmission of MDR-TB involving 2-6 subjects which had escaped detection by routine surveillance studies. Prospective detection of resistance-conferring mutations can identify possible cases of local transmission of MDR-TB in low MDR-TB settings.
| S-EPMC6894303 | biostudies-literature
Project description:BackgroundThe limited knowledge on aetiology, epidemiology and risk factors for multimorbidity especially evident from low and middle-income countries curtail the development and implementation of sustainable healthcare models. Sri Lanka, boasting for one of South Asia's most efficient public health systems that is accessible free-of-charge by the citizens is presently transitioning from lower-middle to upper-middle-income tier. Faced with the triple burden of disease, it is imperative for Sri Lanka to incorporate an integrated model to manage multimorbidity.MethodsA descriptive cross-sectional study was carried out in medical clinics of a tertiary care hospital and a University primary care department. Data were extracted on to a form from the clinical records of patients over the age of 20 years with at least one non-communicable disease (NCD) and analysed.ResultsMultimorbidity was present among 64.1% of patients (n = 1600). Nearly 44.44% of the patients aged 20-35 years have a minimum of two disorders, and by the time they reach 50 years, nearly 64% of the patients have two or more non-communicable diseases. Nearly 7% of those aged over 65 years were diagnosed with four or more disorders. A fourth of the sample was affected by co-morbid diabetes mellitus and hypertension, whereas the combinations of coronary heart disease with hypertension and diabetes mellitus were also found to be significantly prevalent. A salient revelation of the binomial logistic regression analysis was that the number of disorders was positively correlated to the presence of mental disorders 7.25 (95% CI = 5.82-8.68).ConclusionMultimorbidity is highly prevalent among this population and seemingly has a detrimental effect on the psychological wellbeing of those affected. Therefore, the need for horizontal integration of all primary to tertiary care disciplines, including mental health, to manage multimorbidity by policymakers is emphasized as a priority task.
| S-EPMC7732070 | biostudies-literature
Project description:BackgroundWe evaluated the effect of mixed-MTB strain infection on the performance of Line Probe Assay (LPA) and GeneXpert MTB/RIF (Xpert) assays among patients initiating MDR-TB treatment in Uganda.MethodsThis was a cross-sectional study using sputum specimens collected from participants screened for STREAM 2 clinical trial between October 2017 and October 2019. Samples from 62 MTB smear-positive patients and rifampicin-resistant patients from the peripheral health facilities were processed for Xpert and LPA as screening tests for eligibility in the trial. From November 2020, processed stored sputum samples were retrieved and genotyped to determine the presence of mixed-MTB strain infection using a standard 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem-Repeat (MIRU-VNTR). Samples with at least 20/24 MIRU-VNTR loci amplified were considered for analysis. Agar proportional Drug Susceptibility Test (DST) was performed on culture isolates of samples that had discordant results between LPA and Xpert. The impact of the presence of mixed-MTB strain on Xpert and LPA test interpretation was analyzed.ResultsA total of 53/62 (85%) samples had analyzable results from MIRU-VNTR. The overall prevalence of mixed-MTB infection was 5/53 (9.4%). The prevalence was highest among males 3/33 (9.7%) and among middle-aged adults, 4/30 (13.3%). Lineage 4 of MTB contributed 3/33 (9.1%) of the mixed-MTB infection prevalence. Having mixed MTB strain infection increased the odds of false susceptible Xpert test results (OR 7.556, 95% CI 0.88-64.44) but not for LPA. Being HIV-positive (P=0.04) independently predicted the presence of mixed MTB infection.ConclusionsThe presence of mixed-MTB strain infection may affect the performance of the GeneXpert test but not for LPA. For patients with high pre-test probability of rifampicin resistance, an alternative rapid method such as LPA should be considered.
| S-EPMC10571598 | biostudies-literature
Project description:BackgroundMixed M. tuberculosis (MTB) infection occurs when one is infected with more than one clonally distinct MTB strain. This form of infection can assist MTB strains to acquire additional mutations, facilitate the spread of drug-resistant strains, and boost the rate of treatment failure. Hence, the presence of mixed MTB infection could affect the performance of some rapid molecular diagnostic tests such as Line Probe Assay (LPA) and GeneXpert MTB/RIF (Xpert) assays.MethodsThis was a cross-sectional study that used sputum specimens collected from participants screened for STREAM 2 clinical trial between October 2017 and October 2019. Samples from 62 MTB smear-positive patients and rifampicin-resistant patients from peripheral health facilities were processed for Xpert and LPA as screening tests for eligibility in the trial. From November 2020, processed stored sputum samples were retrieved and genotyped to determine the presence of mixed-MTB strain infection using a standard 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem-Repeat (MIRU-VNTR). Samples with at least 20/24 MIRU-VNTR loci amplified were considered for analysis. Agar proportional Drug Susceptibility Test (DST) was performed on culture isolates of samples that had discordant results between LPA and Xpert. The impact of the presence of mixed-MTB strain on Xpert and LPA test interpretation was analyzed.ResultsA total of 53/62 (85%) samples had analyzable results from MIRU-VNTR. The overall prevalence of mixed-MTB infection was 5/53 (9.4%). The prevalence was highest among male's 3/31 (9.7%) and among middle-aged adults, 4/30 (33.3%). Lineage 4 of MTB contributed 3/5 (60.0%) of the mixed-MTB infection prevalence. Having mixed MTB strain infection increased the odds of false susceptible Xpert test results (OR 7.556, 95% CI 0.88-64.44) but not for LPA. Being HIV-positive (P = 0.04) independently predicted the presence of mixed MTB infection.ConclusionsThe presence of mixed-MTB strain infection may affect the performance of the GeneXpert test but not for LPA. For patients with high pre-test probability of rifampicin resistance, an alternative rapid method such as LPA should be considered.
| S-EPMC10782568 | biostudies-literature
Project description:ABSTRACT: BACKGROUND: Most studies of family attitudes and burden have been conducted in developed countries. Thus it is important to test the generalizability of this research in other contexts where social conditions and extended family involvement may be different. The aim of this study was to assess the relationship between the attitudes of caregivers and the burden they experience in such a context, namely Arica, a town located in the northernmost region of Chile, close to the border with Peru and Bolivia. METHODS: We assessed attitudes towards schizophrenia (including affective, cognitive and behavioural components) and burden (including subjective distress, rejection and competence) in 41 main caregivers of patients with schizophrenia, all of whom were users of Public Mental Health Services in Arica. RESULTS: Attitude measures differed significantly according to socio-demographic variables, with parents (mainly mothers) exhibiting a more negative attitude towards the environment than the rest of the family (t = 4.04; p = 0.000).This was also the case for caregivers with a low educational level (t = 3.27; p < 0.003), for the oldest caregivers (r = 0.546; p = 0.000) and for those who had spent more time with the patient (r = 0.377; p = 0.015). Although attitudes had significant association with burden, their explanatory power was modest (R2 = .104, F = 4,55; p = .039). CONCLUSIONS: Similar to finding developed countries, the current study revealed a positive and significant relationship between the attitudes of caregivers and their burden. These findings emphasize the need to support the families of patients with schizophrenia in this social context.
| S-EPMC3191329 | biostudies-literature
Project description:BACKGROUND:The emergence of pre-extensively and extensively drug-resistant tuberculosis (Pre-XDR/XDR-TB) is the major hurdle for TB prevention and care programs especially in developing countries like Ethiopia. The less emphasis on universal access to laboratory techniques for the rapid diagnosis of TB and drug susceptibility testing (DST) makes the management of MDR-TB a challenge. Early detection of second line anti-TB drugs resistance is essential to reduce transmission of Pre-XDR/XDR-TB strains and adjusting the treatment regimen in MDR-TB. OBJECTIVE:To determine the prevalence and resistance pattern of Pre-XDR- and XDR-TB among MDR-TB patients in the Amhara region, Ethiopia. METHODS:A cross sectional study was carried out in nine MDR-TB treatment centers in the Amhara region. Sputum samples were collected from all pulmonary rifampicin resistant (RR) or MDR-TB patients prior to anti-TB treatment. L?wenstein-Jensen (LJ) culture, Ziehl Neelsen (ZN) smear, MTBDRplus and MTBDRsl assays were performed according to the standard procedures. Data were analyzed using SPSS 20 software. Chi-square and/or Fishers exact test was employed. RESULTS:Overall, 6.3% of MDR-TB isolates were resistant to at least one second line drugs. Pre-XDR-TB and XDR-TB isolates accounted 5.7% and 0.6% respectively. Moreover, 3.4% were resistant to FQs and 3.4% were resistant to second line injectable drugs. All isolates were susceptible for low level kanamycin. Almost all pre-XDR-TB strains (90%) were previously treated with anti-TB drugs. Drug resistant Mycobacterium tuberculosis isolates were disproportionately distributed in districts of the Amhara region and the majorities were concentrated in urban areas. CONCLUSIONS:The high proportion of MDR-TB patients resistant to at least one second line drug is alarming. Strengthening the laboratory facilities to monitor pre-XDR and XDR-TB patients is crucial. The TB programs need to give emphasis on the effective and rational use of second line drugs for newly diagnosed MDR-TB patients to prevent the emergence of pre-XDR/XDR-TB strains.
| S-EPMC7018133 | biostudies-literature
Project description:IntroductionTranslation of evidence into clinical practice for use of intravenous thrombolysis in acute stroke care has been slow, especially across low- and middle-income countries. In Malaysia where the average national uptake was poor among the public hospitals in 2018, one hospital intriguingly showed comparable thrombolysis rates to high-income countries. This study aimed to explore and provide in-depth understanding of factors and explanations for the high rates of intravenous stroke thrombolysis in this hospital.MethodsThis single case study sourced data using a multimethod approach: (1) semi-structured in-depth interviews and focus group discussions, (2) surveys, and (3) review of medical records. The Tailored Implementation of Chronic Diseases (TICD) framework was used as a guide to understand the determinants of implementation. Twenty-nine participants comprising the Hospital Director, neurologists, emergency physicians, radiologists, pharmacists, nurses and medical assistants (MAs) were included. Thematic analyses were conducted inductively before triangulated with quantitative analyses and document reviews.ResultsFavorable factors contributing to the uptake included: (1) cohesiveness of team members which comprised of positive interprofessional team dynamics, shared personal beliefs and values, and passionate leadership, and (2) facilitative work process through simplification of workflow and understanding the rationale of the sense of urgency. Patient factors was a limiting factor. Almost two third of ischemic stroke patients arrived at the hospital outside the therapeutic window time, attributing patients' delayed presentation as a main barrier to the uptake of intravenous stroke thrombolysis. One other barrier was the availability of resources, although this was innovatively optimized to minimize its impact on the uptake of the therapy. As such, potential in-hospital delays accounted for only 3.8% of patients who missed the opportunity to receive thrombolysis.ConclusionsDespite the ongoing challenges, the success in implementing intravenous stroke thrombolysis as standard of care was attributed to the cohesiveness of team members and having facilitative work processes. For countries of similar settings, plans to improve the uptake of intravenous stroke thrombolysis should consider the inclusion of interventions targeting on these modifiable factors.
| S-EPMC9729841 | biostudies-literature
Project description:Indispensable for shortening treatment of drug-susceptible tuberculosis (TB), pyrazinamide (PZA, Z) is also essential in the treatment of multidrug-resistant (MDR)-TB. While resistance to PZA in MDR-TB is associated with poor treatment outcome, bacillary susceptibility to PZA along with the use of fluoroquinolone (FQ) and second-line injectable drugs (SLIDs) may predict improved treatment success in MDR-TB. Despite a high prevalence of PZA resistance among MDR-TB patients (10%-85%), PZA susceptibility testing is seldom performed because of technical challenges. To improve treatment of MDR-TB, we propose to: (i) classify MDR-TB into PZA-susceptible MDR-TB (Z(S)-MDR-TB) and PZA-resistant MDR-TB (Z(R)-MDR-TB); (ii) use molecular tests such as DNA sequencing (pncA, gyrA, rrs, etc.) to rapidly identify Z(S)-MDR-TB versus Z(R)-MDR-TB and susceptibility profile for FQ and SLID; (iii) refrain from using PZA in Z(R)-MDR-TB; and (iv) explore the feasibility of shortening the treatment duration of Z(S)-MDR-TB with a regimen comprising PZA plus at least two bactericidal agents especially new agents like TMC207 or PA-824 or delamanid which the bacilli are susceptible to, with one or two other agents. These measures may potentially shorten therapy, save costs, and reduce side effects of MDR-TB treatment.
| S-EPMC3630910 | biostudies-other
Project description:BACKGROUND:MDR-TB is a major threat to global TB control. In 2015, 580,000 were treated for MDR-TB worldwide. The worldwide roll-out of GeneXpert MTB/RIF® has improved diagnosis of MDR-TB; however, in many countries laboratories are unable to assess drug resistance and clinical predictors of MDR-TB could help target suspected patients. In this study, we aimed to determine the clinical factors associated with MDR-TB in Bamako, Mali. METHODS:We performed a cross-sectional study of 214 patients with presumed MDR-TB admitted to University of Bamako Teaching Hospital, Point-G between 2007 and 2016. We calculated crude and adjusted odds ratios for MDR-TB disease diagnosis using SPSS. RESULTS:We found that age ?40years (OR=2.56. 95% CI: 1.44-4.55), two courses of prior TB treatment (OR=3.25, 95% CI: 1.44-7.30), TB treatment failure (OR=3.82, 95% CI 1.82-7.79), sputum microscopy with 3+ bacilli load (OR=1.98, 95% CI: 1.13-3.48) and a history of contact with a TB patient (OR=2.48, 95% CI: 1.11-5.50) were significantly associated with confirmation of MDR-TB disease. HIV was not a risk factor for MDR-TB (aOR=0.88, 95% CI: 0.34-1.94). CONCLUSION:We identified several risk factors that could be used to identify MDR-TB suspects and prioritize them for laboratory confirmation. Prospective studies are needed to understand factors associated with TB incidence and clinical outcomes of TB treatment and disease.
| S-EPMC6481646 | biostudies-literature
Project description:To determine differences in the ability of Mycobacterium tuberculosis strains to withstand antituberculosis drug treatment, we compared the activity of antituberculosis drugs against susceptible Beijing and East-African/Indian genotype M. tuberculosis strains. Beijing genotype strains showed high rates of mutation within a wide range of drug concentrations, possibly explaining this genotype's association with multidrug-resistant tuberculosis.
| S-EPMC3309663 | biostudies-literature