Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda

YesUnderstanding the circulating Mycobacterium tuberculosis resistance mutations is vital for better TB control strategies, especially to inform a new MDR-TB treatment programme. We complemented the phenotypic drug susceptibility testing (DST) based drug resistance surveys (DRSs) conducted in Uganda between 2008 and 2011 with Whole Genome Sequencing (WGS) of 90 Mycobacterium tuberculosis isolates phenotypically resistant to rifampicin and/or isoniazid to better understand the extent of drug resistance. A total of 31 (34.4 %) patients had MDR-TB, 5 (5.6 %) mono-rifampicin resistance and 54 (60.0 %) mono-isoniazid resistance by phenotypic DST. Pyrazinamide resistance mutations were identified in 32.3% of the MDR-TB patients. Resistance to injectable agents was detected in 4/90 (4.4%), and none to fluoroquinolones or novel drugs. Compensatory mutations in rpoC were identified in two patients. The sensitivity and specificity of drug resistance mutations compared to phenotypic DST were for rpoB 88.6% and 98.1%, katG 60.0% and 100%, fabG1 16.5% and 100%, katG and/or fabG1 71.8% and 100%, embCAB 63.0% and 82.5%, rrs 11.4% and 100%, rpsL 20.5% and 95.7% and rrs and/or rpsL 31.8% and 95.7%. Phylogenetic analysis showed dispersed MDR-TB isolate, with only one cluster of three Beijing family from South West Uganda. Among tuberculosis patients in Uganda, resistance beyond first-line drugs as well as compensatory mutations remain low, and MDR-TB isolates did not arise from a dominant clone. Our findings show the potential use of sequencing for complementing DRSs or surveillance in this setting, with good specificity compared to phenotypic DST. The reported high confidence mutations can be included in molecular assays, and population-based studies can track transmission of MDR-TB including the Beijing family strains in the South West of the country.Erasmus Mundus Joint Doctorate Program of the European Union through a training grant to WS and the European Research Council-INTERRUPTB starting grant (nr.311725) to BdJ

The impact of tubal ectopic pregnancy in Papua New Guinea - a retrospective case review

BACKGROUND: Ectopic pregnancy (EP) is an important cause of morbidity and mortality amongst women of reproductive age. Tubal EP is well described in industrialised countries, but less is known about its impact in low-resource countries, in particular in the South Pacific Region. METHODS: We undertook a retrospective review of women with tubal EP treated at a provincial referral hospital in coastal Papua New Guinea over a period of 56 months. Demographic and clinical variables were obtained from patients’ medical records and analysed. The institutional rate of tubal EP was calculated, and diagnosis and management reviewed. Potential risk factors for tubal EP were identified, and delays contributing to increased morbidity described. RESULTS: A total of 73 women had tubal EP. The institutional rate of tubal EP over the study period was 6.3 per 1,000 deliveries. There were no maternal deaths due to EP. The mean age of women was 31.5+/−5.7 years, 85% were parous, 67% were rural dwellers and 62% had a history of sub-fertility. The most commonly used diagnostic aid was culdocentesis. One third of women had clinical evidence of shock on arrival. All women with tubal EP were managed by open salpingectomy. Tubal rupture was confirmed for 48% of patients and was more common amongst rural dwellers. Forty-three percent of women had macroscopic evidence of pelvic infection. Two-thirds of patients received blood transfusions, and post-operative recovery lasted six days on average. Late presentation, lack of clinical suspicion, and delays with receiving appropriate treatments were observed. CONCLUSIONS: Tubal EP is a common gynaecological emergency in a referral hospital in coastal PNG, and causes significant morbidity, in particular amongst women residing in rural areas. Sexually transmitted infections are likely to represent the most important risk factor for tubal EP in PNG. Interventions to reduce the morbidity due to tubal EP include the prevention, detection and treatment of sexually transmitted infections, identification and reduction of barriers to prompt presentation, increasing health workers’ awareness of ectopic pregnancy, providing pregnancy test kits to rural health centres, and strengthening hospital blood transfusion services, including facilities for autotransfusion

Variation and risk factors of drug resistant tuberculosis in sub-Saharan Africa: a systematic review and meta-analysis.

BACKGROUND: Prevalence of multidrug resistant tuberculosis (MDR-TB), defined as in vitro resistance to both rifampicin and isoniazid with or without resistance to other TB drugs, in sub-Saharan Africa (SSA) is reportedly low compared to other regions. These estimates are based on data reported to the World Health Organization (WHO) on drug resistance surveys, which may suffer from a reporting bias. We set out to evaluate the variation in prevalence of drug resistant tuberculosis (DR-TB) and its determinants across SSA countries among new and previously treated TB patients. METHODS: The aim was to perform a systematic review and meta-analysis of DR-TB prevalence and associated risk factors in SSA. PubMed, EMBASE, Cochrane and bibliographies of DR-TB studies were searched. Surveys at national or sub-national level, with reported DR-TB prevalence (or sufficient data to calculate a prevalence) to isoniazid (INH), rifampicin (RMP), ethambutol (EMB), and streptomycin (SM) conducted in SSA excluding the Republic of South Africa, published between 2003 and 2013 with no language restriction were considered. Two authors searched and reviewed the studies for eligibility and extracted the data in pre-defined forms. Forest plots of all prevalence estimates by resistance outcome were performed. Summary estimates were calculated using random effects models, when appropriate. Associations between any DR-TB and MDR-TB with potential risk factors were examined through subgroup analyses stratified by new and previously treated patients. RESULTS: A total of 726 studies were identified, of which 27 articles fulfilled the inclusion criteria. Studies reported drug susceptibility testing (DST) results for a total of 13,465 new and 1,776 previously treated TB patients. Pooled estimate of any DR-TB prevalence among the new cases was 12.6% (95% CI 10.6-15.0) while for MDR-TB this was 1.5% (95% CI 1.0-2.3). Among previously treated patients, these were 27.2% (95% CI 21.4-33.8) and 10.3% (95% CI 5.8-17.4%), respectively. DR-TB (any and MDR-TB) did not vary significantly with respect to study characteristics. CONCLUSIONS: The reported prevalence of DR-TB in SSA is low compared to WHO estimates. MDR-TB in this region does not seem to be driven by the high HIV prevalence rates

Strategies Used by Facilities in Uganda to Integrate Family Planning into HIV Care: What Works and What Doesn't

No Abstract

Implementation of GeneXpert MTB/Rif proficiency testing program: A Case of the Uganda national tuberculosis reference laboratory/supranational reference laboratory.

BackgroundFollowing the WHO's endorsement of GeneXpert MTB/RIF assay for tuberculosis diagnosis in 2010, Uganda's ministry of health introduced the assay in its laboratory network in 2012. However, assessing the quality of the result produced from this technique is one of its major implementation challenges. To bridge this gap, the National tuberculosis reference laboratory (NTRL) introduced the GeneXpert MTB/RIF proficiency testing (PT) Scheme in 2015.MethodsA descriptive cross-sectional study on the GeneXpert PT scheme in Uganda was conducted between 2015 and 2018. Sets of panels each comprising four 1ml cryovial liquid samples were sent out to enrolled participants at preset testing periods. The laboratories' testing accuracies were assessed by comparing their reported results to the expected and participants' consensus results. Percentage scores were assigned and feedback reports were sent back to laboratories. Follow up of sites with unsatisfactory results was done through "on and off-site support". Concurrently, standardization of standard operating procedures (SOPs) and practices to the requirements of the International Organization for Standardization (ISO) 17043:2010 was pursued.ResultsParticipants gradually increased during the program from 56 in the pilot study to 148 in Round 4 (2018). Continual participation of a particular laboratory yielded an odd of 2.5 [95% confidence interval (CI), 1.22 to 4.34] times greater for achieving a score of above 80% with each new round it participated. The "on and off-site" support supervision documented improved performance of failing laboratories. Records of GeneXpert MTB/RIF PT were used to achieve accreditation to ISO 17043:2010 in 2018.ConclusionContinued participation in GeneXpert MTB/RIF PT improves testing accuracy of laboratories. Effective implementation of this scheme requires competent human resources, facility and equipment, functional quality management system, and adherence to ISO 17043:2010

Anti-tuberculosis drug resistance among new and previously treated sputum smear-positive tuberculosis patients in Uganda: results of the first national survey.

BACKGROUND: Multidrug resistant and extensively drug resistant tuberculosis (TB) have become major threats to control of tuberculosis globally. The rates of anti-TB drug resistance in Uganda are not known. We conducted a national drug resistance survey to investigate the levels and patterns of resistance to first and second line anti-TB drugs among new and previously treated sputum smear-positive TB cases. METHODS: Sputum samples were collected from a nationally representative sample of new and previously treated sputum smear-positive TB patients registered at TB diagnostic centers during December 2009 to February 2011 using a weighted cluster sampling method. Culture and drug susceptibility testing was performed at the national TB reference laboratory. RESULTS: A total of 1537 patients (1397 new and 140 previously treated) were enrolled in the survey from 44 health facilities. HIV test result and complete drug susceptibility testing (DST) results were available for 1524 (96.8%) and 1325 (85.9%) patients, respectively. Of the 1209 isolates from new cases, resistance to any anti-TB drug was 10.3%, 5% were resistant to isoniazid, 1.9% to rifampicin, and 1.4% were multi drug resistant. Among the 116 isolates from previously treated cases, the prevalence of resistance was 25.9%, 23.3%, 12.1% and 12.1% respectively. Of the 1524 patients who had HIV testing 469 (30.7%) tested positive. There was no association between anti-TB drug resistance (including MDR) and HIV infection. CONCLUSION: The prevalence of anti-TB drug resistance among new patients in Uganda is low relative to WHO estimates. The higher levels of MDR-TB (12.1%) and resistance to any drug (25.3%) among previously treated patients raises concerns about the quality of directly observed therapy (DOT) and adherence to treatment. This calls for strengthening existing TB control measures, especially DOT, routine DST among the previously treated TB patients or periodic drug resistance surveys, to prevent and monitor development and transmission of drug resistant TB

Sociodemographic and health-related factors associated with exclusive breastfeeding in 77 districts of Uganda

Abstract Background Uganda surpasses many African nations and the global average in exclusive breastfeeding (EBF) rates. Yet, malnutrition is a critical issue, with stunting impacting roughly 29% of children under 5 years. Enhancing EBF could mitigate such nutritional challenges. This study focused on determining the current EBF prevalence and identifying associated factors across 77 surveyed districts. Methods Pooled data from the Lot Quality Assurance Sampling (LQAS) surveys conducted in 77 districts in Uganda during 2021 and 2022 were analyzed. The analysis involved 7,210 mothers of children under 6 months, EBF was considered as the proportion of infants who received breast milk only in the 24 hours before the survey. A mother practicing EBF was (1) currently breastfeeding (2) had not started giving foods other than breastmilk (3) had not given any other probed liquids or (4) semi-solid foods the previous day or night. Multivariable logistic regression was used to identify factors associated with EBF, presenting adjusted odds ratios (aOR) with corresponding 95% confidence intervals at a 5% significance level. Results The prevalence of EBF was 62.3%. In the adjusted analysis, EBF was more common among older mothers 20–24 years, 25–29 years and 30 + years (aOR 1.4; 95% CI 1.2,1.6), (aOR 1.4; 95% CI 1.1, 1.6) and (aOR 1.3; 95% CI 1.1, 1.5) respectively compared to teenage mothers. Also, EBF was more likely among mothers who lived in rural areas compared to urban areas (aOR 1.1; 95% CI 1.0, 1.3) and those who attended antenatal care (ANC) (aOR 2.2; 95% CI 1.5, 3.1). On the contrary, EBF was less common for children aged 3–5 months compared to younger (aOR 0.5; 95% CI 0.5, 0.6) and children who had received Vitamin A supplementation (aOR 0.7; 95% 0.6, 0.8). Conclusion The study suggests that most districts in Uganda might not have made significant strides in improving EBF rates over the last twenty years, pointing to possible ongoing hurdles that need urgent attention. Particularly, there’s a pressing need to focus on teenage mothers. Maintaining and strengthening programs that advocate EBF, such as ANC, is crucial to bridge the gaps and bring about more equitable rates among different groups

Prevalence and patterns of rifampicin and isoniazid resistance conferring mutations in <i>Mycobacterium tuberculosis</i> isolates from Uganda

<div><p>Background</p><p>Accurate diagnosis of tuberculosis, especially by using rapid molecular assays, can reduce transmission of drug resistant tuberculosis in communities. However, the frequency of resistance conferring mutations varies with geographic location of <i>Mycobacterium tuberculosis</i>, and this affects the efficiency of rapid molecular assays in detecting resistance. This has created need for characterizing drug resistant isolates from different settings to investigate frequencies of resistance conferring mutations. Here, we describe the prevalence and patterns of rifampicin- and isoniazid- resistance conferring mutations in isolates from Uganda, which could be useful in the management of MDR-TB patients in Uganda and other countries in sub-Saharan Africa.</p><p>Results</p><p>Ninety seven <i>M</i>. <i>tuberculosis</i> isolates were characterized, of which 38 were MDR, seven rifampicin-resistant, 12 isoniazid-mono-resistant, and 40 susceptible to rifampicin and isoniazid. Sequence analysis of the <i>rpoB</i> rifampicin-resistance determining region (<i>rpoB</i>/RRDR) revealed mutations in six codons: 588, 531, 526, 516, 513, and 511, of which Ser531Leu was the most frequent (40%, 18/45). Overall, the three mutations (Ser531Leu, His526Tyr, Asp516Tyr) frequently associated with rifampicin-resistance occurred in 76% of the rifampicin resistant isolates while 18% (8/45) of the rifampicin-resistant isolates lacked mutations in <i>rpoB</i>/RRDR. Furthermore, sequence analysis of <i>katG</i> and <i>inhA</i> gene promoter revealed mainly the Ser315Thr (76%, 38/50) and C(-15)T (8%, 4/50) mutations, respectively. These two mutations combined, which are frequently associated with isoniazid-resistance, occurred in 88% of the isoniazid resistant isolates. However, 20% (10/50) of the isoniazid-resistant isolates lacked mutations both in <i>katG</i> and <i>inhA</i> gene promoter. The sensitivity of sequence analysis of <i>rpoB</i>/RRDR for rifampicin-resistance via detection of high confidence mutations (Ser531Leu, His526Tyr, Asp516Tyr) was 81%, while it was 77% for analysis of <i>katG</i> and <i>inhA</i> gene promoter to detect isoniazid-resistance via detection of high confidence mutations (Ser315Thr, C(-15)T, T(-8)C). Furthermore, considering the circulating TB genotypes in Uganda, the isoniazid-resistance conferring mutations were more frequent in <i>M</i>. <i>tuberculosis</i> lineage 4/sub-lineage Uganda, perhaps explaining why this genotype is weakly associated with MDR-TB.</p><p>Conclusion</p><p>Sequence analysis of <i>rpoB</i>/RRDR, <i>katG</i> and <i>inhA</i> gene promoter is useful in detecting rifampicin/isoniazid resistant <i>M</i>. <i>tuberculosis</i> isolates in Uganda however, about ≤20% of the resistant isolates lack known resistance-conferring mutations hence rapid molecular assays may not detect them as resistant.</p></div

Frequency of rifampicin/isoniazid-resistance conferring mutations in the circulating <i>M</i>. <i>tuberculosis</i> genotypes/sub-lineages in Uganda (2009–2011).

<p>Frequency of rifampicin/isoniazid-resistance conferring mutations in the circulating <i>M</i>. <i>tuberculosis</i> genotypes/sub-lineages in Uganda (2009–2011).</p

Postpartum family planning uptake in Uganda: findings from the lot quality assurance sampling survey

Abstract Background The initiation and use of family planning (FP) services within the first 12 months following childbirth, postpartum family planning (PPFP), promotes safe motherhood by reducing unintended pregnancies and ensuring appropriate pregnancy spacing. However, there is a paucity of information on PPFP uptake from community surveys. This study aimed to quantify the reported use of PPFP and identify predictors and barriers to PPFP uptake from a large community survey. Methods We analysed data collected from the 2021 Lot Quality Assurance Sampling (LQAS) survey, a cross-sectional community and household survey that covered 68 districts in Uganda. The survey uses small sample sizes to designate health or administrative geographical areas which are assessed to determine whether they achieved the pre-determined target for defined indicators of interest. We abstracted and analysed data collected from mothers of children aged 12 months or younger on reproductive health and FP. PPFP use was defined as the reported use of modern FP by the mother or their partner. Associations were measured using Pearson’s chi-square test at 5% significance. Multivariate logistic regression was performed for variables that were significantly associated with PPFP use to identify the predictors of PPFP. Results Overall, 8103 mothers of children aged less than 12 years were included in the analysis; the majority of mothers, 55.8% (4521/8103) were above 24 years while 11.7% (950/8103) were 19 years and under. 98% (7942/8103) of the mothers attended at least one antenatal care (ANC) visit and 86.3% (6997/8103) delivered at a health facility. Only 10% (814/8103) of mothers who participated in the survey reported PPFP use at the time of the survey. Reporting of PPFP use was 5 times higher among mothers of children aged 7–12 months (AOR 4.9; 95%CI 4.1–5.8), 50% higher among mothers with secondary education (AOR 1.5; 95%CI 1.0-2.3), 80% higher among breastfeeding mothers (AOR 1.8; 95%CI 1.3–2.4) and 30% lower among those that didn’t receive a health worker visit within 3 months preceding the survey (AOR 0.7; 95% CI 0.5–0.8). Among 4.6% (372/8103) who stated a reason for non-use of PPFP, the most cited reasons for not using were breastfeeding 43% (161/372), fear of side effects 26.9% (100/372), respondent/partner opposition 17.6% (48/372) and infrequent sex 12.1% (48/372). Conclusion The analysis showed a low proportion of PPFP uptake among mothers of children under 12 years. Possible barriers included child age, education, a health worker visit, and side effects and perceived benefits of possibly improperly implementing lactation amenorrhea method. Integration of social, community and health services could provide a more holistic approach to improving PPFP uptake