Research articles (Dept of Biomedical Sciences)
http://hdl.handle.net/10311/1260
2024-03-29T09:25:54ZPopulation structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
http://hdl.handle.net/10311/2262
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Hansen, Matthew E.B.; Rubel, Meagan A.; Bailey, Aubrey G; Ranciaro, Alessia; Thompson, Simon R.; Campbell, Michael C.; Beggs, William; Dave, Jaanki R.; Mokone, Gaonyadiwe G; Mpoloka, Sununguko Wata; Nyambo, Thomas; Abnet, Christian; Chanock, Stephen J.; Bushman, Frederic D.; Tishkoff, Sarah A.
Background: Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals
from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region.
Results: We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs
between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual
and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers
are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and
pastoralists were not significantly different from each other. Nearly half of the Bantu-speaking agropastoralists
from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed
metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of
several common industrial pollutants. Within two African populations, we find evidence that bacterial
composition correlates with the genetic relatedness between individuals.
Conclusions: Across the cohort, similarity in bacterial presence/absence compositions between people
increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial
composition varies more significantly with geographic proximity than with genetic relatedness.
2019-01-22T00:00:00ZAssessment of prescribing practices at the primary healthcare facilities in Botswana with an emphasis on antibiotics: findings and implications
http://hdl.handle.net/10311/2252
Assessment of prescribing practices at the primary healthcare facilities in Botswana with an emphasis on antibiotics: findings and implications
Mashalla, Yohana; Setlhare, Vincent; Sepako, Enoch; Tiroyakgosi, Celda; Kgatlwane, Joyce; Chuma, Mpo; Godman, Brian; Massele, Amos
Background and Aims: Inappropriate drug prescribing has increased especially in developing countries where systems for monitoring medicine use are not well developed. This increases the rate of antimicrobial resistance. The study aim was to assess the prescribing patterns among urban primary health facilities in Botswana to provide future guidance including developing future quality indicators.
Methods: Retrospective data from patients’ records between January and December 2013 in 19 clinics were collected in a cross-sectional study. The WHO/International Network for Rational Use of Drugs indicators were used to assess prescribing patterns in the study clinics.
Results: Average number of drugs per prescription was 2.8; 78.6% of the prescribed antibiotics were by International Non-proprietary Name and 96.1% complied with the Botswana Essential Drugs List. Overall rate of antibiotic prescribing was high (42.7%) with 14.7%, 5.9% and 1.3% of prescriptions having two, three and four antibiotics, respectively. Systemic antibiotics (JO1C) accounted for 45.4% of prescribed antibiotics
of which amoxicillin accounted for 28.4% and metronidazole 14.4% of all antibiotic prescriptions.
There was low use of co-amoxiclav (0.3% of all antibiotic prescriptions).
Third generation cephalosporins and macrolides accounted for 9.8% and 6.2% of antibiotic prescriptions respectively, with no prescribing of fluoroquinolones. The majority of indications (87%) for antibiotic prescriptions were according to ICD classification.
Conclusions: While most indications for antibiotic prescriptions were based on signs and symptoms according to ICD, antibiotic prescribing rates were high with some conditions not requiring antibiotics because they are viral infections. There is a need to further improve prescribing practices through induction and training of in-service
prescribers. An effective management tool for monitoring antibiotic prescribing practices at Primary Health Care facilities should be designed and implemented, including developing robust quality indicators.
2017-12-01T00:00:00ZA step toward timely referral and early diagnosis of cancer: implementation and impact on knowledge of a primary care based training program in Botswana
http://hdl.handle.net/10311/2145
A step toward timely referral and early diagnosis of cancer: implementation and impact on knowledge of a primary care based training program in Botswana
Narasimhamurthy, Mohan; Tapela, Neo M.; Peluso, Michael J.; Kohler, Racquel E.; Setlhako, Irene I.; Botebele, Kerapetse; Gabegwe, Kemiso; Nkele, Isaac; Mmalane, Mompati; Grover, Surbhi; Barak, Tomer; Shulman, Lawrence N.; Lockman, Shahin; Dryden-Peterson, Scott
Health system delays in diagnosis of cancer contribute to the glaring disparities in cancer mortality between high-income countries and low- and middle-income countries. In Botswana, approximately 70% of cancers are diagnosed at late stage and median time from first health facility visit for cancer-related symptoms to specialty cancer care was 160 days (IQR 59–653). We describe the implementation and early outcomes of training targeting primary care providers, which is a part of a multi-component implementation study in Kweneng-East district aiming to enhance timely diagnosis of cancers.Methods Health-care providers from all public facilities within the district were invited to participate in an 8-h intensive short-course program developed by a multidisciplinary team and adapted to the Botswana health system context. Participants’ performance was assessed using a 25-multiple choice question tool, with pre- and post-assessments paired by anonymous identifier. Statistical analysis with Wilcoxon signed-rank test to compare performance at the two time points across eight sub-domains (pathophysiology, epidemiology, social context, symptoms, evaluation, treatment, documentation, follow-up). Linear regression and negative binomial modeling were used to determine change in performance. Participants’ satisfaction with the program was measured on a separate survey using a 5-point Likert scale.Results176 participants attended the training over 5 days in April 2016. Pooled linear regression controlling for test version showed an overall performance increase of 16.8% after participation (95% CI 15.2–18.4). Statistically significant improvement was observed for seven out of eight subdomains on test A and all eight subdomains on test B. Overall, 71 (40.3%) trainees achieved a score greater than 70% on the pretest, and 161 (91.5%) did so on the posttest. Participants reported a high degree of satisfaction with the training program’s content and its relevance to their daily work.Conclusion We describe a successfully implemented primary health care provider-focused training component of an innovative intervention aiming to reduce health systems delays in cancer diagnosis in sub-Saharan Africa. The training achieved district-wide participation, and improvement in the knowledge of primary health-care providers in this setting.Clinical Trial Registrationwww.ClinicalTrials.gov, identifier NCT02752061.
2018-05-29T00:00:00ZMolecular detection of human papillomavirus HPV) in highly fragmented DNA from cervical cancer biopsies using double-nested PCR
http://hdl.handle.net/10311/2144
Molecular detection of human papillomavirus HPV) in highly fragmented DNA from cervical cancer biopsies using double-nested PCR
Tawe, Leabaneng; Grover, Surbhi; Moyo, Sikhulile; Narasimhamurthy, Mohan; Kasvosve, Ishmael; Gaseitsiwe, Simani; Paganotti, Giacomo M.
Archived Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens can be a valuable source of human
papillomavirus (HPV) nucleic acids for molecular biological analyses in retrospective studies. Although successful
amplification with polymerase chain reaction (PCR) is essential for analysis of HPV DNA extracted from cervical
FFPE specimens, extensive DNA damage due to cross-linking and fragmentation results in poor yield. Therefore,
techniques to improve the diagnostic rate and sensitivity from FFPE tissues through PCR is highly desired and of
wider interest. To overcome this, a highly sensitive double-nested PCR methodology was designed and optimized
for limited-resource laboratories coupled with an organic extraction of DNA. This method allows the detection of
a broad range of HPV genotypes and also allowing the sequencing of the final amplicon. Validation of the new
approach developed was done with an automated DNA extraction coupled with Real Time PCR. Results showed
that the proposed method achieves 96.3% of HPV detection as compared to 100% Abbott m2000rt used as ‘gold
standard’. Moreover, the concordance rate between the two methods was equal for detecting HPV -16 or -18
genotypes. Nevertheless, the newly introduced assay has an advantage of:
Simultaneously identifying broad range of HPV genotypes besides HPV-16 and -18 from clinical samples.
It is an easy and cost-effective method that can be beneficial in resource-limited setting and can be employed
for various molecular applications.
2018-01-01T00:00:00Z