First report of whole-genome analysis of an extensively drug-resistant Mycobacterium tuberculosis clinical isolate with bedaquiline, linezolid and clofazimine resistance from Uganda.

BACKGROUND: Uganda remains one of the countries with the highest burden of TB/HIV. Drug-resistant TB remains a substantial challenge to TB control globally and requires new strategic effective control approaches. Drug resistance usually develops due to inadequate management of TB patients including improper treatment regimens and failure to complete the treatment course which may be due to an unstable supply or a lack of access to treatment, as well as patient noncompliance. METHODS: Two sputa samples were collected from Xpert MTB/RIF® assay-diagnosed multi-drug resistant tuberculosis (MDR-TB) patient at Lira regional referral hospital in northern Uganda between 2020 and 2021 for comprehensive routine mycobacterial species identification and drug susceptibility testing using culture-based methods. Detection of drug resistance-conferring genes was subsequently performed using whole-genome sequencing with Illumina MiSeq platform at the TB Supranational Reference Laboratory in Uganda. RESULTS: In both isolates, extensively drug-resistant TB (XDR-TB) was identified including resistance to Isoniazid (katG p.Ser315Thr), Rifampicin (rpoB p.Ser450Leu), Moxifloxacin (gyrA p.Asp94Gly), Bedaquiline (Rv0678 Glu49fs), Clofazimine (Rv0678 Glu49fs), Linezolid (rplC Cys154Arg), and Ethionamide (ethA c.477del). Further analysis of these two high quality genomes revealed that this 32 years-old patient was infected with the Latin American Mediterranean TB strain (LAM). CONCLUSIONS: This is the first identification of extensively drug-resistant Mycobacterium tuberculosis clinical isolates with bedaquiline, linezolid and clofazimine resistance from Uganda. These acquired resistances were because of non-adherence as seen in the patient's clinical history. Our study also strongly highlights the importance of combating DR-TB in Africa through implementing next generation sequencing that can test resistance to all drugs while providing a faster turnaround time. This can facilitate timely clinical decisions in managing MDR-TB patients with non-adherence or lost to follow-up.

Knowledge and attitude of secondary school students in Nakaseke, Uganda towards HIV transmission and treatment.

Background: One of the major health concerns in Nakaseke district, Uganda is the high prevalence of HIV/AIDS. According to the Joint United Nations Programme on HIV/AIDS (UNAIDS), as of March 2014, the prevalence rate of the disease in the district was estimated at about 8%, compared to the national average of 6.5%, making Nakaseke district have the sixth-highest prevalence rate of HIV/AIDS in the entire country. We set out to explore the knowledge and attitude of secondary school students in Nakaseke, Uganda on HIV transmission and treatment. Methods: This was a cross sectional survey-based study with data collected during the month of February 2020. Data were analyzed using R programming language version 3.6.2. Results: A total of 163 participants volunteered for the study, 53.37% males and 46.63% females with ages ranging from 12 - 20 years. Participants came from 5 senior classes (S1, S2, S3, S4 and S6). In total, 87.73% participants were aware of HIV/AIDS while 12.27% were not. The major source of information was through teachers/schools. 96.50% knew the mode of transmission of HIV/AIDS and 95.11% were conversant with HIV/AIDS prevention. 63.6% were aware of the terms DNA and genes whereas 36.36% were not. Discussion: Generally, the students in Nakaseke district, Uganda had a high level of awareness of HIV/AIDS. However, with regards to aspects such as the cause and modern prevention methods like taking prep and prevention of mother to child transmission were less known to them. Efforts to find a cure for HIV/AIDS are still in vain. Therefore, strong emphasis on up to date control and prevention methods should be implemented to fight the HIV/AIDS scourge .

Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings.

Background: In January 2020, a previously unknown coronavirus strain was identified as the cause of a severe acute respiratory syndrome (SARS-CoV-2). The first viral whole-genome was sequenced using high-throughput sequencing from a sample collected in Wuhan, China. Whole-genome sequencing (WGS) is imperative in investigating disease outbreak transmission dynamics and guiding decision-making in public health. Methods: We retrieved archived SARS-CoV-2 samples at the Integrated Biorepository of H3Africa Uganda, Makerere University (IBRH3AU). These samples were collected previously from individuals diagnosed with coronavirus disease 2019 (COVID-19) using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). 30 samples with cycle thresholds (Cts) values <25 were selected for WGS using SARS-CoV-2 ARTIC protocol at Makerere University Molecular Diagnostics Laboratory. Results: 28 out of 30 (93.3%) samples generated analyzable genomic sequence reads. We detected SARS-CoV-2 and lineages A (22/28) and B (6/28) from the samples. We further show phylogenetic relatedness of these isolates alongside other 328 Uganda (lineage A = 222, lineage B = 106) SARS-CoV-2 genomes available in GISAID by April 22, 2021 and submitted by the Uganda Virus Research Institute. Conclusions: Our study demonstrated adoption and optimization of the low-cost ARTIC SARS-CoV-2 WGS protocol in a resource limited laboratory setting. This work has set a foundation to enable rapid expansion of SARS-CoV-2 WGS in Uganda as part of the Presidential Scientific Initiative on Epidemics (PRESIDE) CoV-bank project and IBRH3AU.