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

BACKGROUND: Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods for TB diagnosis and detection of drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). This study compared WGS and clinical data in participants with TB. RESULTS: This cohort study performed WGS on 87 from MTBC DNA isolates, 57 (66%) and 30 (34%) patients with drug resistant and susceptible TB, respectively. Drug resistance was determined by Xpert® MTB/RIF assay and phenotypic culture-based drug-susceptibility-testing (DST). WGS and bioinformatics data that predict phenotypic resistance to anti-TB drugs were compared with participant's clinical outcomes. They were 47 female participants (54%) and the median age was 35 years (IQR): 29-44). Twenty (23%) and 26 (30%) of participants had TB/HIV co-infection BMI < 18 kg/m2 respectively. MDR-TB participants had MTBC with multiple mutant genes, compared to those with mono or polyresistant TB, and the majority belonged to lineage 3 Central Asian Strain (CAS). Also, MDR-TB was associated with delayed culture-conversion (median: IQR (83: 60-180 vs. 51:30-66) days). WGS had high concordance with both culture-based DST and Xpert® MTB/RIF assay in detecting drug resistance (kappa = 1.00). CONCLUSION: This study offers comparison of mutations detected by Xpert and WGS with phenotypic DST of M. tuberculosis isolates in Tanzania. The high concordance between the different methods and further insights provided by WGS such as PZA-DST, which is not routinely performed in most resource-limited-settings, provides an avenue for inclusion of WGS into diagnostic matrix of TB including drug-resistant TB.

Bacterial aetiology, antimicrobial susceptibility patterns, and factors associated with urinary tract infection among under-five children at primary health facility, North-Western Tanzania.

BACKGROUND: Urinary tract infections (UTI) are common in under-five children, with significant consequences leading to bacteremia, dehydration, kidney scarring, and renal failure. The incidence of UTI varies with patients' demographics and geographic location. Limited studies have addressed UTI issues, particularly in children. We determined the proportion of UTI, bacterial aetiology, and antimicrobial susceptibility patterns and associated factors among under-five children at the district hospital between March and April 2023. METHODS: We conducted a cross-sectional study using a convenient non-probability sampling technique to collect urine samples from participants with signs and symptoms of UTI. Written informed consent was obtained from parents or guardians. We collected Participants' information using a pretested structured questionnaire. Urine samples were processed at the Regional Referral Hospital. All analyses were conducted using STATA version 15.0. We determined the factors associated with UTI using a modified Poisson model multivariable analysis of the modified Poisson model. The results were presented as a prevalence ratio and 95% confidence interval. The level of significance was specified at 0.05. RESULT: The study recruited 368 under-five children; 194 (52.7%) were males, and the median age (interquartile range) was 24 (13-36) months. Of all, 28.8% (95% CI-24.3-33.6) had culture-confirmed UTI. One hundred and six pathogens were isolated, the majority being Escherichia coli (E. coli), 37 (34.9%), and Staphylococcus aureus (S. aureus), 26 (24.5%). The susceptibility of E. coli to cefepime, piperacillin-tazobactam, nitrofurantoin, and meropenem ranged from 81.1% to 97.3%. S. aureus was most susceptible to nitrofurantoin (96.2%) and ciprofloxacin (92.3%). Multidrug resistance was observed in 33.0% of isolates. The proportion of Methicillin-resistant S. aureus and extended-spectrum beta-lactamases was 23.1% and 25%, respectively. UTI was observed more in patients presenting with vomiting, dysuria, and abdominal pain, patients below 24 months of age, nappy users, and uncircumcised males. CONCLUSION: Our study found a relatively high proportion of UTI among under-five children associated with vomiting, dysuria, abdominal pain, nappy use, and uncircumcision in males. The pathogens were least susceptible to (trimethoprim-sulfamethoxazole, gentamycin, ampicillin, and penicillin) the commonly used antibiotic. We advocate a thorough clinical analysis to detect the predictors of UTI and a periodic review of empirical treatment of UTI based on the antibiotic susceptibility pattern.

Tanzania's first Marburg Viral Disease outbreak response: Describing the roles of FELTP graduates and residents.

Viral Haemorrhagic Fever Outbreak presents a significant public health threat, requiring a timely, robust, and well-coordinated response. This paper aims to describe the roles of the Tanzania Field Epidemiology and Laboratory Training Program (TFELTP) graduates and residents in responding to Tanzania's first Marburg Viral Disease (MVD) outbreak. We performed a secondary data analysis using a range of documents, such as rosters of deployed responders and the TFELTP graduate and resident database, to count and describe them. Additionally, we conducted an exploratory textual analysis of field deployment reports and outbreak situational reports to delineate the roles played by the residents and graduates within each response pillar. A total of 70 TFELTP graduates and residents from different regions were involved in supporting the response efforts. TFELTP graduates and residents actively participated in several interventions, including contact tracing and follow up, sensitising clinicians on surveillance tools such as standard case definitions, alert management, supporting the National and Kagera Regional Public Health Emergency Operations Centres, active case search, risk communication, and community engagement, coordination of logistics, passenger screening at points of entry, and conducting Infection Prevention and Control (IPC) assessments and orientations in 144 Health Facilities. The successes achieved and lessons learned from the MVD response lay a foundation for sustained investment in skilled workforce development. FELTP Training is a key strategy for enhancing global health security and strengthening outbreak response capabilities in Tanzania and beyond.

Molecular Characterization and Phylogenetic Analysis of Dengue Fever Viruses in Three Outbreaks in Tanzania Between 2017 and 2019.

BACKGROUND: Dengue is a disease of public health interest, and Tanzania experienced major outbreaks in 2014 and 2019. Here, we report our findings on the molecular characterization of dengue viruses (DENV) that circulated during two smaller outbreaks (2017 and 2018) and one major epidemic (2019) in Tanzania. METHODOLOGY/PRINCIPAL FINDINGS: We tested archived serum samples from 1,381 suspected dengue fever patients, with a median age of 29 (IQR:22-40) years, referred to the National Public Health Laboratory for confirmation of DENV infection. DENV serotypes were identified by reverse transcription polymerase chain reaction (RT-PCR), and specific genotypes were identified by sequencing the envelope glycoprotein gene and phylogenetic inference methods. DENV was confirmed in 823 (59.6%) cases. More than half (54.7%) of patients with dengue fever infection were males, and nearly three-quarters (73%) of the infected individuals were living in Kinondoni district, Dar es Salaam. DENV-3 Genotype III caused the two smaller outbreaks in 2017 and 2018, while DENV-1 Genotype V caused the 2019 epidemic. DENV-1 Genotype I was also detected in one patient in 2019. CONCLUSION/SIGNIFICANCE: This study has demonstrated the molecular diversity of dengue viruses circulating in Tanzania. We found that contemporary circulating serotypes did not cause the major epidemic of 2019 but rather due to a serotype shift from DENV-3 (2017/2018) to DENV-1 in 2019. Such a change increases the risk for patients previously infected with a particular serotype to develop severe symptoms upon potential re-infection with a heterologous serotype due to antibody-dependent enhancement of infection. Therefore, the circulation of serotypes emphasizes the need to strengthen the country's dengue surveillance system for better management of patients, early detection of outbreaks, and vaccine development.

Compliance to infection prevention and control interventions for slowing down COVID-19 in early phase of disease transmission in Dar es Salaam, Tanzania.

Introduction: on 16th March 2020, Tanzania announced its first COVID-19 case. The country had already developed a 72-hour response plan and had enacted three compulsory infection prevention and control interventions. Here, we describe public compliance to Infection Prevention and Control (IPC) public health measures in Dar es Salaam during the early COVID-19 response and testing of the feasibility of an observational method. Methods: a cross sectional study was conducted between April and May 2020 in Dar es Salaam City. At that time, Dar es Salaam was the epi centre of the epidemic. Respondents were randomly selected from defined population strata (high, medium and low). Data were collected using a structured questionnaire and through observations. Results: a total of 390 subjects were interviewed, response rate was 388 (99.5%). Mean age of the respondents was 34.8 years and 168 (43.1%) had primary level education. Out of the 388 respondents, 384 (98.9%) reported to have heard about COVID-19 public health and social measures, 90.0% had heard from the television and 84.6% from the radio. Covering coughs and sneezes using a handkerchief was the most common behaviour observed among 320 (82.5%) respondents; followed by hand washing hygiene practice, 312 (80.4%) and wearing face masks, 240 (61.9%). Approximately 215 (55.4%) adhered to physical distancing guidance. Age and gender were associated with compliance to IPC measures (both, p<0.05). Conclusion: compliance to public health measures during the early phase of COVID-19 pandemic in this urban setting was encouraging. As the pandemic continues, it is critical to ensure compliance is sustained and capitalize on risk communication via television and radio.

An investigation of pyrexia of unknown origin in Shamva District, Zimbabwe, September 2015.

Outbreak investigation is a key component of public health training. A good outbreak investigation can go beyond determining the causative agent by recommending policies to be formulated by policy makers. This case study simulates a real-life investigation of pyrexia of unknown origin in Shamva District, Zimbabwe, during the period of September to October 2015. It aims at reinforcing principles and skills taught in class on outbreak investigation, study design and policy initiation. The target audience for the case study is Field Epidemiologists at their advanced level of training. It is expected to be completed in approximately 2 hours. General instructions: ideally, 1 to 2 facilitator(s) is/are required to facilitate the case study for 10 to 20 participants. The facilitator should request participants to read a paragraph out loud, going around the room to give each participant a chance to read. When the participant reads a question, the facilitator encourages all participants to engage in discussions, perform calculations, and draw graphs among other tasks. The facilitators request the participants to play different roles or take different sides in answering a question. As a result, participants learn from each other, not just from the facilitators.

Investigating a foodborne illness outbreak at a private girls' school in Mashonaland East Province, Zimbabwe, 2015.

Globally, it is estimated that foodborne-associated illness accounts for 2.2 million deaths. This is caused by contamination of food with toxins, parasites, bacteria or viruses that can lead to increased levels of morbidity and mortality. Although steps to conducting an outbreak investigation have been outlined in most epidemiology textbooks, identifying the causative agent for a foodborne illness outbreak can be complex based on the setting. In view of that, this case study was developed based on a foodborne illness outbreak at agirls' boarding school to model the steps of an investigation. This case study will reinforce skills and theoretical knowledge attained by public health trainees, to be able to build competences in foodborne outbreak investigation. The target audiences are intermediate and advanced public health trainees. Estimated time of facilitation is 3 hours with a class size of 10- 20 students.

Investigating a paralytic shellfish poisoning in Gando Village, Wete District, Tanzania, July 2015.

The investigation of foodborne outbreaks requires a multi-disciplinary set of skills. Frequently, foodborne-related outbreaks are poorly investigated due to lack of all required skills on the part of the investigators. This case study, based on a shellfish poisoning outbreak investigation conducted in Wete, Zanzibar in July 2015 by the Tanzania Field Epidemiology Training Program (TFETP), seeks to reinforce principles and skills in foodborne outbreak investigation. It is primarily intended for training public health practitioners in a classroom setting. Facilitating this case study should take approximately 3 hours.