Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania.

BACKGROUND: Cholera outbreaks have occurred in Tanzania since 1974. To date, the genetic epidemiology of these outbreaks has not been assessed. METHODS: 96 Vibrio cholerae O1 isolates from five regions were characterized, and their genetic relatedness assessed using multi-locus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). RESULTS: Of the 48 MLVA genotypes observed, 3 were genetically unrelated to any others, while the remaining 45 genotypes separated into three MLVA clonal complexes (CCs) - each comprised of genotypes differing by a single allelic change. In Kigoma, two separate outbreaks, 4 months apart (January and May, 2015), were each caused by genetically distinct strains by MLVA and WGS. Remarkably, one MLVA CC contained isolates from both the May outbreak and ones from the 2011/2012 outbreak in Dar-es-Salaam. However, WGS revealed the isolates from the two outbreaks to be distinct clades. The outbreak that started in August 2015 in Dar-es-Salaam and spread to Morogoro, Singida and Mara was comprised of a single MLVA CC and WGS clade. Isolates from within an outbreak were closely related differing at fewer than 5 nucleotides. All isolates were part of the 3rd wave of the 7th pandemic and were found in four clades related to isolates from Kenya and Asia. CONCLUSIONS: We conclude that genetically related V. cholerae cluster in outbreaks, and distinct strains circulate simultaneously.

Results from the first 30 months of national sentinel surveillance for influenza in Tanzania, 2008-2010.

Limited data exist on the burden of influenza in developing countries. In 2008, in order to better understand the epidemiology of influenza virus infection in Tanzania, the Tanzanian Ministry of Health and Social Welfare created a sentinel surveillance system for influenza. At 5 hospitals across the country, patients with influenza-like illness (ILI) and severe acute respiratory illness (SARI) had oropharyngeal and nasopharyngeal samples collected. At the National Influenza Center in Dar es Salaam, specimens were tested for influenza using real-time polymerase chain reaction tests. From May 2008 through November 2010, a total of 1794 samples were collected from 5 sentinel sites, of which 61% were from patients with ILI and 39% were from patients with SARI. Of all ILI and SARI samples, 8.0% were positive for influenza; 6.9% yielded influenza A virus, and 1.1% yielded influenza B virus. Most influenza A virus was subtype H3, which circulated in nearly every month of 2010. The proportion of influenza-positive cases was similar among ILI (8.5%) and SARI (7.3%) patients (P = .39). In multivariate logistic regression, influenza-positive SARI cases were more likely than influenza-negative SARI cases to have had rhonchi (adjusted OR [aOR], 2.31; 95% confidence interval [CI], 1.14-4.67), nasal discharge (aOR, 4.57; 95% CI, 1.30-16.10), and stridor (aOR, 2.63; 95% CI, 1.17-5.90). Influenza-positive ILI patients had a longer duration of fever on presentation, compared with influenza-negative ILI patients (median, 4 vs 3 days; P = .004). Otherwise, there was no difference in signs or symptoms among influenza-positive and influenza-negative ILI patients. During 2.5 years of surveillance for influenza at 5 geographically disbursed sites in Tanzania, we found that influenza circulated year-round. Surveillance should continue in order to fully understand the seasonality and epidemiology of influenza in Tanzania.