Characterization of Vibrio cholerae O1 isolates responsible for cholera outbreaks in Kenya between 1975 and 2017

Kenya is endemic for cholera with different waves of outbreaks having been documented since 1971. In recent years, new variants of Vibrio cholerae O1 have emerged and have replaced most of the traditional El Tor biotype globally. These strains also appear to have increased virulence, and it is important to describe and document their phenotypic and genotypic traits. This study characterized 146 V. cholerae O1 isolates from cholera outbreaks that occurred in Kenya between 1975 and 2017. Our study reports that the 1975–1984 strains had typical classical or El Tor biotype characters. New variants of V. cholerae O1 having traits of both classical and El Tor biotypes were observed from 2007 with all strains isolated between 2015 and 2017 being sensitive to polymyxin B and carrying both classical and El Tor type ctxB. All strains were resistant to Phage IV and harbored rstR, rtxC, hlyA, rtxA and tcpA genes specific for El Tor biotype indicating that the strains had an El Tor backbone. Pulsed field gel electrophoresis (PFGE) genotyping differentiated the isolates into 14 pulsotypes. The clustering also corresponded with the year of isolation signifying that the cholera outbreaks occurred as separate waves of different genetic fingerprints exhibiting different genotypic and phenotypic characteristics. The emergence and prevalence of V. cholerae O1 strains carrying El Tor type and classical type ctxB in Kenya are reported. These strains have replaced the typical El Tor biotype in Kenya and are potentially more virulent and easily transmitted within the population.     

The bounty of minor lakes: the role of small satellite water bodies in evolution and conservation of fishes in the Lake Victoria Region,East Africa

The Lake Victoria Region (LVR) encompasses the large lakes Victoria, Kyoga, Edward, George and Kivu, as well as scores of small satellite lakes within the parent catchments. Taken as a whole, the LVR originally harbored a unique fish fauna that included in excess of 600 endemic species of cichlid fishes. As a result of human influence, including a commercial fishery and the introduction of several exotic species, nearly 200 cichlid species and several endemic genera have become extinct from lakes Victoria and Kyoga. Recently, we have discovered that some of the apparently extinct taxa survive as extant representatives in the satellite lakes. Here, we summarize the findings of our ecological survey of the fish species of the satellite lakes. We also discuss the results of some preliminary genetic analyses, and highlight major genetic and ecological changes in the fish fauna that have taken place in the regional fishery. Minor lakes now play a crucial role in conserving the endangered species of the entire region, and also as living museums of East African ecological history. Our findings allude to the historical importance of minor satellite lakes as natural refugia for the fishes of the Lake Victoria Region, a region characterized by a history of geological and climatic instability.     

Trophic Niche Segregation in the Nilotic Ichthyofauna of Lake Albert (Uganda, Africa)

Synopsis Nile perch, Lates niloticus, and Nile tilapia, Oreochromis niloticus, were originally transplanted from Lake Albert in western Uganda to the African Great Lakes, Lake Victoria and Lake Kyoga, where they are partially implicated in reduction of the fish species diversity. Lake Albert is facing multiple environmental changes, including declining fish species diversity, hyper-eutrophication, hypoxia, and reduced fish catches. To examine the role of Nile perch and Nile tilapia in the food web in their native Lake Albert, we estimated their diets using stable nitrogen and carbon isotopes. In Lake Albert, the tilapiine congeners (closely related species), Tilapia zillii, Oreochromis leucostictus, and Sarethorodon galilaeus, and the centropomid Nile perch congener, Lates macrophthalmus, have narrower diet breath in the presence of the native O. niloticus and L. niloticus. A computerized parameter search of dietary items for five commercially important fish species (Hydrocynus forskahlii, Bagrus bayad, L. niloticus, Alestes baremose and Brycinus nurse) was completed using a static isotopic mixing model. The outcome of the simulation for most fish species compared favorably to previously published stomach contents data for the Lake Albert fishes dating back to 1928, demonstrating agreement between stable isotope values and analyses of stomach contents. While there were some indications of changes in the diets of L. niloticus and A. baremose diets over the past 20 years in parallel with other changes in the lake, for the most part, food web structure in this lake remained stable since 1928. The Lake Albert fish assemblage provides insight into the invasion success of L. niloticus and O. niloticus.     

Alcohol Consumption among HIV-Infected Persons in a Large Urban HIV Clinic in Kampala Uganda: A Constellation of Harmful Behaviors

IntroductionAlcohol use by persons living with HIV/AIDS (PLWHA) negatively impacts the public health benefits of antiretroviral therapy (ART). Using a standardized alcohol assessment tool, we estimate the prevalence of alcohol use, identify associated factors, and test the association of alcohol misuse with sexual risk behaviors among PLWHA in Uganda.MethodsA cross-section of PLWHA in Kampala were interviewed regarding their sexual behavior and self-reported alcohol consumption in the previous 6 months. Alcohol use was assessed using the alcohol use disorders identification test (AUDIT). Gender-stratified log binomial regression analyses were used to identify independent factors associated with alcohol misuse and to test whether alcohol misuse was associated with risky sexual behaviors.ResultsOf the 725 subjects enrolled, 235 (33%) reported any alcohol use and 135 (18.6%) reported alcohol misuse, while 38 (5.2%) drank hazardous levels of alcohol. Alcohol misuse was more likely among subjects not yet on ART (adjusted prevalence ratio [aPR] was 1.65 p=0.043 for males and 1.79, p=0.019 for females) and those with self-reported poor adherence (aPR for males=1.56, p=0.052, and for females=1.93, p=0.0189). Belonging to Pentecostal or Muslim religious denominations was protective against alcohol misuse compared to belonging to Anglican and Catholic denominations in both sexes (aPR=0.11 for men, p<0.001, and aPR=0.32 for women, p=0.003). Alcohol misuse was independently associated with reporting risky sexual behaviors (aPR=1.67; 95% CI: 1.07–2.60, p=0.023) among males, but not significant among females (aPR=1.29; 95% CI: 0.95–1.74, p=0.098). Non-disclosure of HIV positive status to sexual partner was significantly associated with risky sex in both males (aPR=1.69; p=0.014) and females (aPR 2.45; p<0.001).ConclusionAlcohol use among PLWHA was high, and was associated with self-reported medication non-adherence, non-disclosure of HIV positive status to sexual partner(s), and risky sexual behaviors among male subjects. Interventions targeting alcohol use and the associated negative behaviors should be tested in this setting.     

The relationships between relative growth rate,meristematic potential and compensatory growth of semiarid-land shrubs

The submersed macrophyte Vallisneria americana was grown for seven weeks in a greenhouse to test for differences in the ability of three different sediments to support growth stimulation in response to CO₂ enrichment at low pH. Plants accumulated 21- to 24-fold greater biomass at 10 × ambient CO₂ concentrations than at ambient CO₂ on all sediments. At both CO₂ levels, plants grown on sediment from an acidified lake accumulated ca. 81%, and those grown on oligotrophic lake sediment ca. 47% as much biomass as plants grown on alkaline lake sediment. Despite striking CO₂ and sediment effects on biomass accumulation, there was no significant interaction (using log-transformed data) between CO₂ and sediment effects, indicating that all sediments allowed similar proportionate growth responses to CO₂ enrichment. Plants grown on the less fertile sediments showed greater relative allocation to horizontal versus vertical growth by producing more rosette-bearing stolons in relation to plant height (leaf length) than plants grown on relatively fertile, alkaline lake sediment. Tissue analysis suggested that sediment effects on Vallisneria growth could be attributed neither to mineral putrient (nitrogen and phosphorus) limitation nor to aluminum toxicity in these low pH treatments. In any case, CO₂ availability can be an important regulator of submersed macrophyte growth at low pH on a variety of sediment types, including those from oligotrophic and acidic lakes.     

Fish species and trophic diversity of haplochromine cichlids in the Kyoga satellite lakes (Uganda)

Prior to the 1980s, lakes Kyoga and Victoria previously supported an exceptionally diverse haplochromine fish fauna comprising at least 11 trophic groups. The species and trophic diversity in these lakes decreased when the introduced Nile perch depleted haplochromine stocks. From December 1996 to October 1998, we studied species and trophic diversity of haplochromine fishes in six satellite lakes without Nile perch in the Kyoga basin and compared them with the Kyoga main lake against historical data from Lake Victoria where Nile perch were introduced. Forty‐one species were found in the study area, of which, the Kyoga satellite lakes contributed 37 species in comparison to only 14 from the Kyoga main lake. Analysis of trophic diversity based on 24 species that contained food material revealed seven haplochromine trophic groups (insectivores, peadophages, piscivores, algal eaters, higher plant eaters, molluscivores and detritivores) in the Kyoga satellite lakes in comparison to two trophic groups (insectivores and molluscivores) in the Kyoga main lake. Many of the species and trophic groups of haplochromines depleted by the introduced Nile perch in lakes Kyoga and Victoria still survive in the Kyoga satellite lakes. This is attributed to the absence of Nile perch in those lakes. Nile perch has been prevented from spreading into the satellite lakes by swamp vegetation that separate them from the main lakes. If these swamps prevent Nile perch from spreading into the lakes, it is possible to conserve fish species, especially haplochromines, which are threatened by introduction of Nile perch in the main lakes.     

Outcomes in a Cohort of Patients Started on Antiretroviral Treatment and Followed up for a Decade in an Urban Clinic in Uganda

Background

Short-medium term studies from sub-Saharan Africa show that, despite high early mortality, substantial loss to program, and high rates toxicity, patients on antiretroviral treatment have achieved outcomes comparable to those in developed settings. However, these studies were unable to account for long term outcomes of patients as they stayed longer on treatment.

Objectives

We aim to describe ten years outcomes of one of the first cohort of HIV positive patients started on antiretroviral treatment (ART) in Sub-Saharan Africa.

Methods

We report 10-years outcomes including mortality, retention, CD4-count response, virological outcomes, ART regimens change from a prospective cohort of 559 patients initiating ART and followed up for 10 years Uganda.

Results

Of 559 patients, 69.1% were female, median age (IQR) was 38 (33–44) years, median CD4-count (IQR) 98 (21–163) cell/μL; 74% were started on stavudine, lamivudine and nevirapine, 26% on zidovudine, lamivudine and efavirenz. After 10 years 361 (65%) patients were still in the study; 127 (22.7%) had died; 30 (5%) were lost to follow-up; 27 (5%) transferred; 18 (3%) withdrew consent. The probability of death was high in the first year (0.15, 95%, CI 0.12–0.18). The median CD4 count increased from 98 to 589 cell/μL (IQR: 450–739 cell/μL) with a median increase of 357 cells/μL (IQR: 128–600 cells/μL); 7.4% never attained initial viral suppression and of those who did 31.7% experienced viral failure. Three hundred and two patients had at least one drug substitution while on first line after a median of 40 months; 66 (11.9%) of the patients were switched to a second line PI-based regimen due to confirmed treatment failure.

Conclusions

Despite the high rate of early mortality due to advanced disease at presentation the outcomes from this cohort are encouraging, particularly the remarkable and incremental immune-recovery and a satisfactory rate of virologic suppression.