New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission.

Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region. To better characterize regional transmission, we generated and analyzed 118 Vibrio cholerae genomes collected between 2007-2019 from five different countries in Southern and Eastern Africa. We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, Zambia, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. We also find evidence that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.

Enhanced cholera surveillance to improve vaccination campaign efficiency.

Systematic testing for Vibrio cholerae O1 is rare, which means that the world's limited supply of oral cholera vaccines (OCVs) may not be delivered to areas with the highest true cholera burden. Here we used a phenomenological model with subnational geographic targeting and fine-scale vaccine effects to model how expanding V. cholerae testing affected impact and cost-effectiveness for preventive vaccination campaigns across different bacteriological confirmation and vaccine targeting assumptions in 35 African countries. Systematic testing followed by OCV targeting based on confirmed cholera yielded higher efficiency and cost-effectiveness and slightly fewer averted cases than status quo scenarios targeting suspected cholera. Targeting vaccine to populations with an annual incidence rate greater than 10 per 10,000, the testing scenario averted 10.8 (95% prediction interval (PI) 9.4-12.6) cases per 1,000 fully vaccinated persons while the status quo scenario averted 6.9 (95% PI 6.0-7.8) cases per 1,000 fully vaccinated persons. In the testing scenario, testing costs increased by US$31 (95% PI 25-39) while vaccination costs reduced by US$248 (95% PI 176-326) per averted case compared to the status quo. Introduction of systematic testing into cholera surveillance could improve efficiency and reach of global OCV supply for preventive vaccination.

Estimating the proportion of clinically suspected cholera cases that are true Vibrio cholerae infections: A systematic review and meta-analysis.

BACKGROUND: Cholera surveillance relies on clinical diagnosis of acute watery diarrhea. Suspected cholera case definitions have high sensitivity but low specificity, challenging our ability to characterize cholera burden and epidemiology. Our objective was to estimate the proportion of clinically suspected cholera that are true Vibrio cholerae infections and identify factors that explain variation in positivity. METHODS AND FINDINGS: We conducted a systematic review of studies that tested ≥10 suspected cholera cases for V. cholerae O1/O139 using culture, PCR, and/or a rapid diagnostic test. We searched PubMed, Embase, Scopus, and Google Scholar for studies that sampled at least one suspected case between January 1, 2000 and April 19, 2023, to reflect contemporary patterns in V. cholerae positivity. We estimated diagnostic test sensitivity and specificity using a latent class meta-analysis. We estimated V. cholerae positivity using a random-effects meta-analysis, adjusting for test performance. We included 119 studies from 30 countries. V. cholerae positivity was lower in studies with representative sampling and in studies that set minimum ages in suspected case definitions. After adjusting for test performance, on average, 52% (95% credible interval (CrI): 24%, 80%) of suspected cases represented true V. cholerae infections. After adjusting for test performance and study methodology, the odds of a suspected case having a true infection were 5.71 (odds ratio 95% CrI: 1.53, 15.43) times higher when surveillance was initiated in response to an outbreak than in non-outbreak settings. Variation across studies was high, and a limitation of our approach was that we were unable to explain all the heterogeneity with study-level attributes, including diagnostic test used, setting, and case definitions. CONCLUSIONS: In this study, we found that burden estimates based on suspected cases alone may overestimate the incidence of medically attended cholera by 2-fold. However, accounting for cases missed by traditional clinical surveillance is key to unbiased cholera burden estimates. Given the substantial variability in positivity between settings, extrapolations from suspected to confirmed cases, which is necessary to estimate cholera incidence rates without exhaustive testing, should be based on local data.

Cholera and COVID-19 pandemic prevention in multiple hotspot districts of Uganda: vaccine coverage, adverse events following immunization and WASH conditions survey.

BACKGROUND: Between March, 2020 and December, 2021 due to cholera and coronavirus disease 2019 (COVID-19) pandemics, there were 1,534 cholera cases with 14 deaths and 136,065 COVID-19 cases with 3,285 deaths reported respectively in Uganda. This study investigated mass vaccination campaigns for the prevention of the two pandemics namely: oral cholera vaccine (OCV) and COVID-19 vaccine coverage; adverse events following immunization (AEFI); barriers and enablers for the vaccine uptake and assessed water, sanitation and hygiene (WASH) conditions in the six cholera and COVID-19 hotspot districts of Uganda. METHODS: A household survey was conducted between January and February, 2022 in the six cholera hotspot districts of Uganda which had recently conducted OCV mass vaccination campaigns and had ongoing COVID-19 mass vaccination campaigns. The survey randomly enrolled 900 households with 4,315 persons of whom 2,085 were above 18 years. Data were collected using a data entry application designed in KoBoToolbox and analysed using STATA version 14. Frequencies, percentages, odds ratios, means, confidence intervals and maps were generated and interpreted. RESULTS: The OCV coverage for dose one and two were 85% (95% CI: 84.2-86.4) and 67% (95% CI: 65.6-68.4) respectively. Among the 4,315 OCV recipients, 2% reported mild AEFI, 0.16% reported moderate AEFI and none reported severe AEFI. The COVID-19 vaccination coverage for dose one and two were 69.8% (95% CI: 67.8-71.8) and 18.8% (95% CI: 17.1-20.5) respectively. Approximately, 23% (478/2,085) of COVID-19 vaccine recipient reported AEFI; most 94% were mild, 0.6% were moderate and 2 cases were severe. The commonest reason for missing COVID-19 vaccine was fear of the side effects. For most districts (5/6), sanitation (latrine/toilet) coverage were low at 7.4%-37.4%. CONCLUSION: There is high OCV coverage but low COVID-19 vaccine and sanitation coverage with high number of moderate cases of AEFI recorded due to COVID-19 vaccines. The low COVID-19 vaccine coverage could indicate vaccine hesitancy for COVID-19 vaccines. Furthermore, incorporation of WASH conditions assessment in the OCV coverage surveys is recommended for similar settings to generate data for better planning. However, more studies are required on COVID-19 vaccine hesitancy.

Development of a Scorecard to Monitor Progress toward National Cholera Elimination: Its Application in Uganda.

In 2017, the Global Task Force for Cholera Control (GTFCC) set a goal to eliminate cholera from ≥ 20 countries and to reduce cholera deaths by 90% by 2030. Many countries have included oral cholera vaccine (OCV) in their cholera control plans. We felt that a simple, user-friendly monitoring tool would be useful to guide national progress toward cholera elimination. We reviewed cholera surveillance data of Uganda from 2015 to 2021 by date and district. We defined a district as having eliminated cholera if cholera was not reported in that district for at least 4 years. We prepared maps to show districts with cholera, districts that had eliminated it, and districts that had eliminated it but then "relapsed." These maps were compared with districts where OCV was used and the hotspot map recommended by the GTFCC. Between 2018 and 2021, OCV was administered in 16 districts previously identified as hotspots. In 2018, cholera was reported during at least one of the four previous years from 36 of the 146 districts of Uganda. This number decreased to 18 districts by 2021. Cholera was deemed "eliminated" from four of these 18 districts but then "relapsed." The cholera elimination scorecard effectively demonstrated national progress toward cholera elimination and identified districts where additional resources are needed to achieve elimination by 2030. Identification of the districts that have eliminated cholera and those that have relapsed will assist the national programs to focus on addressing the factors that result in elimination or relapse of cholera.

The COVID-19 pandemic in the African continent.

In December 2019, a new coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and associated disease, coronavirus disease 2019 (COVID-19), was identified in China. This virus spread quickly and in March, 2020, it was declared a pandemic. Scientists predicted the worst scenario to occur in Africa since it was the least developed of the continents in terms of human development index, lagged behind others in achievement of the United Nations sustainable development goals (SDGs), has inadequate resources for provision of social services, and has many fragile states. In addition, there were relatively few research reporting findings on COVID-19 in Africa. On the contrary, the more developed countries reported higher disease incidences and mortality rates. However, for Africa, the earlier predictions and modelling into COVID-19 incidence and mortality did not fit into the reality. Therefore, the main objective of this forum is to bring together infectious diseases and public health experts to give an overview of COVID-19 in Africa and share their thoughts and opinions on why Africa behaved the way it did. Furthermore, the experts highlight what needs to be done to support Africa to consolidate the status quo and overcome the negative effects of COVID-19 so as to accelerate attainment of the SDGs.

Cholera epidemic amidst the COVID-19 pandemic in Moroto district, Uganda: Hurdles and opportunities for control.

INTRODUCTION: On 21st March 2020, the first COVID-19 case was detected in Uganda and a COVID-19 pandemic declared. On the same date, a nationwide lockdown was instituted in response to the pandemic. Subsequently, more cases were detected amongst the returning international travelers as the disease continued to spread across the country. On May 14th, 2020, a cholera epidemic was confirmed in Moroto district at a time when the district had registered several COVID-19 cases and was in lockdown. This study aimed to describe the cholera epidemic and response activities during the COVID-19 pandemic as well as the hurdles and opportunities for cholera control encountered during the response. MATERIALS AND METHODS: In a cross-sectional study design, we reviewed Moroto district's weekly epidemiological records on cholera and COVID-19 from April to July 2020. We obtained additional information through a review of the outbreak investigation and control reports. Data were analyzed and presented in frequencies, proportions, attack rates, case fatality rates, graphs, and maps. RESULTS: As of June 28th, 2020, 458 cases presenting with severe diarrhea and/or vomiting were line listed in Moroto district. The most affected age group was 15-30 years, 30.1% (138/458). The females, 59.0% [270/458], were the majority. The Case Fatality Rate (CFR) was 0.4% (2/458). Whereas home use of contaminated water following the vandalization of the only clean water source in Natapar Kocuc village, Moroto district, could have elicited the epidemic, implementing COVID-19 preventive and control measures presented some hurdles and opportunities for cholera control. The significant hurdles were observing the COVID-19 control measures such as social distancing, wearing of masks, and limited time in the community due to the need to observe curfew rules starting at 6.00 pm. The opportunities from COVID-19 measures complementary to cholera control measures included frequent hand washing, travel restrictions within the district & surrounding areas, and closure of markets. CONCLUSION: COVID-19 preventive and control measures such as social distancing, wearing of masks, and curfew rules may be a hurdle to cholera control whereas frequent hand washing, travel restrictions within the district & surrounding areas, and closure of markets may present opportunities for cholera control. Other settings experiencing concurrent cholera and COVID-19 outbreaks can borrow lessons from this study.

A framework to support the integration of priority setting in the preparedness, alert, control and evaluation stages of a disease pandemic.

The COVID-19 pandemic, where the need-resource gap has necessitated decision makers in some contexts to ration access to life-saving interventions, has demonstrated the critical need for systematic and fair priority setting and resource allocation mechanisms. Disease outbreaks are becoming increasingly common and priority setting lessons from previous disease outbreaks could be better harnessed to inform decision making and planning for future disease outbreaks. The purpose of this paper is to discuss how priority setting and resource allocation could, ideally, be integrated into the WHO pandemic planning and preparedness framework and used to inform the COVID-19 pandemic recovery plans and plans for future outbreaks. Priority setting and resource allocation during disease outbreaks tend to evoke a process similar to the 'rule of rescue'. This results in inefficient and unfair resource allocation, negative effects on health and non-health programs and increased health inequities. Integrating priority setting and resource allocation activities throughout the four phases of the WHO emergency preparedness framework could ensure that priority setting during health emergencies is systematic, evidence informed and fair.

Cholera risk in cities in Uganda: understanding cases and contacts centered strategy (3CS) for rapid cholera outbreak control.

INTRODUCTION: in the recent past, cities in sub-Saharan Africa have reported serious cholera outbreaks that last for several months. Uganda is one of the African countries where cities are prone to cholera outbreaks. Studies on cholera in Bangladesh show increased risk of cholera for the immediate household members (contacts) yet the control interventions mainly target cases with little or no focus on contacts. This study aimed to describe the rapid control of cholera outbreaks in Kampala and Mbale cities, Uganda, using, "Cases and Contacts Centered Strategy (3CS)" that consisted of identification and treatment of cases, promotion of safe water, sanitation, hygiene (WaSH) and selective chemoprophylaxis for the contacts. METHODS: a cross-sectional study was conducted in 2015-2016 in the Kampala and Mbale cities during cholera outbreaks. Cholera cases were treated and 816 contacts from 188 households were listed and given cholera preventive packages. Data were collected, cleaned, analysed and stored in spreadsheet. Comparison of categories was done using Chi-Square test. RESULTS: a total of 58 and 41 confirmed cholera cases out of 318 and 153 suspected cases were recorded in Kampala and Mbale cities respectively. The outbreaks lasted for 41 days in both cities. Case fatality rates were high; 12.1% (5/41) for Mbale city and 1.7% (1/58) for Kampala city. Fifty-five percent (210/379) of stool samples were tested by culture to confirm V. choleraeO1. No contacts listed and given cholera preventive package developed cholera. Both sexes and all age groups were affected. In Kampala city, the males were more affected than the females in the age groups less than 14 years, p-value of 0.0097. CONCLUSION: this study showed that by implementing 3CS, it was possible to rapidly control cholera outbreaks in Kampala and Mbale cities and no cholera cases were reported amongst the listed household contacts. The findings on 3CS and specifically, selective antibiotic chemoprophylaxis for cholera prevention, could be used in similar manner to oral cholera vaccines to complement the core cholera control interventions (disease surveillance, treatment of cases and WaSH). However, studies are needed to guide such rollout and to understand the age-sex differences in Kampala city.

Contrasting Epidemiology of Cholera in Bangladesh and Africa.

In Bangladesh and West Bengal cholera is seasonal, transmission occurs consistently annually. By contrast, in most African countries, cholera has inconsistent seasonal patterns and long periods without obvious transmission. Transmission patterns in Africa occur during intermittent outbreaks followed by elimination of that genetic lineage. Later another outbreak may occur because of reintroduction of new or evolved lineages from adjacent areas, often by human travelers. These then subsequently undergo subsequent elimination. The frequent elimination and reintroduction has several implications when planning for cholera's elimination including: a) reconsidering concepts of definition of elimination, b) stress on rapid detection and response to outbreaks, c) more effective use of oral cholera vaccine and WASH, d) need to readjust estimates of disease burden for Africa, e) re-examination of water as a reservoir for maintaining endemicity in Africa. This paper reviews major features of cholera's epidemiology in African countries which appear different from the Ganges Delta.

Refugee Settlements and Cholera Risks in Uganda, 2016-2019.

During 2016 to 2019, cholera outbreaks were reported commonly to the Ministry of Health from refugee settlements. To further understand the risks cholera posed to refugees, a review of surveillance data on cholera in Uganda for the period 2016-2019 was carried out. During this 4-year period, there were seven such outbreaks with 1,495 cases and 30 deaths in five refugee settlements and one refugee reception center. Most deaths occurred early in the outbreak, often in the settlements or before arrival at a treatment center rather than after arrival at a treatment center. During the different years, these outbreaks occurred during different times of the year but simultaneously in settlements that were geographically separated and affected all ages and genders. Some outbreaks spread to the local populations within Uganda. Cholera control prevention measures are currently being implemented; however, additional measures are needed to reduce the risk of cholera among refugees including oral cholera vaccination and a water, sanitation and hygiene package during the refugee registration process. A standardized protocol is needed to quickly conduct case-control studies to generate information to guide future cholera outbreak prevention in refugees and the host population.

Use of surveys to evaluate an integrated oral cholera vaccine campaign in response to a cholera outbreak in Hoima district, Uganda.

OBJECTIVES: To evaluate the quality and coverage of the campaign to distribute oral cholera vaccine (OCV) during a cholera outbreak in Hoima, Uganda to guide future campaigns of cholera vaccine. DESIGN: Survey of communities targeted for vaccination to determine vaccine coverage rates and perceptions of the vaccination campaign, and a separate survey of vaccine staff who carried out the campaign. SETTING: Hoima district, Uganda. PARTICIPANTS: Representative clusters of households residing in the communities targeted for vaccination and staff members who conducted the vaccine campaign. RESULTS: Among 209 households (1274 individuals) included in the coverage survey, 1193 (94%; 95% CI 92% to 95%) reported receiving at least one OCV dose and 998 (78%; 95% CI 76% to 81%) reported receiving two doses. Among vaccinated individuals, minor complaints were reported by 71 persons (5.6%). Individuals with 'some' education (primary school or above) were more knowledgeable regarding the required OCV doses compared with non-educated (p=0.03). Factors negatively associated with campaign implementation included community sensitisation time, staff payment and problems with field transport. Although the campaign was carried out quickly, the outbreak was over before the campaign started. Most staff involved in the campaign (93%) were knowledgeable about cholera control; however, 29% did not clearly understand how to detect and manage adverse events following immunisation. CONCLUSION: The campaign achieved high OCV coverage, but the surveys provided insights for improvement. To achieve high vaccine coverage, more effort is needed for community sensitisation, and additional resources for staff transportation and timely payment for campaign staff is required. Pretest and post-test assessment of staff training can identify and address knowledge and skill gaps.

A prolonged cholera outbreak caused by drinking contaminated stream water, Kyangwali refugee settlement, Hoima District, Western Uganda: 2018.

BACKGROUND: On 23 February 2018, the Uganda Ministry of Health (MOH) declared a cholera outbreak affecting more than 60 persons in Kyangwali Refugee Settlement, Hoima District, bordering the Democratic Republic of Congo (DRC). We investigated to determine the outbreak scope and risk factors for transmission, and recommend evidence-based control measures. METHODS: We defined a suspected case as sudden onset of watery diarrhoea in any person aged ≥ 2 years in Hoima District, 1 February-9 May 2018. A confirmed case was a suspected case with Vibrio cholerae cultured from a stool sample. We found cases by active community search and record reviews at Cholera Treatment Centres. We calculated case-fatality rates (CFR) and attack rates (AR) by sub-county and nationality. In a case-control study, we compared exposure factors among case- and control-households. We estimated the association between the exposures and outcome using Mantel-Haenszel method. We conducted an environmental assessment in the refugee settlement, including testing samples of stream water, tank water, and spring water for presence of fecal coliforms. We tested suspected cholera cases using cholera rapid diagnostic test (RDT) kits followed by culture for confirmation. RESULTS: We identified 2122 case-patients and 44 deaths (CFR = 2.1%). Case-patients originating from Demographic Republic of Congo were the most affected (AR = 15/1000). The overall attack rate in Hoima District was 3.2/1000, with Kyangwali sub-county being the most affected (AR = 13/1000). The outbreak lasted 4 months, which was a multiple point-source. Environmental assessment showed that a stream separating two villages in Kyangwali Refugee Settlement was a site of open defecation for refugees. Among three water sources tested, only stream water was feacally-contaminated, yielding > 100 CFU/100 ml. Of 130 stool samples tested, 124 (95%) yielded V. cholerae by culture. Stream water was most strongly associated with illness (odds ratio [OR] = 14.2, 95% CI: 1.5-133), although tank water also appeared to be independently associated with illness (OR = 11.6, 95% CI: 1.4-94). Persons who drank tank and stream water had a 17-fold higher odds of illness compared with persons who drank from other sources (OR = 17.3, 95% CI: 2.2-137). CONCLUSIONS: Our investigation demonstrated that this was a prolonged cholera outbreak that affected four sub-counties and two divisions in Hoima District, and was associated with drinking of contaminated stream water. In addition, tank water also appears to be unsafe. We recommended boiling drinking water, increasing latrine coverage, and provision of safe water by the District and entire High Commission for refugees.

The quality of drinking and domestic water from the surface water sources (lakes, rivers, irrigation canals and ponds) and springs in cholera prone communities of Uganda: an analysis of vital physicochemical parameters.

BACKGROUND: Water is the most abundant resource on earth, however water scarcity affects more than 40% of people worldwide. Access to safe drinking water is a basic human right and is a United Nations Sustainable Development Goal (SDG) 6. Globally, waterborne diseases such as cholera are responsible for over two million deaths annually. Cholera is a major cause of ill-health in Africa and Uganda. This study aimed to determine the physicochemical characteristics of the surface and spring water in cholera endemic communities of Uganda in order to promote access to safe drinking water. METHODS: A longitudinal study was carried out between February 2015 and January 2016 in cholera prone communities of Uganda. Surface and spring water used for domestic purposes including drinking from 27 sites (lakes, rivers, irrigation canal, springs and ponds) were tested monthly to determine the vital physicochemical parameters, namely pH, temperature, dissolved oxygen, conductivity and turbidity. RESULTS: Overall, 318 water samples were tested. Twenty-six percent (36/135) of the tested samples had mean test results that were outside the World Health Organization (WHO) recommended drinking water range. All sites (100%, 27/27) had mean water turbidity values greater than the WHO drinking water recommended standards and the temperature of above 17 °C. In addition, 27% (3/11) of the lake sites and 2/5 of the ponds had pH and dissolved oxygen respectively outside the WHO recommended range of 6.5-8.5 for pH and less than 5 mg/L for dissolved oxygen. These physicochemical conditions were ideal for survival of Vibrio. cholerae. CONCLUSIONS: This study showed that surface water and springs in the study area were unsafe for drinking and had favourable physicochemical parameters for propagation of waterborne diseases including cholera. Therefore, for Uganda to attain the SDG 6 targets and to eliminate cholera by 2030, more efforts are needed to promote access to safe drinking water. Also, since this study only established the vital water physicochemical parameters, further studies are recommended to determine the other water physicochemical parameters such as the nitrates and copper. Studies are also needed to establish the causal-effect relationship between V. cholerae and the physicochemical parameters.

Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application for Vibrio cholerae.

BACKGROUND: Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks for subtyping pathogens causing foodborne and water-borne disease outbreaks. However, Whole Genome Sequencing (WGS) has recently emerged as the new more powerful reference for pathogen subtyping, making a data conversion method necessary which enables the users to compare the MLVA identified by either method. The MLVAType shiny application was designed to extract MLVA profiles of Vibrio cholerae isolates from WGS data while ensuring backward compatibility with traditional MLVA typing methods. METHODS: To test and validate the MLVAType algorithm, WGS-derived MLVA profiles of nineteen Vibrio cholerae isolates from Democratic Republic of the Congo (n = 9) and Uganda (n = 10) were compared to MLVA profiles generated by an in silico PCR approach and Sanger sequencing, the latter being used as the reference method. RESULTS: Results obtained by Sanger sequencing and MLVAType were totally concordant. However, the latter were affected by censored estimations whose percentage was inversely proportional to the k-mer parameter used during genome assembly. With a k-mer of 127, less than 15% estimation of V. cholerae VNTR was censored. Preventing censored estimation was only achievable when using a longer k-mer size (i.e. 175), which is not proposed in the SPAdes v.3.13.0 software. CONCLUSION: As NGS read lengths and qualities tend to increase with time, one may expect the increase of k-mer size in a near future. Using MLVAType application with a longer k-mer size will then efficiently retrieve MLVA profiles from WGS data while avoiding censored estimation.

Environmental Surveillance of Vibrio cholerae O1/O139 in the Five African Great Lakes and Other Major Surface Water Sources in Uganda.

Cholera is a major public health problem in the African Great Lakes basin. Two hypotheses might explain this observation, namely the lakes are reservoirs of toxigenic Vibrio cholerae O1 and O139 bacteria, or cholera outbreaks are a result of repeated pathogen introduction from the neighboring communities/countries but the lakes facilitate the introductions. A prospective study was conducted in Uganda between February 2015 and January 2016 in which 28 selected surface water sources were tested for the presence of V. cholerae species using cholera rapid test and multiplex polymerase chain reaction. Of 322 water samples tested, 35 (10.8%) were positive for V. cholerae non O1/non O139 and two samples tested positive for non-toxigenic atypical V. cholerae O139. None of the samples tested had toxigenic V. cholerae O1 or O139 that are responsible for cholera epidemics. The Lake Albert region registered the highest number of positive tests for V. cholerae non O1/non O139 at 47% (9/19). The peak period for V. cholerae non O1/non O139 positive tests was in March-July 2015 which coincided with the first rainy season in Uganda. This study showed that the surface water sources, including the African Great Lakes in Uganda, are less likely to be reservoirs for the observed V. cholerae O1 or O139 epidemics, though they are natural habitats for V. cholerae non O1/non O139 and atypical non-toxigenic V. cholerae O139. Further studies by WGS tests of non-toxigenic atypical V. cholerae O139 and physicochemical tests of surface water sources that supports V. cholerae should be done to provide more information. Since V. cholerae non O1/non O139 may cause other human infections, their continued surveillance is needed to understand their potential pathogenicity.

Molecular characterization of Vibrio cholerae responsible for cholera epidemics in Uganda by PCR, MLVA and WGS.

BACKGROUND: For almost 50 years sub-Saharan Africa, including Uganda, has experienced several outbreaks due to Vibrio cholerae. Our aim was to determine the genetic relatedness and spread of strains responsible for cholera outbreaks in Uganda. METHODOLOGY/PRINCIPAL FINDINGS: Sixty-three V. cholerae isolates collected from outbreaks in Uganda between 2014 and 2016 were tested using multiplex polymerase chain reaction (PCR), multi-locus variable number of tandem repeat analysis (MLVA) and whole genome sequencing (WGS). Three closely related MLVA clonal complexes (CC) were identified: CC1, 32% (20/63); CC2, 40% (25/63) and CC3, 28% (18/63). Each CC contained isolates from a different WGS clade. These clades were contained in the third wave of the 7th cholera pandemic strain, two clades were contained in the transmission event (T)10 lineage and other in T13. Analysing the dates and genetic relatedness revealed that V. cholerae genetic lineages spread between districts within Uganda and across national borders. CONCLUSION: The V. cholerae strains showed local and regional transmission within Uganda and the East African region. To prevent, control and eliminate cholera, these countries should implement strong cross-border collaboration and regional coordination of preventive activities.