Use of Vibrio cholerae vaccine in an outbreak in Guinea.

BACKGROUND: The use of vaccines to prevent and control cholera is currently under debate. Shanchol is one of the two oral cholera vaccines prequalified by the World Health Organization; however, its effectiveness under field conditions and the protection it confers in the first months after administration remain unknown. The main objective of this study was to estimate the short-term effectiveness of two doses of Shanchol used as a part of the integrated response to a cholera outbreak in Africa. METHODS: We conducted a matched case-control study in Guinea between May 20 and October 19, 2012. Suspected cholera cases were confirmed by means of a rapid test, and controls were selected among neighbors of the same age and sex as the case patients. The odds of vaccination were compared between case patients and controls in bivariate and adjusted conditional logistic-regression models. Vaccine effectiveness was calculated as (1-odds ratio)×100. RESULTS: Between June 8 and October 19, 2012, we enrolled 40 case patients and 160 controls in the study for the primary analysis. After adjustment for potentially confounding variables, vaccination with two complete doses was associated with significant protection against cholera (effectiveness, 86.6%; 95% confidence interval, 56.7 to 95.8; P=0.001). CONCLUSIONS: In this study, Shanchol was effective when used in response to a cholera outbreak in Guinea. This study provides evidence supporting the addition of vaccination as part of the response to an outbreak. It also supports the ongoing efforts to establish a cholera vaccine stockpile for emergency use, which would enhance outbreak prevention and control strategies. (Funded by Médecins sans Frontières.).

Use of Viremia to Evaluate the Baseline Case Fatality Ratio of Ebola Virus Disease and Inform Treatment Studies: A Retrospective Cohort Study.

BACKGROUND: The case fatality ratio (CFR) of Ebola virus disease (EVD) can vary over time and space for reasons that are not fully understood. This makes it difficult to define the baseline CFRs needed to evaluate treatments in the absence of randomized controls. Here, we investigate whether viremia in EVD patients may be used to evaluate baseline EVD CFRs. METHODS AND FINDINGS: We analyzed the laboratory and epidemiological records of patients with EVD confirmed by reverse transcription PCR hospitalized in the Conakry area, Guinea, between 1 March 2014 and 28 February 2015. We used viremia and other variables to model the CFR. Data for 699 EVD patients were analyzed. In the week following symptom onset, mean viremia remained stable, and the CFR increased with viremia, V, from 21% (95% CI 16%-27%) for low viremia (V < 104.4 copies/ml) to 53% (95% CI 44%-61%) for intermediate viremia (104.4 ≤ V < 105.2 copies/ml) and 81% (95% CI 75%-87%) for high viremia (V ≥ 105.2 copies/ml). Compared to adults (15-44 y old [y.o.]), the CFR was larger in young children (0-4 y.o.) (odds ratio [OR]: 2.44; 95% CI 1.02-5.86) and older adults (≥ 45 y.o.) (OR: 2.84; 95% CI 1.81-4.46) but lower in children (5-14 y.o.) (OR: 0.46; 95% CI 0.24-0.86). An order of magnitude increase in mean viremia in cases after July 2014 compared to those before coincided with a 14% increase in the CFR. Our findings come from a large hospital-based study in Conakry and may not be generalizable to settings with different case profiles, such as with individuals who never sought care. CONCLUSIONS: Viremia in EVD patients was a strong predictor of death that partly explained variations in CFR in the study population. This study provides baseline CFRs by viremia group, which allow appropriate adjustment when estimating efficacy in treatment studies. In randomized controlled trials, stratifying analysis on viremia groups could reduce sample size requirements by 25%. We hypothesize that monitoring the viremia of hospitalized patients may inform the ability of surveillance systems to detect EVD patients from the different severity strata.

Development and deployment of a rapid recombinase polymerase amplification Ebola virus detection assay in Guinea in 2015.

In the absence of a vaccine or specific treatments for Ebola virus disease (EVD), early identification of cases is crucial for the control of EVD epidemics. We evaluated a new extraction kit (SpeedXtract (SE), Qiagen) on sera and swabs in combination with an improved diagnostic reverse transcription recombinase polymerase amplification assay for the detection of Ebola virus (EBOV-RT-RPA). The performance of combined extraction and detection was best for swabs. Sensitivity and specificity of the combined SE and EBOV-RT-RPA were tested in a mobile laboratory consisting of a mobile glovebox and a Diagnostics-in-a-Suitcase powered by a battery and solar panel, deployed to Matoto Conakry, Guinea as part of the reinforced surveillance strategy in April 2015 to reach the goal of zero cases. The EBOV-RT-RPA was evaluated in comparison to two real-time PCR assays. Of 928 post-mortem swabs, 120 tested positive, and the combined SE and EBOV-RT-RPA yielded a sensitivity and specificity of 100% in reference to one real-time RT-PCR assay. Another widely used real-time RT-PCR was much less sensitive than expected. Results were provided very fast within 30 to 60 min, and the field deployment of the mobile laboratory helped improve burial management and community engagement.

A novel MLSA allelic profile 'A15' of Mycoplasma mycoides subsp mycoides in Niger.

Mycoplasma mycoides subsp. mycoides (Mmm) is the aetiological agent of contagious bovine pleuropneumonia (CBPP). The aim of the present study was to identify the profiles of the Mmm strains isolated in Niger using the 'Multilocus Sequence Analysis' (MLSA) typing technique based on polymorphism analysis of housekeeping and non-coding genes. The investigation was conducted on samples (n=22) comprising of lung tissues, lymph node and pleural fluids. Following classical PCR, Mmm positive amplicons (n=6) were identified. These positive amplicons were then amplified using eight loci of the PG1 reference strain (LocPG1-0001, Loc-PG1-0103, Loc-PG1-0287, Loc-PG1-0431, Loc-PG1-0489, Loc-PG1-0523, Loc-PG1-0710 and Loc-PG1-0827). Sequencing followed by the determination of the profile of each strain by the combination of the allele numbers revealed three different MLSA profiles namely; A11, E01 and A15. The profiles A11 and E01 were previously identified. The novel profile identified in this study was named profile A15. The difference was detected while comparing sequences of non-coding loci. This novel profile was named 'A15' according to the similarities with African reference strain profile 'A00' at the seven loci level (loc-0103, loc-0287, loc-0431, loc-0489, loc-0523, loc-0710 and loc-0827). For CBPP control measures, identification and molecular characterization of Mmm strains is very important. Thus, the use of MLSA technique is relevant to identify profiles of Mmm circulating in Niger. Other countries where CBPP is still endemic are encouraged to use a MLSA scheme to address this issue and, most importantly, to rapidly trace back the origin of outbreaks, which will help reduce the transmission and spread of the disease. In addition, mapping the profiles of strains circulating in each of the countries of the sub-region is necessary for effective control of CBPP.

Transboundary spread of equine influenza viruses (H3N8) in West and Central Africa: Molecular characterization of identified viruses during outbreaks in Niger and Senegal, in 2019.

Since November 2018, several countries in West and Central Africa have reported mortalities in donkeys and horses. Specifically, more than 66,000 horses and donkeys have succumbed to disease in Burkina Faso, Chad, Cameroon, The Gambia, Ghana, Mali, Niger, Nigeria, and Senegal. Strangles caused by Streptococcus equi subsp equi, African Horse Sickness (AHS) virus, and Equine influenza virus (EIV) were all suspected as potential causative agents. This study reports the identification of EIV in field samples collected in Niger and Senegal. Phylogenetic analysis of the hemagglutinin and neuraminidase genes revealed that the identified viruses belonged to clade 1 of the Florida sublineage and were very similar to viruses identified in Nigeria in 2019. Interestingly, they were also more similar to EIVs from recent outbreaks in South America than to those in Europe and the USA. This is one of the first reports providing detailed description and characterization of EIVs in West and Central Africa region.

Serological Prevalence of Contagious Bovine Pleuropneumonia in Niger in 2017.

Contagious bovine pleuropneumonia (CBPP) is a highly contagious disease of cattle caused by Mycoplasma mycoides subsp. mycoides Biotype Small Colony (MmmSC). The disease currently occurs in most of sub-Saharan Africa and where it is endemic and a major constraint for improving pastoral productivity. Following the persistence of this scourge, and in order to control this disease, a serological survey was conducted to determine the prevalence of CBPP in Niger. In fact, 1,590 sera were collected following a stratified sampling plan based on the risk factor of dissemination of CBPP. The analysis were performed at the Central Livestock Laboratory using the c-Elisa test. The results obtained show a wide distribution of the disease with an overall prevalence of 4.15% at individual level. The highest prevalences were recorded in the South-East regions [Zinder (7.5%), Diffa (7.5%)] and the West part [Tahoua (6.9%)]. The prevalence at the commune level was about 36.55%, which was relatively high. The prevalence at strata level was 36.55% (95% PI 0.2428-0.4882). The expected prevalences did not match those found. The results of this serological survey are considered the reference situation (T0) of CBPP in Niger with the PRAPS project, and allowed to the country to redefine control policies for better control of the disease at national and sub-regional level.

Mixing of Shiga toxin-producing and enteropathogenic Escherichia coli in a wastewater treatment plant receiving city and slaughterhouse wastewater.

Wastewater of human and animal may contain Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli. We evaluated the prevalence of such strains in a wastewater treatment plant (WWTP) receiving both city and slaughterhouse wastewater. PCR screenings were performed on 12,248 E. coli isolates. The prevalence of STEC in city wastewater, slaughterhouse wastewater and treated effluent was 0.22%, 0.07% and 0.22%, respectively. The prevalence of EPEC at the same sampling sites was 0.63%, 0.90% and 0.55%. No significant difference was observed between the sampling points. Treatment had no impact on these prevalences. Enterohemorrhagic E. coli (EHEC) O157:H7 and O111:H8 were isolated from the treated effluent rejected into the river. The characteristics of STEC and EPEC differed according to their origin. City wastewater contained STEC with various stx subtypes associated with serious human disease, whereas slaughterhouse wastewater contained exclusively STEC with stx2e subtype. All the EPEC strains were classified as atypical and were screened for the ε, γ1 and ß1 subtypes, known to be associated with the EHEC mainly involved in human infections in France. In city wastewater, eae subtypes remained largely unidentified; whereas eae-ß1 was the most frequent subtype in slaughterhouse wastewater. Moreover, the EPEC isolated from slaughterhouse wastewater were positive for other EHEC-associated virulence markers, including top five serotypes, the ehxA gene, putative adherence genes and OI-122 associated genes. The possibility that city wastewater could contain a pool of stx genes associated with human disease and that slaughterhouse wastewater could contain a pool of EPEC sharing similar virulence genes with EHEC, was highlighted. Mixing of such strains in WWTP could lead to the emergence of EHEC by horizontal gene transfer.

Pregnancy Outcomes after a Mass Vaccination Campaign with an Oral Cholera Vaccine in Guinea: A Retrospective Cohort Study.

INTRODUCTION: Since 2010, WHO has recommended oral cholera vaccines as an additional strategy for cholera control. During a cholera episode, pregnant women are at high risk of complications, and the risk of fetal death has been reported to be 2-36%. Due to a lack of safety data, pregnant women have been excluded from most cholera vaccination campaigns. In 2012, reactive campaigns using the bivalent killed whole-cell oral cholera vaccine (BivWC), included all people living in the targeted areas aged ≥ 1 year regardless of pregnancy status, were implemented in Guinea. We aimed to determine whether there was a difference in pregnancy outcomes between vaccinated and non-vaccinated pregnant women. METHODS AND FINDINGS: From 11 November to 4 December 2013, we conducted a retrospective cohort study in Boffa prefecture among women who were pregnant in 2012 during or after the vaccination campaign. The primary outcome was pregnancy loss, as reported by the mother, and fetal malformations, after clinical examination. Primary exposure was the intake of the BivWC vaccine (Shanchol) during pregnancy, as determined by a vaccination card or oral history. We compared the risk of pregnancy loss between vaccinated and non-vaccinated women through binomial regression analysis. A total of 2,494 pregnancies were included in the analysis. The crude incidence of pregnancy loss was 3.7% (95%CI 2.7-4.8) for fetuses exposed to BivWC vaccine and 2.6% (0.7-4.5) for non-exposed fetuses. The incidence of malformation was 0.6% (0.1-1.0) and 1.2% (0.0-2.5) in BivWC-exposed and non-exposed fetuses, respectively. In both crude and adjusted analyses, fetal exposure to BivWC was not significantly associated with pregnancy loss (adjusted risk ratio (aRR = 1.09 [95%CI: 0.5-2.25], p = 0.818) or malformations (aRR = 0.50 [95%CI: 0.13-1.91], p = 0.314). CONCLUSIONS: In this large retrospective cohort study, we found no association between fetal exposure to BivWC and risk of pregnancy loss or malformation. Despite the weaknesses of a retrospective design, we can conclude that if a risk exists, it is very low. Additional prospective studies are warranted to add to the evidence base on OCV use during pregnancy. Pregnant women are particularly vulnerable during cholera episodes and should be included in vaccination campaigns when the risk of cholera is high, such as during outbreaks.

Persistence and prevalence of pathogenic and extended-spectrum beta-lactamase-producing Escherichia coli in municipal wastewater treatment plant receiving slaughterhouse wastewater.

We compared the prevalence of pathogenic and extended-spectrum beta-lactamase (ESBL) - producing Escherichia coli in effluents of a municipal wastewater treatment plant (WWTP) receiving wastewater from a slaughterhouse. A total of 1248 isolates were screened for the presence of virulence genes associated with enterohemorrhagic E. coli (EHEC) (stx1, stx2, and eae) and extraintestinal pathogenic E. coli (ExPEC) (sfa/focDE, kpsMT K1, hlyA, papEF, afa/draBC, clbN, f17A and cnf). The prevalence of atypical enteropathogenic E. coli (EPEC) was 0.7%, 0.2% and 0.5% in city wastewater, slaughterhouse wastewater and in the treated effluent, respectively. One stx1a and stx2b-positive E. coli isolate was detected in city wastewater. The prevalence of ExPEC was significantly higher in city wastewater (8.4%), compared to slaughterhouse wastewater (1.2%). Treatment in the WWTP did not significantly impact the prevalence of ExPEC in the outlet effluent (5.0%) compared to city wastewater. Moreover, the most potentially pathogenic ExPEC were isolated from city wastewater and from the treated effluent. ESBL-producing E. coli was also mainly detected in city wastewater (1.7%), compared to slaughterhouse wastewater (0.2%), and treated effluent (0.2%). One ESBL-producing E. coli, isolated from city wastewater, was eae-ß1 positive. These results showed that pathogenic and/or ESBL-producing E. coli were mainly detected in human wastewater, and at a lesser extend in animal wastewater. Treatment failed to eliminate these strains which were discharged into the river, and then these strains could be transmitted to animals and humans via the environment.