• Face to Face with Ebola - An Emergency Care Center in Sierra Leone.

      Wolz, Anja (Massachusetts Medical Society, 2014-08-27)
      At 6 a.m., our medical team arrives at the Ebola case-management center in the Kailahun district of Sierra Leone to take blood samples. At our 80-bed center here near the borders of Liberia and Guinea, 8 new patients were admitted yesterday, 9 need to have a repeat test 72 hours after their symptoms began, and some we hope to discharge today: at least 18 blood samples to obtain. The center currently houses 64 patients in all, 4 of them children less than 5 years of age. We have already seen 2 patients die today. I have been here for 7 . . .
    • The factors affecting household transmission dynamics and community compliance with Ebola control measures: a mixed-methods study in a rural village in Sierra Leone

      Caleo, G; Duncombe, J; Jephcott, F; Lokuge, K; Mills, C; Looijen, E; Theoharaki, F; Kremer, R; Kleijer, K; Squire, J; et al. (BioMed Central, 2018-02-13)
      Little is understood of Ebola virus disease (EVD) transmission dynamics and community compliance with control measures over time. Understanding these interactions is essential if interventions are to be effective in future outbreaks. We conducted a mixed-methods study to explore these factors in a rural village that experienced sustained EVD transmission in Kailahun District, Sierra Leone.
    • Factors Affecting Perceived Stigma in Leprosy Affected Persons in Western Nepal

      Adhikari, Bipin; Kaehler, Nils; Chapman, Robert S.; Raut, Shristi; Roche, Paul; Akogun, Oladele B. (Public Library of Science, 2014-06-05)
      Background There are various factors which construct the perception of stigma in both leprosy affected persons and unaffected persons. The main purpose of this study was to determine the level of perceived stigma and the risk factors contributing to it among leprosy affected person attending the Green Pastures Hospital, Pokhara municipality of western Nepal. Methods A cross-sectional study was conducted among 135 people affected by leprosy at Green Pastures Hospital and Rehabilitation Centre. Persons above the age of 18 were interviewed using a set of questionnaire form and Explanatory Model Interview Catalogue (EMIC). In addition, two sets of focused group discussions each containing 10 participants from the ward were conducted with the objectives of answering the frequently affected EMIC items. Results Among 135 leprosy affected persons, the median score of perceived stigma was 10 while it ranged from 0–34. Higher perceived stigma score was found in illiterate persons (p = 0.008), participants whose incomes were self-described as inadequate (p = 0.014) and who had changed their occupation due to leprosy (p = 0.018). Patients who lacked information on leprosy (p = 0.025), knowledge about the causes (p = 0.02) and transmission of leprosy (p = 0.046) and those who had perception that leprosy is a severe disease (p<0.001) and is difficult to treat (p<0.001) had higher perceived stigma score. Participants with disfigurement or deformities (p = 0.014), ulcers (p = 0.022) and odorous ulcers (p = 0.043) had higher perceived stigma score. Conclusion The factors associated with higher stigma were illiteracy, perceived economical inadequacy, change of occupation due to leprosy, lack of knowledge about leprosy, perception of leprosy as a severe disease and difficult to treat. Similarly, visible deformities and ulcers were associated with higher stigma. There is an urgent need of stigma reduction strategies focused on health education and health awareness programs in addition to the necessary rehabilitation support.
    • Factors Associated with Marburg Hemorrhagic Fever:

      Roddy, Paul; Sara L Thomas; Benjamin Jeffs; Pascoal Nascimento Folo; Pedro Pablo Palma; Bengi Moco Henrique; Luis Villa; Fernando Paixao Damiao Machado; Oscar Bernal; Steven M. Jones; et al. (Infectious Disease Society of America, 2010-06-15)
      Background. Reliable on-site polymerase chain reaction (PCR) testing for Marburg hemorrhagic fever (MHF) is not always available. Therefore, clinicians triage patients on the basis of presenting symptoms and contact history. Using patient data collected in Uige, Angola, in 2005, we assessed the sensitivity and specificity of these factors to evaluate the validity of World Health Organization (WHO)–recommended case definitions for MHF. Methods. Multivariable logistic regression was used to identify independent predictors of PCR confirmation of MHF. A data-derived algorithm was developed to obtain new MHF case definitions with improved sensitivity and specificity. Results. A MHF case definition comprising (1) an epidemiological link or (2) the combination of myalgia or arthralgia and any hemorrhage could potentially serve as an alternative to current case definitions. Our dataderived case definitions maintained the sensitivity and improved the specificity of current WHO-recommended case definitions. Conclusions. Continued efforts to improve clinical documentation during filovirus outbreaks would aid in the refinement of case definitions and facilitate outbreak control.
    • Favipiravir Pharmacokinetics in Ebola-Infected Patients of the JIKI Trial Reveals Concentrations Lower Than Targeted

      Nguyen, TH; Guedj, J; Anglaret, X; Laouénan, C; Madelain, V; Taburet, AM; Baize, S; Sissoko, D; Pastorino, B; Rodallec, A; et al. (PLoS, 2017-02-23)
      In 2014-2015, we assessed favipiravir tolerance and efficacy in patients with Ebola virus (EBOV) disease (EVD) in Guinea (JIKI trial). Because the drug had never been used before for this indication and that high concentrations of the drugs were needed to achieve antiviral efficacy against EBOV, a pharmacokinetic model had been used to propose relevant dosing regimen. Here we report the favipiravir plasma concentrations that were achieved in participants in the JIKI trial and put them in perspective with the model-based targeted concentrations.
    • Favipiravir--a prophylactic treatment for Ebola contacts?

      Van Herp, Michel; Declerck, Hilde; Decroo, Tom (Elsevier, 2015-06-13)
    • Feasibility of Xpert Ebola Assay in Médecins Sans Frontières Ebola Program, Guinea

      Van den Bergh, R; Chaillet, P; Sow, MS; Amand, M; van Vyve, C; Jonckheere, S; Crestani, R; Sprecher, A; Van Herp, M; Chua, A; et al. (Center for Disease Control and Prevention, 2016-02-01)
      Rapid diagnostic methods are essential in control of Ebola outbreaks and lead to timely isolation of cases and improved epidemiologic surveillance. Diagnosis during Ebola outbreaks in West Africa has relied on PCR performed in laboratories outside this region. Because time between sampling and PCR results can be considerable, we assessed the feasibility and added value of using the Xpert Ebola Assay in an Ebola control program in Guinea. A total of 218 samples were collected during diagnosis, treatment, and convalescence of patients. Median time for obtaining results was reduced from 334 min to 165 min. Twenty-six samples were positive for Ebola virus. Xpert cycle thresholds were consistently lower, and 8 (31%) samples were negative by routine PCR. Several logistic and safety issues were identified. We suggest that implementation of the Xpert Ebola Assay under programmatic conditions is feasible and represents a major advance in diagnosis of Ebola virus disease without apparent loss of assay sensitivity.
    • Field challenges to measles elimination in the Democratic Republic of the Congo

      Coulborn, RM; Nackers, F; Bachy, C; Porten, K; Vochten, H; Ndele, E; Van Herp, M; Bibala-Faray, E; Cohuet, S; Panunzi, I (Elsevier, 2020-02-25)
      BACKGROUND: During a measles epidemic, the Ministry of Public Health (MOH) of the Democratic Republic of the Congo conducted supplementary immunization activities (2016-SIA) from August 28-September 3, 2016 throughout Maniema Province. From October 29-November 4, 2016, Médecins Sans Frontières and the MOH conducted a reactive measles vaccination campaign (2016-RVC) targeting children six months to 14 years old in seven health areas with heavy ongoing transmission despite inclusion in the 2016-SIA, and a post-vaccination survey. We report the measles vaccine coverage (VC) and effectiveness (VE) of the 2016-SIA and VC of the 2016-RVC. METHODS: A cross-sectional VC cluster survey stratified by semi-urban/rural health area and age was conducted. A retrospective cohort analysis of measles reported by the parent/guardian allowed calculation of the cumulative measles incidence according to vaccination status after the 2016-SIA for an estimation of crude and adjusted VE. RESULTS: In November 2016, 1145 children (6-59 months old) in the semi-urban and 1158 in the rural areas were surveyed. Post-2016-SIA VC (documentation/declaration) was 81.6% (95%CI: 76.5-85.7) in the semi-urban and 91.0% (95%CI: 84.9-94.7) in the rural areas. The reported measles incidence in October among children less than 5 years old was 5.0% for 2016-SIA-vaccinated and 11.2% for 2016-SIA-non-vaccinated in the semi-urban area, and 0.7% for 2016-SIA-vaccinated and 4.0% for 2016-SIA-non-vaccinated in the rural area. Post-2016-SIA VE (adjusted for age, sex) was 53.9% (95%CI: 2.9-78.8) in the semi-urban and 78.7% (95%CI: 0-97.1) in the rural areas. Post 2016-RVC VC (documentation/declaration) was 99.1% (95%CI: 98.2-99.6) in the semi-urban and 98.8% (95%CI: 96.5-99.6) in the rural areas. CONCLUSIONS: Although our VE estimates could be underestimated due to misclassification of measles status, the VC and VE point estimates of the 2016-SIA in the semi-urban area appear suboptimal, and in combination, could not limit the epidemic. Further research is needed on vaccination strategies adapted to urban contexts.
    • Field evaluation of capillary blood samples as a collection specimen for the rapid diagnosis of Ebola virus infection during an outbreak emergency

      Strecker, Thomas; Palyi, Bernadett; Ellerbrok, Heinz; Jonckheere, Sylvie; de Clerck, Hilde; Bore, Joseph Akoi; Gabriel, Martin; Stoecker, Kilian; Eickmann, Markus; van Herp, Michel; et al. (Oxford University Press, 2015-05-19)
      Reliable reverse-transcriptase polymerase chain reaction (RT-PCR)-based diagnosis of Ebola virus infection currently requires a blood sample obtained by intravenous puncture. During the current Ebola outbreak in Guinea, we evaluated the usability of capillary blood samples collected from fingersticks of patients suspected of having Ebola virus disease (EVD) for field diagnostics during an outbreak emergency.
    • Field evaluation of GeneXpert® (Cepheid) HCV performance for RNA quantification in a genotype 1 and 6 predominant patient population in Cambodia.

      Iwamoto, M; Calzia, A; Dublineau, A; Rouet, F; Nouhin, J; Yann, S; Pin, S; Sun, C; Sann, K; Dimanche, C; et al. (Wiley-Blackwell, 2018-12-03)
      GeneXpert® (Cepheid) is the only WHO prequalified platform for hepatitis C virus (HCV) nucleic acid amplification testing that is suitable for point-of-care use in resource-limited contexts. However, its application is constrained by the lack of evidence on genotype 6 (GT6) HCV. We evaluated its field performance among a patient population in Cambodia predominantly infected with GT6. Between August and September 2017, we tested plasma samples obtained from consenting patients at Médecins Sans Frontières' HCV clinic at Preah Kossamak Hospital for HCV viral load (VL) using GeneXpert® and compared its results to those obtained using COBAS® AmpliPrep/Cobas® TaqMan® HCV Quantitative Test, v2.0 (Roche) at the Institut Pasteur du Cambodge. Among 769 patients, 77% of the seropositive patients (n = 454/590) had detectable and quantifiable VL using Roche and 43% (n = 195/454) were GT6. The sensitivity and specificity of GeneXpert® against Roche were 100% (95% CI 99.2, 100.0) and 98.5% (95% CI 94.8, 99.8). The mean VL difference was -0.01 (95% CI -0.05, 0.02) log10  IU/mL for 454 samples quantifiable on Roche and -0.07 (95% CI -0.12, -0.02) log10  IU/mL for GT6 (n = 195). The limit of agreement (LOA) was -0.76 to 0.73 log10  IU/mL for all GTs and -0.76 to 0.62 log10 IU/mL for GT6. Twenty-nine GeneXpert® results were outside the LOA. Frequency of error and the median turnaround time (TAT) for GeneXpert® were 1% and 0 days (4 days using Roche). We demonstrated that the GeneXpert® HCV assay has good sensitivity, specificity, quantitative agreement, and TAT in a real-world, resource-limited clinical setting among GT6 HCV patients.
    • Field evaluation of two rapid diagnostic tests for Neisseria meningitidis serogroup A during the 2006 outbreak in Niger.

      Rose, Angela M C; Gerstl, Sibylle; Mahamane, Ali E-H; Sidikou, Fati; Djibo, Saacou; Bonte, Laurence; Caugant, Dominique A; Guerin, Philippe J; Chanteau, Suzanne; Epicentre, Paris, France. angela.rose@cavehill.uwi.edu (2009-10)
      The Pastorex((R)) (BioRad) rapid agglutination test is one of the main rapid diagnostic tests (RDTs) for meningococcal disease currently in use in the "meningitis belt". Earlier evaluations, performed after heating and centrifugation of cerebrospinal fluid (CSF) samples, under good laboratory conditions, showed high sensitivity and specificity. However, during an epidemic, the test may be used without prior sample preparation. Recently a new, easy-to-use dipstick RDT for meningococcal disease detection on CSF was developed by the Centre de Recherche Médicale et Sanitaire in Niger and the Pasteur Institute in France. We estimate diagnostic accuracy in the field during the 2006 outbreak of Neisseria meningitidis serogroup A in Maradi, Niger, for the dipstick RDT and Pastorex((R)) on unprepared CSF, (a) by comparing each test's sensitivity and specificity with previously reported values; and (b) by comparing results for each test on paired samples, using McNemar's test. We also (c) estimate diagnostic accuracy of the dipstick RDT on diluted whole blood. We tested unprepared CSF and diluted whole blood from 126 patients with suspected meningococcal disease presenting at four health posts. (a) Pastorex((R)) sensitivity (69%; 95%CI 57-79) was significantly lower than found previously for prepared CSF samples [87% (81-91); or 88% (85-91)], as was specificity [81% (95%CI 68-91) vs 93% (90-95); or 93% (87-96)]. Sensitivity of the dipstick RDT [89% (95%CI 80-95)] was similar to previously reported values for ideal laboratory conditions [89% (84-93) and 94% (90-96)]. Specificity, at 62% (95%CI 48-75), was significantly lower than found previously [94% (92-96) and 97% (94-99)]. (b) McNemar's test for the dipstick RDT vs Pastorex((R)) was statistically significant (p<0.001). (c) The dipstick RDT did not perform satisfactorily on diluted whole blood (sensitivity 73%; specificity 57%).Sensitivity and specificity of Pastorex((R)) without prior CSF preparation were poorer than previously reported results from prepared samples; therefore we caution against using this test during an epidemic if sample preparation is not possible. For the dipstick RDT, sensitivity was similar to, while specificity was not as high as previously reported during a more stable context. Further studies are needed to evaluate its field performance, especially for different populations and other serogroups.
    • Field research in humanitarian medical programmes. Treatment of neuropathic pain in Sierra Leone.

      Lacoux, P A; Lassalle, X; McGoldrick, P M; Crombie, I K; Macrae, W A; Médecins Sans Frontières, Paris, France. phil@lacoux.u-net.com (Elsevier, 2008-01-31)
      A pilot study was carried out among 223 war wounded and amputees in Sierra Leone in 2001 to investigate whether an intervention using proven medication for clinically diagnosed neuropathic pain would work in a developing country with limited health services. Compliance with medication was assessed in 79 patients and their pain and mood scores were assessed by questionnaire before medication and 6-10 months later. The pain and mood scores of 33 patients who stopped taking medication were compared for the initial and follow-up assessments indicating that, although the scores showed an improvement at follow-up, there was no significant improvement. Compliance was reasonable in 46 patients who continued with their medication, with 86.5% of possible doses collected although many had difficulty understanding how to take the drugs properly. Their pain and mood scores showed significant improvement at reassessment indicating that pain will be reduced with a longer duration of treatment. This study showed that it is possible to run an effective intervention for neuropathic pain in Sierra Leone with intermittent expert involvement and MSF have been able to develop a protocol for the assessment and treatment of neuropathic pain that may be useful in other difficult settings in which they work.
    • Filovirus Hemorrhagic Fever Outbreak Case Management: A Review of Current and Future Treatment Options

      Roddy, P.; Colebunders, R.; Jeffs, B.; Palma, P. P.; Van Herp, M.; Borchert, M. (2011-10)
    • First external Quality Assurance Program for bloodstream Real-Time PCR monitoring of treatment response in clinical trials of Chagas disease

      Ramírez, JC; Parrado, R; Sulleiro, E; de la Barra, A; Rodríguez, M; Villarroel, S; Irazu, L; Alonso-Vega, C; Alves, F; Curto, MA; et al. (Public Library of Science, 2017-11-27)
      Real-Time PCR (qPCR) testing is recommended as both a diagnostic and outcome measurement of etiological treatment in clinical practice and clinical trials of Chagas disease (CD), but no external quality assurance (EQA) program provides performance assessment of the assays in use. We implemented an EQA system to evaluate the performance of molecular biology laboratories involved in qPCR based follow-up in clinical trials of CD. An EQA program was devised for three clinical trials of CD: the E1224 (NCT01489228), a pro-drug of ravuconazole; the Sampling Study (NCT01678599), that used benznidazole, both conducted in Bolivia; and the CHAGASAZOL (NCT01162967), that tested posaconazole, conducted in Spain. Four proficiency testing panels containing negative controls and seronegative blood samples spiked with 1, 10 and 100 parasite equivalents (par. eq.)/mL of four Trypanosoma cruzi stocks, were sent from the Core Lab in Argentina to the participating laboratories located in Bolivia and Spain. Panels were analyzed simultaneously, blinded to sample allocation, at 4-month intervals. In addition, 302 random blood samples from both trials carried out in Bolivia were sent to Core Lab for retesting analysis. The analysis of proficiency testing panels gave 100% of accordance (within laboratory agreement) and concordance (between laboratory agreement) for all T. cruzi stocks at 100 par. eq./mL; whereas their values ranged from 71 to 100% and from 62 to 100% at 1 and 10 par. eq./mL, respectively, depending on the T. cruzi stock. The results obtained after twelve months of preparation confirmed the stability of blood samples in guanidine-EDTA buffer. No significant differences were found between qPCR results from Bolivian laboratory and Core Lab for retested clinical samples. This EQA program for qPCR analysis of CD patient samples may significantly contribute to ensuring the quality of laboratory data generated in clinical trials and molecular diagnostics laboratories of CD.
    • Foci of Schistosomiasis mekongi, Northern Cambodia: II. Distribution of infection and morbidity.

      Stich, A H; Biays, S; Odermatt, P; Men, C; Saem, C; Sokha, K; Ly, C S; Legros, P; Philips, M; Lormand, J D; et al. (Wiley-Blackwell, 1999-10)
      In the province of Kracheh, in Northern Cambodia, a baseline epidemiological survey on Schistosoma mekongi was conducted along the Mekong River between December 1994 and April 1995. The results of household surveys of highly affected villages of the East and the West bank of the river and of school surveys in 20 primary schools are presented. In household surveys 1396 people were examined. An overall prevalence of infection of 49.3% was detected by a single stool examination with the Kato-Katz technique. The overall intensity of infection was 118.2 eggs per gram of stool (epg). There was no difference between the population of the east and west shore of the Mekong for prevalence (P = 0.3) or intensity (P = 0.9) of infection. Severe morbidity was very frequent. Hepatomegaly of the left lobe was detected in 48.7% of the population. Splenomegaly was seen in 26.8% of the study participants. Visible diverted circulation was found in 7.2% of the population, and ascites in 0.1%. Significantly more hepatomegaly (P = 0.001), splenomegaly (P = 0. 001) and patients with diverted circulation (P = 0.001) were present on the west bank of the Mekong. The age group of 10-14 years was most affected. The prevalence of infection in this group was 71.8% and 71.9% in the population of the West and East of the Mekong, respectively. The intensity of infection was 172.4 and 194.2 epg on the West and the East bank, respectively. In the peak age group hepatomegaly reached a prevalence of 88.1% on the west and 82.8% on the east bank. In the 20 schools 2391 children aged 6-16 years were examined. The overall prevalence of infection was 40.0%, ranging from 7.7% to 72.9% per school. The overalls mean intensity of infection was 110.1 epg (range by school: 26.7-187.5 epg). Both prevalence (P = 0.001) and intensity of infection (P = 0.001) were significantly higher in schools on the east side of the Mekong. Hepatomegaly (55.2%), splenomegaly (23.6%), diverted circulation (4. 1%), ascites (0.5%), reported blood (26.7%) and mucus (24.3%) were very frequent. Hepatomegaly (P = 0.001), splenomegaly (P = 0.001), diverted circulation (P = 0.001) and blood in stool (P = 0.001) were significantly more frequent in schools of the east side of the Mekong. Boys suffered more frequently from splenomegaly (P = 0.05), ascites (P = 0.05) and bloody stools (P = 0.004) than girls. No difference in sex was found for the prevalence and intensity of infection and prevalence of hepatomegaly. On the school level prevalence and intensity of infection were highly associated (r = 0. 93, P = 0.0001). The intensity of infection was significantly associated only with the prevalence of hepatomegaly (r = 0.44, P = 0. 05) and blood in stool (r = 0.40, P = 0.02). This comprehensive epidemiological study documents for the first time the public health importance of schistosomiasis mekongi in the Province of Kracheh, Northern Cambodia and points at key epidemiological features of this schistosome species, in particular the high level of morbidity associated with infection.
    • From Risk to Care: The Hepatitis C Screening and Diagnostic Cascade in a Primary Health Care Clinic in Karachi, Pakistan—a Cohort Study

      Khalid, GG; Kyaw, KWY; Bousquet, C; Auat, R; Donchuk, D; Trickey, A; Hamid, S; Qureshi, H; Mazzeo, V; Aslam, K; et al. (Oxford University Press, 2018-12-28)
      Background In the high-prevalence setting of Pakistan, screening, diagnosis and treatment services for chronic hepatitis C (CHC) patients are commonly offered in specialized facilities. We aimed to describe the cascade of care in a Médecins Sans Frontières primary health care clinic offering CHC care in an informal settlement in Karachi, Pakistan. Methods This was a retrospective cohort analysis using routinely collected data. Three different screening algorithms were assessed among patients with one or more CHC risk factors. Results Among the 87 348 patients attending the outpatient clinic, 5003 (6%) presented with one or more risk factors. Rapid diagnostic test (RDT) positivity was 38% overall. Approximately 60% of the CHC patients across all risk categories were in the early stage of the disease, with an aspartate aminotransferase:platelet ratio index score <1. The sequential delays in the cascade differed between the three groups, with the interval between screening and treatment initiation being the shortest in the cohort tested with GeneXpert onsite. Conclusions Delays between screening and treatment can be reduced by putting in place more patient-centric testing algorithms. New strategies, to better identify and treat the hidden at-risk populations, should be developed and implemented.
    • Genetic heterogeneity of hepatitis E virus in Darfur, Sudan, and neighboring Chad.

      Nicand, E; Armstrong, G L; Enouf, V; Guthmann, J P; Guerin, J P; Caron, M; Nizou, J Y; Andraghetti, R; National Reference Centre for Hepatitis E, Teaching Military Hospital Val de Grâce, Paris, France. en.biol-vdg@filnet.fr (2005-12)
      The within-outbreak diversity of hepatitis E virus (HEV) was studied during the outbreak of hepatitis E that occurred in Sudan in 2004. Specimens were collected from internally displaced persons living in a Sudanese refugee camp and two camps implanted in Chad. A comparison of the sequences in the ORF2 region of 23 Sudanese isolates and five HEV samples from the two Chadian camps displayed a high similarity (>99.7%) to strains belonging to Genotype 1. But four isolates collected in one of the Chadian camps were close to Genotype 2. Circulation of divergent strains argues for possible multiple sources of infection.
    • Genomic History of the seventh Pandemic of Cholera in Africa

      Weill, FX; Domman, D; Njamkepo, E; Tarr, C; Rauzier, J; Fawal, N; Keddy, KH; Salje, H; Moore, S; Mukhopadhyay, AK; et al. (American Association for the Advancement of Science, 2017-11-10)
      The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa.
    • Genomic Insights into the 2016-2017 Cholera Epidemic in Yemen

      Weill, FX; Domman, D; Njamkepo, E; Almesbahi, AA; Naji, M; Nasher, SS; Rakesh, A; Assiri, AM; Sharma, NC; Kariuki, S; et al. (Nature Publishing Group, 2019-01-02)
      Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.
    • Geographic Distribution and Mortality Risk Factors during the Cholera Outbreak in a Rural Region of Haiti, 2010-2011

      Page, Anne-Laure; Ciglenecki, Iza; Jasmin, Ernest Robert; Desvignes, Laurence; Grandesso, Francesco; Polonsky, Jonathan; Nicholas, Sarala; Alberti, Kathryn P; Porten, Klaudia; Luquero, Francisco J (Public Library of Science, 2015-03-26)
      In 2010 and 2011, Haiti was heavily affected by a large cholera outbreak that spread throughout the country. Although national health structure-based cholera surveillance was rapidly initiated, a substantial number of community cases might have been missed, particularly in remote areas. We conducted a community-based survey in a large rural, mountainous area across four districts of the Nord department including areas with good versus poor accessibility by road, and rapid versus delayed response to the outbreak to document the true cholera burden and assess geographic distribution and risk factors for cholera mortality.