High genetic diversity among Mycobacterium tuberculosis complex strains from Sierra Leone

<p>Abstract</p> <p>Background</p> <p>Among tuberculosis (TB) high incidence regions, Sub-Saharan Africa is particularly affected with approx. 1.6 million new cases every year. Besides this dramatic situation, data on the diversity of <it>Mycobacterium tuberculosis </it>complex (MTBC) strains causing this epidemic in this area are only sparsely available. Here we analyzed the population structure of strains from Sierra Leone with a special focus on the prevalence of <it>M. africanum</it>.</p> <p>Results</p> <p>A total of 97 strains isolated from smear positive cases registered for re-treatment in the Western Area and Kenema districts in years 2003/2004 were investigated by susceptibility testing (first line drugs) and molecular typing (IS<it>6110 </it>fingerprinting, spoligotyping, and MIRU-VNTR typing).</p> <p>Among the strains analyzed, 32 were resistant to isoniazid, and 11 were multidrug resistant (at least resistant to isoniazid and rifampin). The population diversity was high with two previously described <it>M. africanum </it>lineages (West African-1, n = 6; West African-2, n = 17) and seven <it>M. tuberculosis </it>lineages (Haarlem, n = 14; LAM, n = 15; EAI, n = 4; Beijing, n = 4; S-type, n = 4, X-type, n = 1; Cameroon, n = 4). Furthermore, two new <it>M. tuberculosis </it>genotypes Sierra Leone-1 (n = 7) and -2 (n = 10) were found. Strain classification according to a 7 bp deletion in pks1/15 revealed that the majority of <it>M. tuberculosis </it>strains belonged to the Euro American lineage (66 out of 74).</p> <p>Conclusion</p> <p>Resistance rates in Sierra Leone have reached an alarming level. The population structure of MTBC strains shows an intriguing diversity raising the question of possible consequences for TB epidemic and for the introduction of new diagnostic tests or treatment strategies in West Africa.</p

Exposure Patterns Driving Ebola Transmission in West Africa:A Retrospective Observational Study

BackgroundThe ongoing West African Ebola epidemic began in December 2013 in Guinea, probably from a single zoonotic introduction. As a result of ineffective initial control efforts, an Ebola outbreak of unprecedented scale emerged. As of 4 May 2015, it had resulted in more than 19,000 probable and confirmed Ebola cases, mainly in Guinea (3,529), Liberia (5,343), and Sierra Leone (10,746). Here, we present analyses of data collected during the outbreak identifying drivers of transmission and highlighting areas where control could be improved.Methods and findingsOver 19,000 confirmed and probable Ebola cases were reported in West Africa by 4 May 2015. Individuals with confirmed or probable Ebola ("cases") were asked if they had exposure to other potential Ebola cases ("potential source contacts") in a funeral or non-funeral context prior to becoming ill. We performed retrospective analyses of a case line-list, collated from national databases of case investigation forms that have been reported to WHO. These analyses were initially performed to assist WHO's response during the epidemic, and have been updated for publication. We analysed data from 3,529 cases in Guinea, 5,343 in Liberia, and 10,746 in Sierra Leone; exposures were reported by 33% of cases. The proportion of cases reporting a funeral exposure decreased over time. We found a positive correlation (r = 0.35, p ConclusionsAchieving elimination of Ebola is challenging, partly because of super-spreading. Safe funeral practices and fast hospitalisation contributed to the containment of this Ebola epidemic. Continued real-time data capture, reporting, and analysis are vital to track transmission patterns, inform resource deployment, and thus hasten and maintain elimination of the virus from the human population

Ebola Virus Outbreak Investigation, Sierra Leone, September 28–November 11, 2014

During 2014–2015, an outbreak of Ebola virus disease (EVD) swept across parts of West Africa. The China Mobile Laboratory Testing Team was dispatched to support response efforts; during September 28–November 11, 2014, they conducted PCR testing on samples from 1,635 suspected EVD patients. Of those patients, 50.4% were positive, of whom 84.6% lived within a 3-km zone along main roads connecting rural towns and densely populated cities. The median time from symptom onset to testing was 5 days. At testing, 75.7% of the confirmed patients had fever, and 94.1% reported at least 1 gastrointestinal symptom; all symptoms, except rash and hemorrhage, were more frequent in confirmed than nonconfirmed patients. Virus loads were significantly higher in EVD patients with fever, diarrhea, fatigue, or headache. The case-fatality rate was lower among patients 15–44 years of age and with virus loads of <100,000 RNA copies/mL. These findings are key for optimizing EVD control and treatment measures

All SPSS Tables and Outputs from Assessments of Ebola knowledge, attitudes and practices in Forécariah, Guinea and Kambia, Sierra Leone, July–August 2015

The border region of Forécariah (Guinea) and Kambia (Sierra Leone) was of immense interest to the West Africa Ebola response. Cross-sectional household surveys with multi-stage cluster sampling procedure were used to collect random samples from Kambia (<i>n</i> = 635) in July 2015 and Forécariah (<i>n</i> = 502) in August 2015 to assess public knowledge, attitudes and practices related to Ebola. Knowledge of the disease was high in both places, and handwashing with soap and water was the most widespread prevention practice. Acceptance of safe alternatives to traditional burials was significantly lower in Forécariah compared with Kambia. In both locations, there was a minority who held discriminatory attitudes towards survivors. Radio was the predominant source of information in both locations, but those from Kambia were more likely to have received Ebola information from community sources (mosques/churches, community meetings or health workers) compared with those in Forécariah. These findings contextualize the utility of Ebola health messaging during the epidemic and suggest the importance of continued partnership with community leaders, including religious leaders, as a prominent part of future public health protection.This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’

Rapid deployment of a mobile biosafety level-3 laboratory in Sierra Leone during the 2014 Ebola virus epidemic

<div><p>Background</p><p>Ebola virus emerged in West Africa in December 2013. The high population mobility and poor public health infrastructure in this region led to the development of the largest Ebola virus disease (EVD) outbreak to date.</p><p>Methodology/Principal findings</p><p>On September 26, 2014, China dispatched a Mobile Biosafety Level-3 Laboratory (MBSL-3 Lab) and a well-trained diagnostic team to Sierra Leone to assist in EVD diagnosis using quantitative real-time PCR, which allowed the diagnosis of suspected EVD cases in less than 4 hours from the time of sample receiving. This laboratory was composed of three container vehicles equipped with advanced ventilation system, communication system, electricity and gas supply system. We strictly applied multiple safety precautions to reduce exposure risks. Personnel, materials, water and air flow management were the key elements of the biosafety measures in the MBSL-3 Lab. Air samples were regularly collected from the MBSL-3 Lab, but no evidence of Ebola virus infectious aerosols was detected. Potentially contaminated objects were also tested by collecting swabs. On one occasion, a pipette tested positive for EVD. A total of 1,635 suspected EVD cases (824 positive [50.4%]) were tested from September 28 to November 11, 2014, and no member of the diagnostic team was infected with Ebola virus or other pathogens, including Lassa fever. The specimens tested included blood (69.2%) and oral swabs (30.8%) with positivity rates of 54.2% and 41.9%, respectively. The China mobile laboratory was thus instrumental in the EVD outbreak response by providing timely and reliable diagnostics.</p><p>Conclusions/Significance</p><p>The MBSL-3 Lab significantly contributed to establishing a suitable laboratory response capacity during the emergence of EVD in Sierra Leone.</p></div

Layout of the mobile biosafety level-3 laboratory.

<p>The main and auxiliary containers were connected by an airtight soft connection and together formed a complete biosafety level-3 (BSL-3) lab. The instruments represented by letters were listed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005622#pntd.0005622.s003" target="_blank">S1 Table</a>.</p