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Objectives Lassa fever (LF), a priority emerging pathogen likely to cause major epidemics, is endemic in much of West Africa and is difficult to distinguish from other viral hemorrhagic fevers, including Ebola virus disease (EVD). Definitive diagnosis requires laboratory confirmation, which is not widely available in affected settings. The public health action to contain a LF outbreak and the challenges encountered in an EVD-affected setting are reported herein. Methods In February 2016, a rapid response team was deployed in Liberia in response to a cluster of LF cases. Active case finding, case investigation, contact tracing, laboratory testing, environmental investigation, risk communication, and community awareness raising were undertaken. Results From January to June 2016, 53 suspected LF cases were reported through the Integrated Disease Surveillance and Response system (IDSR). Fourteen cases (26%) were confirmed for LF, 14 (26%) did not have a sample tested, and 25 (47%) were classified as not a case following laboratory analysis. The case fatality rate in the confirmed cases was 29%. One case of international exportation was reported from Sweden. Difficulties were identified in timely specimen collection, packaging, and transportation (in confirmed cases, the time from sample collection to sample result ranged from 2 to 64 days) and a lack of response interventions for early cases. Conclusions The delay in response to this outbreak could have been related to a number of challenges in this EVD-affected setting: a need to strengthen the IDSR system, develop preparedness plans, train rapid response teams, and build laboratory capacity. Prioritizing these actions will aid in the timely response to future outbreaks.

On April 25, 2017, the Sinoe County Health Team (CHT) notified the Liberia Ministry of Health (MoH) and the National Public Health Institute of Liberia of an unknown illness among 14 persons that resulted in eight deaths in Sinoe County. On April 26, the National Rapid Response Team and epidemiologists from CDC, the World Health Organization (WHO) and the African Field Epidemiology Network (AFENET) in Liberia were deployed to support the county-led response. Measures were immediately implemented to identify all cases, ascertain the cause of illness, and control the outbreak. Illness was associated with attendance at a funeral event, and laboratory testing confirmed Neisseria meningitidis in biologic specimens from cases. The 2014-2015 Ebola virus disease (Ebola) outbreak in West Africa devastated Liberia's already fragile health system, and it took many months for the country to mount an effective response to control the outbreak. Substantial efforts have been made to strengthen Liberia's health system to prevent, detect, and respond to health threats. The rapid and efficient field response to this outbreak of N. meningitidis resulted in implementation of appropriate steps to prevent a widespread outbreak and reflects improved public health and outbreak response capacity in Liberia.

Introduction Early detection of disease outbreaks is paramount to averting associated morbidity and mortality. In January 2018, nine cases including four deaths associated with meningococcal disease were reported in three communities of Foya district, Lofa County, Liberia. Due to the porous borders between Lofa County and communities in neighboring Sierra Leone and Guinea, the possibility of epidemic spread of meningococcal disease could not be underestimated. Methods The county incidence management system (IMS) was activated that coordinated the response activities. Daily meetings were conducted to review response activities progress and challenges. The district rapid response team (DRRT) was the frontline responders. The case based investigation form; case line list and contacts list were used for data collection. A data base was established and analysed daily for action. Tablets Ciprofloxacin were given for chemoprophylaxis. Results Sixty-seven percent (67%) of the cases were males and also 67% of the affected age range was 3 to 14 years and attending primary school. The attack rate was 7/1,000 population and case fatality rate was 44.4 % with majority of the deaths occurring within 24-48 hours of symptoms onset. Three of the cases tested positive for Neisseria Meningitidis sero-type W while six cases were Epi-linked. None of the cases had recent meningococcal vaccination and no health-worker infections were registered. Conclusion This cluster of cases of meningococcal disease during the meningitis season in a country that is not traditionally part of the meningitis belt emphasized the need for strengthening surveillance, preparedness and response capacity to meningitis.

Summary Background On April 25, 2017, a cluster of unexplained illnesses and deaths associated with a funeral was reported in Sinoe County, Liberia. Molecular testing identified Neisseria meningitidis serogroup C (NmC) in specimens from patients. We describe the epidemiological investigation of this cluster and metagenomic characterisation of the outbreak strain. Methods We collected epidemiological data from the field investigation and medical records review. Confirmed, probable, and suspected cases were defined on the basis of molecular testing and signs or symptoms of meningococcal disease. Metagenomic sequences from patient specimens were compared with 141 meningococcal isolate genomes to determine strain lineage. Findings 28 meningococcal disease cases were identified, with dates of symptom onset from April 21 to April 30, 2017: 13 confirmed, three probable, and 12 suspected. 13 patients died. Six (21%) patients reported fever and 23 (82%) reported gastrointestinal symptoms. The attack rate for confirmed and probable cases among funeral attendees was 10%. Metagenomic sequences from six patient specimens were similar to a sequence type (ST) 10217 (clonal complex [CC] 10217) isolate genome from Niger, 2015. Multilocus sequencing identified five of seven alleles from one specimen that matched ST-9367, which is represented in the PubMLST database by one carriage isolate from Burkina Faso, in 2011, and belongs to CC10217. Interpretation This outbreak featured high attack and case fatality rates. Clinical presentation was broadly consistent with previous meningococcal disease outbreaks, but predominance of gastrointestinal symptoms was unusual compared with previous African meningitis epidemics. The outbreak strain was genetically similar to NmC CC10217, which caused meningococcal disease outbreaks in Niger and Nigeria. CC10217 had previously been identified only in the African meningitis belt. Funding US Global Health Security.

Background Multi-drug resistant (MDR) Enterobacteriaceae are on the increase worldwide and their spread has become a global challenge. Escalating the challenge is the possibility that many of these are Carbapenemase-producing Enterobacteriaceae (CPE). This further complicates patient management. The magnitude of MDR-CPE in many developed settings has been reported, however, there is paucity of data from resource limited settings. We evaluated the epidemiology of MDR-CPE of clinical origin in South Western Uganda. Methods From September 2013 to June 2014, all Enterobacteriaceae isolated from diverse specimens obtained from patients attending Mbarara Regional Referral Hospital, South-western Uganda, were screened for MDR in a laboratory-based cross sectional study. Isolates found to be MDR were screened for carbapenem susceptibility/resistance phenotypically by Kirby Bauer disc diffusion method following CLSI guidelines and genetically using the multiplex real-time Polymerase Chain Reaction (RT-PCR). Results Of the 658 strains isolated, 183 (27.8%) were MDR and 68 (37.15%) of those MDR exhibited at least one form of carbapenem resistance with 23 (12.57%) and 56 (30.60%) isolates expressing phenotypic and genetic resistance, respectively. Eleven MDR-CPE (6.01%) isolates exhibited both phenotypic and genotypic resistance to carbapenems. Only blaVIM and blaOXA-48 genes were detected among the genetically resistant isolates. Conclusion The high prevalence of MDR-CPE calls for aggressive infection control and prevention strategies, including reinforcement of hand hygiene, using contact precautions and early detection of CPE through use of targeted surveillance and molecular techniques in resource limited settings.

On April 25, 2017, a cluster of unexplained illness and deaths among persons who had attended a funeral during April 21-22 was reported in Sinoe County, Liberia (1). Using a broad initial case definition, 31 cases were identified, including 13 (42%) deaths. Twenty-seven cases were from Sinoe County (1), and two cases each were from Grand Bassa and Monsterrado counties, respectively. On May 5, 2017, initial multipathogen testing of specimens from four fatal cases using the Taqman Array Card (TAC) assay identified Neisseria meningitidis in all specimens. Subsequent testing using direct real-time polymerase chain reaction (PCR) confirmed N. meningitidis in 14 (58%) of 24 patients with available specimens and identified N. meningitidis serogroup C (NmC) in 13 (54%) patients. N. meningitidis was detected in specimens from 11 of the 13 patients who died; no specimens were available from the other two fatal cases. On May 16, 2017, the National Public Health Institute of Liberia and the Ministry of Health of Liberia issued a press release confirming serogroup C meningococcal disease as the cause of this outbreak in Liberia.

Introduction While the laboratory represents more than 70% of clinical diagnosis and patient management, access to reliable and quality laboratory diagnostics in sub-Saharan Africa remains a challenge. To gain knowledge and suggest evidence based interventions towards laboratory improvement in Southwestern Uganda, we assessed the baseline laboratory quality standards in three medical and research laboratories in Southwestern Uganda. Methods We conducted a cross sectional survey from October, 2013 to April, 2014. Selected laboratories, including one private research, one private for profit and one public laboratory, were assessed using the WHO AFRO_SLIPTA checklist and baseline scores were determined. Results The three laboratories assessed met basic facility requirements, had trained personnel, and safety measures in place. Sample reception was properly designed and executed with a well designated chain of custody. All laboratories had sufficient equipment for the nature of work they were involved in. However, we found that standard operating procedures were incomplete in all three laboratories, lack of quality audit schemes by two laboratories and only one laboratory enrolled into external quality assurance schemes. The SLIPTA scores were one star for the research laboratory and no star for both the public and private-for-profit laboratories. Conclusion While most of the laboratory systems were in place, the low scores obtained by the assessed laboratories reflect the need for improvement to reach standards of quality assured diagnostics in the region. Therefore, routine mentorship and regional supportive supervision are necessary to increase the quality of laboratory services.

The 2014–16 Ebola Virus Disease (EVD) outbreak in West Africa highlighted the necessity for readily available, accurate and rapid diagnostics. The magnitude of the outbreak and the re-emergence of clusters of EVD cases following the declaration of interrupted transmission in Liberia, reinforced the need for sustained diagnostics to support surveillance and emergency preparedness. We describe implementation of the Xpert Ebola Assay, a rapid molecular diagnostic test run on the GeneXpert platform, at a mobile laboratory in Liberia and the subsequent impact on EVD outbreak response, case management and laboratory system strengthening. During the period of operation, site coordination, management and operational capacity was supported through a successful collaboration between Ministry of Health (MoH), World Health Organization (WHO) and international partners. A team of Liberian laboratory technicians were trained to conduct EVD diagnostics and the laboratory had capacity to test 64–100 blood specimens per day. Establishment of the laboratory significantly increased the daily testing capacity for EVD in Liberia, from 180 to 250 specimens at a time when the effectiveness of the surveillance system was threatened by insufficient diagnostic capacity. During the 18 months of operation, the laboratory tested a total of 9,063 blood specimens, including 21 EVD positives from six confirmed cases during two outbreaks. Following clearance of the significant backlog of untested EVD specimens in November 2015, a new cluster of EVD cases was detected at the laboratory. Collaboration between surveillance and laboratory coordination teams during this and a later outbreak in March 2016, facilitated timely and targeted response interventions. Specimens taken from cases during both outbreaks were analysed at the laboratory with results informing clinical management of patients and discharge decisions. The GeneXpert platform is easy to use, has relatively low running costs and can be integrated into other national diagnostic algorithms. The technology has on average a 2-hour sample-to-result time and allows for single specimen testing to overcome potential delays of batching. This model of a mobile laboratory equipped with Xpert Ebola test, staffed by local laboratory technicians, could serve to strengthen outbreak preparedness and response for future outbreaks of EVD in Liberia and the region., Author summary We describe a model of a mobile laboratory co-located at an Ebola treatment unit (ETU) equipped with GeneXpert molecular diagnostic platform and automated qRT-PCR test for Ebola virus disease (EVD). The laboratory contributed significantly to the EVD response in Liberia, including supporting surveillance, outbreak detection, contact tracing and management of confirmed cases. The laboratory was run by local laboratory technicians as opposed to international experts on short missions, making it a more sustainable option in prolonged outbreaks and early recovery phases. The redeployment and strategic placement of these GeneXpert instruments to complement EVD isolation facilities throughout the country has strengthened preparedness and response capabilities for future EVD outbreaks in Liberia.

Background The international impact, rapid widespread transmission, and reporting delays during the 2014 Ebola outbreak in West Africa highlighted the need for a global, centralized database to inform outbreak response. The World Health Organization and Emerging and Dangerous Pathogens Laboratory Network addressed this need by supporting the development of a global laboratory database. Methods Specimens were collected in the affected countries from patients and dead bodies meeting the case definitions for Ebola virus disease. Test results were entered in nationally standardized spreadsheets and consolidated onto a central server. Results From March 2014 through August 2016, 256343 specimens tested for Ebola virus disease were captured in the database. Thirty-one specimen types were collected, and a variety of diagnostic tests were performed. Regular analysis of data described the functionality of laboratory and response systems, positivity rates, and the geographic distribution of specimens. Conclusion With data standardization and end user buy-in, the collection and analysis of large amounts of data with multiple stakeholders and collaborators across various user-access levels was made possible and contributed to outbreak response needs. The usefulness and value of a multifunctional global laboratory database is far reaching, with uses including virtual biobanking, disease forecasting, and adaption to other disease outbreaks.

There is an urgent need to identify new treatments for tuberculosis (TB), a major infectious disease caused by Mycobacterium tuberculosis (Mtb), which results in 1.5 million deaths each year. We have targeted two essential enzymes in this organism that are promising for antibacterial therapy and reported to be inhibited by naphthoquinones. ThyX is an essential thymidylate synthase that is mechanistically and structurally unrelated to the human enzyme. DNA gyrase is a DNA topoisomerase present in bacteria and plants but not animals. The current study set out to understand the structure-activity relationships of these targets in Mtb using a combination of cheminformatics and in vitro screening. Here, we report the identification of new Mtb ThyX inhibitors, 2-chloro-3-(4-methanesulfonylpiperazin-1-yl)-1,4-dihydronaphthalene-1,4-dione) and idebenone, which show modest whole-cell activity and appear to act, at least in part, by targeting ThyX in Mtb.

Multi-drug resistant (MDR) Enterobacteriaceae are on the increase worldwide and their spread has become a global challenge. Escalating the challenge is the possibility that many of these are Carbapenemase-producing Enterobacteriaceae (CPE). This further complicates patient management. The magnitude of MDR-CPE in many developed settings has been reported, however, there is paucity of data from resource limited settings.

Background: Point-of-care tests have the capacity to improve healthcare delivery by reducing costs and delay associated with care. A novel point-of-care immunochromatographic test for dual diagnosis of both HIV and syphilis by detecting IgG, IgM and IgA antibodies to HIV, and specific and recombinant Treponema pallidum antigens has recently been developed, but has not been evaluated in rural field settings. We evaluated the performance of the SD Bioline Syphilis/HIV Duo (Duo) assay at a healthcare center in rural Uganda. Methods: A convenience sample of pregnant women attending Kinoni Health Centre IV from March to May, 2013 was enrolled. Venous blood was collected and centrifuged for plasma isolation. Samples were tested with the Duo assay and compared with the Treponema pallidum hemaglutination assay and paired HIV rapid antibody tests as the reference standards. The ease of use and time required for the Duo assay were also assessed by laboratory technicians. Results: Two hundred twenty women were enrolled with a mean age of 25.00 years (SD 5.41). The sensitivity and specificity of the Duo assay were 100% (95% CI 79.0 – 100%) and 100% (95% CI 97.6 – 100.0) respectively, for syphilis, and, 100% (75.9 – 100%) and 99.5% (96.8 – 99.9%) respectively, for HIV. The duo kit was found to be faster and easier to use than the current HIV and syphilis testing techniques. Conclusion: The sensitivity and specificity of the SD Bioline HIV/Syphilis Duo test were excellent in a field setting in Uganda. The Duo assay should be further evaluated in alternate populations and with point-of-care specimens (e.g. whole blood from finger stick specimens), but shows promise as a tool for improved HIV and syphilis surveillance, diagnosis, and treatment in field settings.

Background: The resazurin microtiter assay (classic REMA), a colorimetric liquid culture-based drug susceptibility assay for Mycobacterium tuberculosis (MTB), has been endorsed by the World Health Organization. The assay requires 8-16 days to obtain results, delaying management of drug resistant tuberculosis patients. A modified REMA which allows results in as little as 24 hours for bacterial strains, has been developed and validated using Staphylococcus aureus, but has not yet been evaluated for MTB. Therefore we assessed the performance of the modified REMA for rifampicin (RIF) and isoniazid (INH) susceptibility, using the classic REMA as the reference standard. We also compared simplicity (from the technicians’ point of view), time taken to obtain results (rank-sum testing), specificity and Kappa statistics of the two methods. Results: The modified REMA, which is a one-step procedure, was found to be simpler to perform and results were obtained in a significantly shorter time (5 versus 9 days, p < 0.0001) compared to the classic REMA due to addition of indicator and strain at the same time. The specificity of the modified REMA was low {46.8% (35.5% - 58.4%) for RIF and 13.9% (7.2% - 23.5%) for INH}. Kappa statistics were 16.0% for RIF and 2.0% for INH. Low specificity and kappa statistics are due to indicator reduction by the strains before complete drug activity. Conclusion: Although modified REMA is faster and simpler compared to classic REMA, it is not reliable for MTB drug susceptibility testing.