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Modeling the impact of COVID-19-mitigation strategies on malarial case management and prevention by health services in sub-Saharan Africa predicts 81,000 additional deaths in Nigeria and 769,000 in sub-Saharan Africa in 2020.

The natural ecology of Ebola virus infection remains enigmatic. No clear reservoir species has been confirmed but there is evidence of infection in a wide spectrum of mammals, including humans, non-human primates, domestic and wild ungulates and a variety of bat species, both frugivorous and insectivorous. Humans and most other species examined appear to be spillover hosts and suffer disease. Bats are the exception and are tolerant to infection in some laboratory studies. Some surveys show a low prevalence of antibodies against Zaire Ebola virus (ZEBOV) strains in bats during human outbreaks and inter-epidemic periods, and this order of mammals is considered to be the likely reservoir for the virus. Other putative sources include insects but this hypothesis is unproven in the field or laboratory. Moreover, some potential sources, such as aquatic species, have yet to be investigated. There are a number of environmental, human behavioural and ecological risk factors proposed with respect to spillover and spread. In the West African outbreak, which was unprecedented in scale and geographic spread, the source of the spillover remains unproven, although an association exists between the proposed index case and a colony of insectivorous bats. In all but a few Ebola virus disease events, spillover has only been superficially investigated and this was also the case in the West African epidemic. The authors suggest that, to address risks at the human-animal-environmental interface, using a One Health approach, more effort is needed to investigate spillover factors at the time of a ZEBOV epidemic, in addition to conducting inter-epidemic surveys in peridomestic environments. The true prevalence of ZEBOV infection in any species of bats remains unknown. Large-scale, expensive, non-randomised surveys, with low sampling numbers per species, are unlikely to provide evidence for Ebola virus reservoirs or to improve our epidemiological understanding.

The 2014-16 outbreak of ebola virus disease (EVD) in West Africa resulted in 11,308 deaths. During the outbreak only 60% of patients were laboratory confirmed and global health authorities have identified the need for accurate and readily deployable molecular diagnostics as an important component of the ideal response to future outbreaks, to quickly identify and isolate patients. Areas covered: Currently PCR-based techniques and rapid diagnostic tests (RDTs) that detect antigens specific to EVD infections dominate the diagnostic landscape, but recent advances in biosensor technologies have led to novel approaches for the development of EVD diagnostics. This review summarises the literature and available performance data of currently available molecular diagnostics for ebolavirus, identifies knowledge gaps and maps out future priorities for research in this field. Expert opinion: While there are now a plethora of diagnostic tests for EVD at various stages of development, there is an acute need for studies to compare their clinical performance, but the sporadic nature of EVD outbreaks makes this extremely challenging, demanding pragmatic new modalities of research funding and ethical/institutional approval, to enable responsive research in outbreak settings. Retrospective head-to-head diagnostic comparisons could also be implemented using biobanked specimens, providing this can be done safely.

Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014&ndash, 2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.

The World Health Organization defines a zoonosis as any infection naturally transmissible from vertebrate animals to humans. The pandemic of Coronavirus disease (COVID-19) caused by SARS-CoV-2 has been classified as a zoonotic disease, however, no animal reservoir has yet been found, so this classification is premature. We propose that COVID-19 should instead be classified an “emerging infectious disease (EID) of probable animal origin.” To explore if COVID-19 infection fits our proposed re-categorization vs. the contemporary definitions of zoonoses, we reviewed current evidence of infection origin and transmission routes of SARS-CoV-2 virus and described this in the context of known zoonoses, EIDs and “spill-over” events. Although the initial one hundred COVID-19 patients were presumably exposed to the virus at a seafood Market in China, and despite the fact that 33 of 585 swab samples collected from surfaces and cages in the market tested positive for SARS-CoV-2, no virus was isolated directly from animals and no animal reservoir was detected. Elsewhere, SARS-CoV-2 has been detected in animals including domesticated cats, dogs, and ferrets, as well as captive-managed mink, lions, tigers, deer, and mice confirming zooanthroponosis. Other than circumstantial evidence of zoonotic cases in mink farms in the Netherlands, no cases of natural transmission from wild or domesticated animals have been confirmed. More than 40 million human COVID-19 infections reported appear to be exclusively through human-human transmission. SARS-CoV-2 virus and COVID-19 do not meet the WHO definition of zoonoses. We suggest SARS-CoV-2 should be re-classified as an EID of probable animal origin.

IntroductionPrevalence of cardiovascular disease risk factors (CVDRFs) is increasing, especially in low-income countries. In Sierra Leone, there is limited empirical data on the prevalence of CVDRFs, and there are no previous studies on the access to care for these conditions.MethodsThis study in rural and urban Sierra Leone collected demographic, anthropometric measurements and clinical data from randomly sampled individuals over 40 years old using a household survey. We describe the prevalence of the following risk factors: diabetes, hypertension, dyslipidaemia, overweight or obesity, smoking and having at least one of these risk factors. Cascades of care were constructed for diabetes and hypertension using % of the population with the disease who had previously been tested (‘screened’), knew of their condition (‘diagnosed’), were on treatment (‘treated’) or were controlled to target (‘controlled’). Multivariable regression was used to test associations between prevalence of CVDRFs and progress through the cascade for hypertension with demographic and socioeconomic variables. In those with recognised disease who did not seek care, reasons for not accessing care were recorded.ResultsOf 2071 people, 49.6% (95% CI 49.3% to 50.0%) of the population had hypertension, 3.5% (3.4% to 3.6%) had diabetes, 6.7% (6.5% to 7.0%) had dyslipidaemia, 25.6% (25.4% to 25.9%) smoked and 26.5% (26.3% to 26.8%) were overweight/obese; a total of 77.1% (76.6% to 77.5%) had at least one CVDRF. People in urban areas were more likely to have diabetes and be overweight than those living in rural areas. Moreover, being female, more educated or wealthier increased the risk of having all CVDRFs except for smoking. There is a substantial loss of patients at each step of the care cascade for both diabetes and hypertension, with less than 10% of the total population with the conditions being screened, diagnosed, treated and controlled. The most common reasons for not seeking care were lack of knowledge and cost.ConclusionsIn Sierra Leone, CVDRFs are prevalent and access to care is low. Health system strengthening with a focus on increased access to quality care for CVDRFs is urgently needed.

Febrile illnesses are among the most common reasons for visits to hospitals and clinics worldwide. Since fevers can arise from a wide range of diseases, identifying the causative pathogen is essential not only for effective personal treatment but also for early detection of outbreaks. The Defense Threat Reduction Agency (DTRA) tasked a coalition of commercial, academic, and government researchers with moving diagnostic technology concepts from ideation to field use as rapidly as possible using scientifically sound evaluations. DTRA's 24 Month Challenge program examined >30 technologies before fielding four technologies on four continents. >10,000 in field test results were recorded. Here we discuss our tiered evaluation system to assess candidate technologies developed by commercial partners and the process of field testing those technologies at various front-line clinics in Sierra Leone, Thailand, Peru, and Australia. We discuss successes and challenges for introducing two multiplexed lateral flow immunoassay (LFI) tests that detect malaria, dengue fever, melioidosis, and the plague. Additionally we discuss the use of a LFI reader that assisted the interpretation of the assay, communicated results to a data cloud, and greatly facilitated reach-back support. Lastly, we discuss the concurrent field testing of a multiplexed PCR assay on the FilmArray platform, which had an assay pouch specially designed for the 24 Month Challenge. Either standard-of-care or gold-standard testing were run alongside our fielded technologies to benchmark their performance. Keywords: Diagnostic device, Lateral flow immunoassay, Nested PCR, Field testing, Malaria, Dengue fever

Malaria remains a significant cause of morbidity and mortality in West Africa, but the contribution of other vector-borne infections (VBIs) to the burden of disease has been understudied. We used rapid diagnostic tests (RDTs) for three VBIs to test blood samples from 1,795 febrile residents of Bo City, Sierra Leone, over a 1-year period in 2012–2013. In total, 24% of the tests were positive for malaria, fewer than 5% were positive for markers of dengue virus infection, and 39% were positive for IgM directed against chikungunya virus (CHIKV) or a related alphavirus. In total, more than half (55%) of these febrile individuals tested positive for at least one of the three VBIs, which highlights the very high burden of vector-borne diseases in this population. The prevalence of positives on the Chikungunya IgM and dengue tests did not vary significantly with age (P > 0.36), but higher rates of malaria were observed in children < 15 years of age (P < 0.001). Positive results on the Chikungunya IgM RDTs were moderately correlated with rainfall (r2 = 0.599). Based on the high prevalence of positive results on the Chikungunya IgM RDTs from individuals Bo and its environs, there is a need to examine whether an ecological shift toward a greater burden from CHIKV or related alphaviruses is occurring in other parts of Sierra Leone or the West African region.

Recent Ebola virus disease outbreaks affirm the dire need for treatments with proven efficacy. Randomized controlled clinical trials remain the gold standard but, during disease outbreaks, may be difficult to conduct due to ethical concerns and challenging field conditions. In the absence of a randomized control group, statistical modeling to create a control group could be a possibility. Such a model-based reference control would only be credible if it had the same mortality risk as that of the experimental group in the absence of treatment. One way to test this counterfactual assumption is to evaluate whether reasonable similarity exists across nonrandomized control groups from different clinical studies, which might suggest that a future control group would be similarly homogeneous. We evaluated similarity across six clinical studies conducted during the 2013-2016 West Africa outbreak of Ebola virus disease. These studies evaluated favipiravir, the biologic ZMapp, the antimalarial drug amodiaquine, or administration of convalescent plasma or convalescent whole blood. We compared the nonrandomized control groups of these six studies comprising 1147 individuals infected with Ebola virus. We found considerable heterogeneity, which did not disappear after statistical modeling to adjust for prognostic variables. Mortality risk varied widely (31 to 66%) across the nonrandomized control arms of these six studies. Models adjusting for baseline covariates (age, sex, and cycle threshold, a proxy for viral load) failed to sufficiently recalibrate these studies and showed that heterogeneity remained. Our findings highlight concerns about making invalid conclusions when comparing nonrandomized control groups to cohorts receiving experimental treatments.

Background This is the third paper in a 3-paper series evaluating alternative models for rapidly estimating neighborhood populations using limited survey data, augmented with aerial imagery. Methods Bayesian methods were used to sample the large solution space of candidate regression models for estimating population density. Results We accurately estimated the population densities and counts of 20 neighborhoods in the city of Bo, Sierra Leone, using statistical measures derived from Landsat multi-band satellite imagery. The best regression model proposed estimated the latter with an absolute median proportional error of 8.0%, while the total population of the 20 neighborhoods was estimated with an error of less than 1.0%. We also compare our results with those obtained using an empirical Bayes approach. Conclusions Our approach provides a rapid and effective method for constructing predictive models for population densities and counts utilizing remote sensing imagery. Our results, including cross-validation analysis, suggest that masking non-urban areas in the Landsat section images prior to computing the candidate covariate regressors should further improve model generality.

The multimammate mouse (Mastomys natalensis) is the reservoir for Lassa virus (LASV). Zoonotic transmission occurs when humans are directly or indirectly exposed to fluids of the multimammate mouse, such as urine, saliva, and blood. Housing characteristics and domestic organization affect rodent density in and around households and villages, and are likely to be a risk factor for Lassa fever in humans where the reservoir exists. We use semi-structured interviews (N = 51), a quantitative survey (N = 429), direct observations, and a rodent ecology study to provide new insights into how the organization of domestic spaces brings together humans and rodents and creates pathways for infection in rural settlements in Bo District, Sierra Leone. Rodents were frequently reported inside houses (92.4% of respondents), in which we predominantly trapped M. natalensis (57% of trapped rodents) and Rattus rattus (38% of trapped rodents). Building design and materials provide hiding and nesting places for rodents and lead to close proximity with humans. Patterns of contact are both unintentional and intentional and research participants reported high levels of contact with rodents (34.2% of respondents) and rodent fluids (52.8% of respondents). Rodents are also perceived as a serious threat to food security. These results present detailed knowledge about how humans live with and come into contact with rodents, including the LASV reservoir. Our results argue for further collaborative research in housing and environmental modification such as ceiling construction, food storage, and sanitation as prevention against zoonotic LASV transmission.

Although research on the epidemiology and ecology of Ebola has expanded since the 2014-15 outbreak in West Africa, less attention has been paid to the mental health implications and the psychosocial context of the disease for providers working in primary health facilities (rather than Ebola-specific treatment units). This study draws on 54 qualitative interviews with 35 providers working in eight peripheral health units of Sierra Leone's Bo and Kenema Districts. Data collection started near the height of the outbreak in December 2014 and lasted 1 month. Providers recounted changes in their professional, personal and social lives as they became de facto first responders in the outbreak. A theme articulated across interviews was Ebola's destruction of social connectedness and sense of trust within and across health facilities, communities and families. Providers described feeling lonely, ostracized, unloved, afraid, saddened and no longer respected. They also discussed restrictions on behaviors that enhance coping including attending burials and engaging in physical touch (hugging, handshaking, sitting near, or eating with colleagues, patients and family members). Providers described infection prevention measures as necessary but divisive because screening booths and protective equipment inhibited bonding or 'suffering with' patients. To mitigate psychiatric morbidities and maladaptive coping mechanisms-and to prevent the spread of Ebola-researchers and program planners must consider the psychosocial context of this disease and mechanisms to enhance psychological first aid to all health providers, including those in peripheral health settings.

ObjectivesPrevalence of cardiovascular disease risk factors (CVDRF) is increasing, especially in low-income countries. In Sierra Leone, there are no previous studies on the knowledge and the awareness of these conditions in the community. This study aimed to explore the knowledge and understanding of CVDRF, as well as the perceptions of the barriers and facilitators to accessing care for these conditions, among patients and community leaders in Sierra Leone.DesignQualitative study employing semistructured interviews and focus group discussions.SettingUrban and rural Bo District, Sierra Leone.ParticipantsInterviews with a purposive sample of 37 patients and two focus groups with six to nine community leaders.ResultsWhile participants possessed general knowledge of their conditions, the level and complexity of this knowledge varied widely. There were clear gaps in knowledge regarding the coexistence of CVDRF and their consequences, as well as the link between behavioural factors and CVDRF. An overarching theme from the data was the need to create an understanding and awareness of CVDRF in the community in order to prevent and improve management of these conditions. Cost was also seen as a major barrier to accessing care for CVDRFs.ConclusionsThe knowledge gaps identified in this study highlight the need to design strategies and interventions that improve knowledge and recognition of CVDRF in the community. Interventions should specifically consider how to develop and enhance awareness about CVDRF and their consequences. They should also consider how patients seek help and where they access it.

Lockdown measures have been introduced worldwide to contain the transmission of COVID-19. However, the term ‘lockdown’ is not well-defined. Indeed, WHO’s reference to ‘so-called lockdown measures’ indicates the absence of a clear and universally accepted definition of the\ud term ‘lockdown’. We propose a definition of ‘lockdown’ based on a two-by-two matrix that categorises different communicable disease measures based on whether\ud they are compulsory or voluntary; and whether they are targeted at identifiable individuals or facilities, or whether they are applied indiscriminately to a general population\ud or area. Using this definition, we describe the design, timing and implementation of lockdown measures in nine countries in sub-Saharan Africa: Ghana, Nigeria, South Africa, Sierra Leone, Sudan, Tanzania, Uganda, Zambia\ud and Zimbabwe. While there were some commonalities in the implementation of lockdown across these countries,\ud a more notable finding was the variation in the design, timing and implementation of lockdown measures. We\ud also found that the number of reported cases is heavily dependent on the number of tests carried out, and that testing rates ranged from 2031 to 63 928 per million population up until 7 September 2020. The reported number of COVID-19 deaths per million population also varies (0.4 to 250 up until 7 September 2020), but is generally low when compared with countries in Europe and North America. While lockdown measures may have helped inhibit community transmission, the pattern and nature of the epidemic remains unclear. However, there are signs\ud of lockdown harming health by affecting the functioning of the health system and causing social and economic disruption.

A large proportion of ongoing malaria parasite transmission is attributed to low-density subclinical infections not readily detected by available rapid diagnostic tests (RDTs) or microscopy. Plasmodium falciparum gametocyte carriage is subclinical, but gametocytemic individuals comprise the parasite reservoir that leads to infection of mosquitoes and local transmission. Effective detection and quantification of these carriers can help advance malaria elimination strategies. However, no point-of-need (PON) RDTs for gametocyte detection exist, much less one that can perform noninvasive sampling of saliva outside a clinical setting. Here, we report on the discovery of 35 parasite markers from which we selected a single candidate for use in a PON RDT. We performed a cross-sectional, multi-omics study of saliva from 364 children with subclinical infection in Cameroon and Zambia and produced a prototype saliva-based PON lateral flow immunoassay test for P. falciparum gametocyte carriers. The test is capable of identifying submicroscopic carriage in both clinical and nonclinical settings and is compatible with archived saliva samples.

Following the 2013–2016 outbreak of Ebola virus disease (EVD) in West Africa, governments across the region imposed a ban on the hunting and consumption of meat from wild animals. This injunction was accompanied by public health messages emphasising the infectious potential of wild meat, or ‘bushmeat.’ Using a qualitative methodology, we examine the local reception and impact of these interventions. Fieldwork was focused in 9 villages in the Eastern and Southern provinces of Sierra Leone between August and December 2015. We conducted 47 semi-structured interviews, coordinated 12 informal group discussions, and conducted direct observations throughout. We also draw from research undertaken in Sierra Leone immediately before the outbreak, and from our participation in the EVD response in Guinea and Sierra Leone. Our findings underscore the social and political reverberations of hunting proscriptions. Messaging that unilaterally stressed the health risk posed by wild meat contradicted the experiences of target publics, who consume wild meat without incident. This epistemic dissonance radically undercut the effectiveness of the ban, which merely served to proliferate informal networks of wild animal trade and sale—rendering the development of acceptable, evidence-based surveillance and mitigation strategies for zoonotic spillovers almost impossible. Further, the criminalisation of wild meat consumption fuelled fears and rumours within communities under considerable strain from the health, social, and economic effects of the epidemic, entrenching distrust towards outbreak responders and exacerbating pre-existing tensions within villages. These unintended consequences are instructive for public health emergency response and preparedness. While wild meat is a risk for zoonotic infection, mitigating those risks entails interventions that fully take into account the local significances of hunting—including a communicative engagement that is designed, validated, and continually refined before emergency situations. Ultimately, our research questions the value of legal sanctions as a means of behavioural change in an emergency context.

Objective The aim of this study was to determine the prevalence of hepatitis B surface antigen (HBsAg) among febrile individuals tested at Mercy Hospital Research Laboratory (MHRL) in Bo, Sierra Leone. Results A total of 860 febrile individuals ages 5 years and older were tested by MHRL between July 2012 and June 2013 with a Standard Diagnostics Bioline HBsAg rapid diagnostic test. The overall HBsAg prevalence rate was 13.7%, including a rate of 15.5% among males and 12.6% among females. The HBsAg rate did not differ by child or adult age group (p > 0.5). The prevalence rate in Bo was similar to the 11–15% HBsAg prevalence rates reported in the past decade from other studies across West Africa. Scaling up the infant hepatitis B vaccination program in Sierra Leone will be important for reducing the future burden of disease and premature death attributable to chronic viral hepatitis B disease.

Objective The goal of this study was to examine the prevalence of HIV among febrile patients seeking care in Mercy Hospital, Bo, Sierra Leone, in 2012–2013. Results A total of 1207 febrile persons were tested for HIV with Determine™ and SD Bioline rapid diagnostic tests kits that detect the presence of HIV antibodies and HIV p24 antigens. The overall prevalence of HIV among the tested patients was 8.9%, which is considerably higher than the

Intra-abdominal infections (IAI) are an important cause of morbidity and are frequently associated with poor prognosis, particularly in high-risk patients. The cornerstones in the management of complicated IAIs are timely effective source control with appropriate antimicrobial therapy. Empiric antimicrobial therapy is important in the management of intra-abdominal infections and must be broad enough to cover all likely organisms because inappropriate initial antimicrobial therapy is associated with poor patient outcomes and the development of bacterial resistance. The overuse of antimicrobials is widely accepted as a major driver of some emerging infections (such as C. difficile), the selection of resistant pathogens in individual patients, and for the continued development of antimicrobial resistance globally. The growing emergence of multi-drug resistant organisms and the limited development of new agents available to counteract them have caused an impending crisis with alarming implications, especially with regards to Gram-negative bacteria. An international task force from 79 different countries has joined this project by sharing a document on the rational use of antimicrobials for patients with IAIs. The project has been termed AGORA (Antimicrobials: A Global Alliance for Optimizing their Rational Use in Intra-Abdominal Infections). The authors hope that AGORA, involving many of the world's leading experts, can actively raise awareness in health workers and can improve prescribing behavior in treating IAIs.

New and re-emerging infectious diseases cause much human suffering worldwide. Many of these diseases are zoonoses with epidemic potential. All sub-Saharan African regions are highly biodiverse with large rural populations that are highly dependent on livestock agriculture. Movement of pathogens between animals and people increases as the domestic populations expand, creating novel ecotones and ecosystemic perturbation. With increasing food security demands, intensification of livestock and agriculture is required and further evolution and spill over of novel zoonoses to humans is inevitable. The emergence this century of previously unknown zoonotic respiratory tract infectious diseases with epidemic potential, such as Avian influenza, Severe Acute Respiratory Syndrome (SARS), and Middle East Respiratory Syndrome (MERS), highlights an urgent need to change the current global status quo. The 2015 west African Ebola virus epidemic illustrated that once an infectious disease

Background Across low-income settings, community volunteers and health committee members support the formal health system - both routinely and amid emergencies - by engaging in health services such as referrals and health education. During the 2014–2015 Ebola epidemic, emerging reports suggest that community engagement was instrumental in interrupting transmission. Nevertheless, literature regarding community volunteers’ roles during emergencies generally, and Ebola specifically, is scarce. This research outlines what this cadre of the workforce did, how they coped, and the facilitators and barriers they faced to providing care in Sierra Leone. Methods Thirteen focus group discussions (FGD) were conducted with community members (including members of Health Management Committees (HMC)) near the height of the Ebola epidemic in two districts of Sierra Leone: Bo and Kenema. Conducted in either Krio or Mende, each FGD lasted an average of two hours and was led by a trained moderator who was accompanied by a note taker. All FGDs were audio recorded, transcribed, and translated into English by the data collection team. Analysis followed a modified framework approach, which entailed coding (both inductive and deductive), arrangement of codes into themes, and drafting, distribution and discussion of analytic summaries across the study team. Results Community volunteers and HMC members described engaging in labor-related tasks (e.g. building isolation structures, digging graves) and administrative/community-outreach tasks (e.g. screening, contact tracing, and encouraging care seeking within facilities). Through their dual orientation as community members and as individuals linked to the health system, respondents described building community trust and support for Ebola prevention and treatment, while also enabling formal health workers to better understand and address people’s fears and needs. Community volunteers’ main concerns included inadequate communication with - and a sense of being forgotten by - the health system, negative perceptions of their role within their communities, and concerns regarding the amount and nature of their compensation. Discussion & Conclusion Respondents described commitment to supporting their health system and their communities during the Ebola crisis. The health system could more effectively harness the potential of local responders by recognizing community strengths and weaknesses, as well as community volunteers’ motivations and limitations. Clarifying the roles, responsibilities, and remuneration of health volunteers to the recipients themselves, facility-based staff, and the wider community will enable organizations that partner with health committees to bolster trust, manage expectations, and reinforce collaboration.

Citrobacter freundiiis a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence ofC. freundiistrain SL151, a highly multidrug-resistant human urine isolate.

Highlights • Twenty-eight percent of the world's 9.6 million new tuberculosis (TB) cases are in the World Health Organization Africa Region. The Mano River Union (MRU) countries of West Africa have made incremental investments into TB control programs over the past two decades. • The devastating 2014–2015 Ebola virus disease (EVD) outbreak in Guinea, Liberia, and Sierra Leone had a significant impact on all sectors of the healthcare system, including TB prevention and control programs. • Vaccination of the under-fives for TB with BCG was adversely affected by the EVD epidemic, and the deaths of numerous healthcare workers deprived the weak healthcare systems of much needed human resources. • There is an urgent need to improve the ability of countries and regions to sustain functioning health systems during outbreaks so that other disease control programs (like those for TB, malaria, and HIV) are not compromised during the emergency measures of a severe epidemic., Summary The World Health Organization (WHO) Global Tuberculosis Report 2015 states that 28% of the world's 9.6 million new tuberculosis (TB) cases are in the WHO Africa Region. The Mano River Union (MRU) countries of West Africa–Guinea, Sierra Leone, and Liberia–have made incremental sustained investments into TB control programmes over the past two decades. The devastating Ebola virus disease (EVD) outbreak of 2014–2015 in West Africa impacted significantly on all sectors of the healthcare systems in the MRU countries, including the TB prevention and control programmes. The EVD outbreak also had an adverse impact on the healthcare workforce and healthcare service delivery. At the height of the EVD outbreak, numerous staff members in all MRU countries contracted EBV at the Ebola treatment units and died. Many healthcare workers were also infected in healthcare facilities that were not Ebola treatment units but were national hospitals and peripheral health units that were unprepared for receiving patients with EVD. In all three MRU countries, the disruption to TB services due to the EVD epidemic will no doubt have increased Mycobacterium tuberculosis transmission, TB morbidity and mortality, and decreased patient adherence to TB treatment, and the likely impact will not be known for several years to come. In this viewpoint, the impact that the EVD outbreak had on TB diagnostic, management, and prevention services is described. Vaccination against TB with BCG in children under 5 years of age was affected adversely by the EVD epidemic. The EVD outbreak was a result of global failure and represents yet another ‘wake-up call’ to the international community, and particularly to African governments, to reach a consensus on new ways of thinking at the national, regional, and global levels for building healthcare systems that can sustain their function during outbreaks. This is necessary so that other disease control programmes (like those for TB, malaria, and HIV) are not compromised during the emergency measures of a severe epidemic.

A collection of 74 Enterobacteriaceae isolates found in Bo, Sierra Leone, were tested for quinolone antibiotic susceptibility and resistance mechanisms. The majority of isolates (62%) were resistant to quinolones, and 61% harbored chromosomal gyrA and/or parC mutations. Plasmid-mediated quinolone resistance genes were ubiquitous, with qnrB and aac(6′)-Ib-cr being the most prevalent. Mutated LexA binding sites were found in all qnrB1 genes, and truncated qnrB pseudogenes were found in the majority of Citrobacter isolates.

Introduction: bypassing refers to a person's decision to seek care at a healthcare facility that is not the nearest one of its type to the person's home. Methods: this study examined inpatient care facility bypassing in urban Bo, Sierra Leone using data from 1,980 women with children 15 years of age and younger who were interviewed in 2010-2011. The locations of residential structures and hospitals were identified using a geographic information system (GIS), and the road distances from participating households to the nearest and preferred inpatient care facilities were measured. Results: nine inpatient care facilities serve Bo residents, but more than 70% of the participating women reported that the city's main public hospital (Bo Government Hospital), located in the city center, was their preferred inpatient care provider. Participants resided within a median distance of 0.9 km (Interquartile range (IQR): 0.6, 1.8) from their closest inpatient facility, but they would travel a median distance of 2.4 km (IQR: 1.0, 3.3) to reach their preferred providers. About 87% of the women would bypass their nearest inpatient care facility to access care at a preferred provider. Bypassing rates were similar for various demographic and socioeconomic groups, but higher for women living farther from the city center. Conclusion: although Bo has a diverse healthcare marketplace, access to affordable advanced care options is limited. Most women in Bo would choose to bypass facilities nearer to their homes to seek the low-cost and comprehensive care offered by Bo Government Hospital.The Pan African Medical Journal 2016;23

Summary Background Convalescent blood therapy has been a promising form of treatment for Ebola Virus Disease (EVD), but less attention has been focused on it for treatment. Method We assessed the effectiveness of convalescent whole blood (CWB) in the treatment of consented EVD patients. We recruited 69 subjects in December 2014 up to April 2015, at the 34 Military Hospital in Wilberforce and the PTS 1 Ebola Treatment Unit in Hastings, Freetown. Forty-four were given CWB, and 25 who consented but preferred to be exempted from the CWB treatment were used to compare clinical outcomes. All were given routine treatment used at the Ebola Treatment Unit. Results One of 44 subjects treated with CWB dropped out of the study and 31 recovered while 12 succumbed to the disease with a case fatality rate of 27.9%. For the group that was given routine treatment without CWB, 11 died with a case fatality rate of 44%. There was a significant difference between admission viral load and viral load after the first 24 h of treatment with convalescent whole blood (P, Highlights • We evaluated convalescent whole blood (CWB) to treat EVD. • We recruited 69 subjects: 44 were enrolled on CWB. • There was a significant difference between admission viral load and viral load after 24 h of treatment with CWB. • Case fatality rates were 27.9% for the CWB group and 44% for the control group. • CWB could still be important in the treatment of EVD.

Highlights • The appearance, disappearance, and re-emergence of pathogens of humans with epidemic potential and high mortality rates have threatened global health security for centuries. • Global public health authorities should have been better prepared for the recent Ebola virus disease (EVD) epidemic in West Africa. • The current Zika virus outbreak is diverting the attention of public authorities and governments from other important infectious diseases that continue to threaten global public health security; one such disease lurking in the background is the Middle East respiratory syndrome (MERS). • The emergence of the MERS coronavirus (MERS-CoV) in 2012 was the second time (after severe acute respiratory syndrome coronavirus (SARS-CoV)) that a new coronavirus, highly pathogenic for humans, emerged in the 21st century. Whilst most MERS cases have been reported from the Middle East, MERS cases have been reported from 27 countries in all continents. • MERS-CoV has been found in camel populations of Eastern Africa and the Middle East, and with millions of pilgrims visiting Saudi Arabia and returning home every year, the movement of MERS-CoV to new locations presents a real threat to global health security. • With animal, human, and environmental factors playing a critical role in its evolution, MERS-CoV represents a classical zoonosis. • A serious and more collaborative and coordinated MERS-CoV response plan is required to better define MERS-CoV epidemiology, transmission dynamics, molecular evolution, optimal treatment and prevention measures, and development of vaccines for humans and camels. • The ‘One Health’ concept focuses on the relationship and interconnectedness between humans, animals, and the environment, and recognizes that the health and wellbeing of humans is intimately connected to the health of animals and their environment (and vice versa). • A ‘One Health’ approach is ideally suited to the MERS-CoV situation and requires close cooperation between those who provide human health, animal health, and promote environmental and ecosystems health. • Critical to the establishment of a ‘One Health’ platform is the creation of a multidisciplinary team with a range of expertise to learn more about zoonotic spread between animals, humans, and the environment, and to monitor, respond to, and prevent major outbreaks conductive sociopolitical and economic framework for action. • The persistence of MERS-CoV 4 years since its first discovery has created major opportunities for Saudi Arabia or one of the other Middle Eastern countries to take leadership of the ‘One Health’ approach to tackling new emerging and re-emerging infectious diseases with epidemic potential in their region. • Parallel initiatives across Africa and the tropics could be harmonized to create regional networks that can serve as a repository for expert ‘One Health’ advice on safe and sustainable agricultural systems, especially for livestock, in support of human development., Summary The appearance of novel pathogens of humans with epidemic potential and high mortality rates have threatened global health security for centuries. Over the past few decades new zoonotic infectious diseases of humans caused by pathogens arising from animal reservoirs have included West Nile virus, Yellow fever virus, Ebola virus, Nipah virus, Lassa Fever virus, Hanta virus, Dengue fever virus, Rift Valley fever virus, Crimean-Congo haemorrhagic fever virus, severe acute respiratory syndrome coronavirus, highly pathogenic avian influenza viruses, Middle East Respiratory Syndrome Coronavirus, and Zika virus. The recent Ebola Virus Disease epidemic in West Africa and the ongoing Zika Virus outbreak in South America highlight the urgent need for local, regional and international public health systems to be be more coordinated and better prepared. The One Health concept focuses on the relationship and interconnectedness between Humans, Animals and the Environment, and recognizes that the health and wellbeing of humans is intimately connected to the health of animals and their environment (and vice versa). Critical to the establishment of a One Health platform is the creation of a multidisciplinary team with a range of expertise including public health officers, physicians, veterinarians, animal husbandry specialists, agriculturalists, ecologists, vector biologists, viral phylogeneticists, and researchers to co-operate, collaborate to learn more about zoonotic spread between animals, humans and the environment and to monitor, respond to and prevent major outbreaks. We discuss the unique opportunities for Middle Eastern and African stakeholders to take leadership in building equitable and effective partnerships with all stakeholders involved in human and health systems to take forward a ‘One Health’ approach to control such zoonotic pathogens with epidemic potential.

Background Accomplishing infection prevention and control (IPC) in health facilities in Sub-Saharan Africa is challenging. Owing to poor IPC, healthcare workers (HCWs) were frequently infected during Sierra Leone9s Ebola epidemic. In late 2014, IPC was rapidly and nationally scaled up. We carried out workshops in sampled facilities to further improve adherence to IPC. We investigated HCW experiences and observed practice gaps, before and after the workshops. Methods We conducted an uncontrolled, before and after, mixed-methods study in eight health facilities in Bo and Kenema Districts during December 2014 and January 2015. Quantitative methods administered to HCWs at baseline and follow-up included a survey on attitudes and self-efficacy towards IPC, and structured observations of behaviours. The intervention involved a workshop for HCWs to develop improvement plans for their facility. We analysed the changes between rounds in survey responses and behaviours. We used interviews to explore attitudes and self-efficacy throughout the study period. Results HCWs described IPC as ‘life-saving’ and personal protective equipment (PPE) as uncomfortable for providers and frightening for patients. At baseline, self-efficacy was high (median=4/strongly agree). Responses reflecting unfavourable attitudes were low for glove use (median=1/strongly disagree, IQR, 1–2) and PPE use with ill family members (median=1, IQR, 1–2), and mixed for PPE use with ill HCWs (median=2/disagree, IQR, 1–4). Observations demonstrated consistent glove reuse and poor HCW handwashing. The maintenance of distance (RR 1.09, 95% CI 1.02 to 1.16) and patient handwashing (RR 1.19, 95% CI 1.3 to 1.25) improved to >90%. Conclusions We found favourable attitudes towards IPC and gaps in practice. Risk perceptions of HCWs and tendencies to ration PPE where chronic supply chain issues normally lead to PPE stock-outs may affect practice. As Sierra Leone9s Ebola Recovery Strategy aims to make all facilities IPC compliant, socio-behavioural improvements and a secure supply chain are essential.

Lassa fever is a zoonotic hemorrhagic illness predominant in areas across Nigeria, Sierra Leone, Guinea, Liberia, and southern Mali. The reservoir of Lassa virus is the multimammate mouse (Mastomys natalensis), a highly commensal species in West Africa. Primary transmission to humans occurs through direct or indirect contact with rodent body fluids such as urine, feces, saliva, or blood. Our research draws together qualitative and quantitative methods to provide a fuller and more nuanced perspective on these varied points of human–animal contact. In this article, we focus on the hunting, preparation, and consumption of rodents as possible routes of exposure in Bo, Sierra Leone. We found that the consumption of rodents, including the reservoir species, is widespread and does not neatly tally against generational or gender lines. Further, we found that the reasons for rodent consumption are multifactorial, including taste preferences, food security, and opportunistic behavior. We argue that on certain topics, such as rodent consumption, establishing trust with communities, and using qualitative research methods, is key to investigate sensitive issues and situate them in their wider context. To conclude, we recommend ways to refine sensitization campaigns to account for these socio-cultural contexts.

Intra-abdominal infections (IAI) are an important cause of morbidity and are frequently associated with poor prognosis, particularly in high-risk patients. The cornerstones in the management of complicated IAIs are timely effective source control with appropriate antimicrobial therapy. Empiric antimicrobial therapy is important in the management of intra-abdominal infections and must be broad enough to cover all likely organisms because inappropriate initial antimicrobial therapy is associated with poor patient outcomes and the development of bacterial resistance. The overuse of antimicrobials is widely accepted as a major driver of some emerging infections (such as C. difficile), the selection of resistant pathogens in individual patients, and for the continued development of antimicrobial resistance globally. The growing emergence of multi-drug resistant organisms and the limited development of new agents available to counteract them have caused an impending crisis with alarming implications, especially with regards to Gram-negative bacteria. An international task force from 79 different countries has joined this project by sharing a document on the rational use of antimicrobials for patients with IAIs. The project has been termed AGORA (Antimicrobials: A Global Alliance for Optimizing their Rational Use in Intra-Abdominal Infections). The authors hope that AGORA, involving many of the world's leading experts, can actively raise awareness in health workers and can improve prescribing behavior in treating IAIs., 0, SCOPUS: ar.j, info:eu-repo/semantics/published

To examine the diversity of the health-care providers in urban Bo, Sierra Leone, identify the types of health-care facilities preferred by women for fevers, and analyze the road network distances from homes to preferred health-care providers. A population-based random sampling method was used to recruit 2419 women from Bo. A geographic information system was used to measure the road distance from each woman’s home to her preferred provider. Preferred health-care providers for acute febrile illnesses (commonly referred to as “malaria” in the study communities) were hospitals (62.3 %), clinics (12.6 %), and pharmacies (12.4 %). Participants lived a median distance of 0.6 km from the nearest provider, but on average each woman lived 2.2 km one-way from her preferred provider. Women living farther from the city center had preferred providers significantly farther from home than women living downtown. The diverse health-care marketplace in Bo allows women to select clinical facilities from across the city. Most women prefer a malaria care provider farther from home than they could comfortably walk when ill.

This study demonstrates the use of bootstrap methods to estimate the total population of urban and periurban areas using satellite imagery and limited survey data. We conducted complete household surveys in 20 neighborhoods in the city of Bo, Sierra Leone, which collectively were home to 25,954 persons living in 1,979 residential structures. For five of those twenty sections, we quantized the rooftop areas of structures extracted from satellite images. We used bootstrap statistical methods to estimate the total population of the pooled sections, including the associated uncertainty intervals, as a function of sample size. Evaluations based either on rooftop area per person or on the mean number of occupants per residence both converged on the true population size. We demonstrate with this simulation that demographic surveys of a relatively small proportion of residences can provide a foundation for accurately estimating the total population in conjunction with aerial photographs.

Background Infectious diseases contribute to a high burden of diseases globally. Surveillance using low-cost technology, combined with cutting edge platforms offers a path for understanding the disease ecology of locations of interest in resource-poor countries. Our goal was to pilot a bio surveillance system comprising of rapid lateral flow immunoassays, rapid PCR and a cloud database. Methods The study was carried out in Bo, Sierra Leone at the Mercy Hospital. We recruited 1570 subjects over a period of two years. Inclusion criteria for the study were being febrile, being at least five years of age, living within the city of Bo or its neighbouring villages and agreeing to participate in the study. The assays used included a DPP multiplex lateral flow assay for dengue, Burkholderia pseudomallei , Yersinia pestis , malaria Pf/Pan, a Film Array PCR platform with multiplex Biothreat and SASFI panels that together detect over 30 pathogen targets. We used a Deki Reader to upload lateral flow images to the cloud database. The Deki reader quantitates test results, such that scores at ≥1.75 are considered positive. A special computer program was designed to upload pdf images of PCR results to the cloud database. The cloud database was designed for automated quality assessment and remote monitoring. Results Preliminary results show that out of 1570 samples processed by DPP, 30(1.9%) were positive for Burkholderia, 41(2.6%) were positive for Dengue NS1 antigen, 22(1.4%) were positive for Yesinia pestis fraction 1 antigen, and 340(21.7%) were positive for malaria. When a cross-section of results obtained by eye was compared with results automatically detected by the D2C platform, there was 95.2% concordance between results obtained by eye and those obtained automatically by the Deki reader to the cloud database. Conclusions Active disease surveillance and the ability to remotely monitor activities in peripheral health units are critical needs in many poor countries. Our results provide additional perspectives on the twin problem of surveillance and remote quality assessment.

Background The rising level of antimicrobial resistance among bacterial pathogens is one of the most significant public health problems globally. While the antibiotic resistance of clinically important bacteria is closely tracked in many developed countries, the types and levels of resistance and multidrug resistance (MDR) among pathogens currently circulating in most countries of sub-Saharan Africa are virtually unknown. Methods From December 2013 to April 2014, we collected 93 urine specimens from all outpatients showing symptoms of urinary tract infection (UTI) and 189 fomite swabs from a small hospital in Bo, Sierra Leone. Culture on chromogenic agar combined with biochemical and DNA sequence-based assays was used to detect and identify the bacterial isolates. Their antimicrobial susceptibilities were determined using a panel of 11 antibiotics or antibiotic combinations. Results The 70 Enterobacteriaceae urine isolates were identified as Citrobacter freundii (n = 22), Klebsiella pneumoniae (n = 15), Enterobacter cloacae (n = 15), Escherichia coli (n = 13), Enterobacter sp./Leclercia sp. (n = 4) and Escherichia hermannii (n = 1). Antimicrobial susceptibility testing demonstrated that 85.7 % of these isolates were MDR while 64.3 % produced an extended-spectrum ß-lactamase (ESBL). The most notable observations included widespread resistance to sulphonamides (91.4 %), chloramphenicol (72.9 %), gentamycin (72.9 %), ampicillin with sulbactam (51.4 %) and ciprofloxacin (47.1 %) with C. freundii exhibiting the highest and E. coli the lowest prevalence of multidrug resistance. The environmental cultures resulted in only five Enterobacteriaceae isolates out of 189 collected with lower overall antibiotic resistance. Conclusions The surprisingly high proportion of C. freundii found in urine of patients with suspected UTI supports earlier findings of the growing role of this pathogen in UTIs in low-resource countries. The isolates of all analyzed species showed worryingly high levels of resistance to both first- and second-line antibiotics as well as a high frequency of MDR and ESBL phenotypes, which likely resulted from the lack of consistent antibiotic stewardship policies in Sierra Leone. Analysis of hospital environmental isolates however suggested that fomites in this naturally ventilated hospital were not a major reservoir for Enterobacteriaceae or antibiotic resistance determinants. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1495-1) contains supplementary material, which is available to authorized users.