A compendium of multi-omics data illuminating host responses to lethal human virus infections.

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

Molecular characterization of an outbreak-involved Bacillus anthracis strain confirms the spillover of anthrax from West Africa.

BACKGROUND: Anthrax, a zoonotic disease caused by the spore-forming bacterium Bacillus anthracis, remains a major global public health concern, especially in countries with limited resources. Sierra Leone, a West African country historically plagued by anthrax, has almost been out of report on this disease in recent decades. In this study, we described a large-scale anthrax outbreak affecting both animals and humans and attempted to characterize the pathogen using molecular techniques. METHODS: The causative agent of the animal outbreak in Port Loko District, Sierra Leone, between March and May 2022 was identified using the nanopore sequencing technique. A nationwide active surveillance was implemented from May 2022 to June 2023 to monitor the occurrence of anthrax-specific symptoms in humans. Suspected cases were subsequently verified using quantitative polymerase chain reaction. Full-genome sequencing was accomplished by combining long-read and short-read sequencing methods. Subsequent phylogenetic analysis was performed based on the full-chromosome single nucleotide polymorphisms. RESULTS: The outbreak in Port Loko District, Sierra Leone, led to the death of 233 animals between March 26th and May 16th, 2022. We ruled out the initial suspicion of Anaplasma species and successfully identified B. anthracis as the causative agent of the outbreak. As a result of the government's prompt response, out of the 49 suspected human cases identified during the one-year active surveillance, only 6 human cases tested positive, all within the first month after the official declaration of the outbreak. The phylogenetic analysis indicated that the BaSL2022 isolate responsible for the outbreak was positioned in the A.Br.153 clade within the TransEuroAsian group of B. anthracis. CONCLUSIONS: We successfully identified a large-scale anthrax outbreak in Sierra Leone. The causative isolate of B. anthracis, BaSL2022, phylogenetically bridged other lineages in A.Br.153 clade and neighboring genetic groups, A.Br.144 and A.Br.148, eventually confirming the spillover of anthrax from West Africa. Given the wide dissemination of B. anthracis spores, it is highly advisable to effectively monitor the potential reoccurrence of anthrax outbreaks and to launch campaigns to improve public awareness regarding anthrax in Sierra Leone.

Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa.

The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (Mastomys natalensis), and also in two Guinean multimammate mice (Mastomys erythroleucus) in northern Sierra Leone and two rusty-bellied brush-furred mice (Lophuromys sikapusi) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316-374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.

Determinants of incomplete childhood hepatitis B vaccination in Sierra Leone, Liberia, and Guinea: Analysis of national surveys (2018-2020).

Vaccination against hepatitis B virus (HBV) is effective at preventing vertical transmission. Sierra Leone, Liberia, and Guinea are hyperendemic West African countries; yet, childhood vaccination coverage is suboptimal, and the determinants of incomplete vaccination are poorly understood. We analyzed national survey data (2018-2020) of children aged 4-35 months to assess complete HBV vaccination (receiving 3 doses of the pentavalent vaccine) and incomplete vaccination (receiving <3 doses). Statistical analysis was conducted using the complex sample command in SPSS (version 28). Multivariate logistic regression was used to identify determinants of incomplete immunization. Overall, 11,181 mothers were analyzed (4,846 from Sierra Leone, 2,788 from Liberia, and 3,547 from Guinea). Sierra Leone had the highest HBV childhood vaccination coverage (70.3%), followed by Liberia (64.6%) and Guinea (39.3%). Within countries, HBV vaccination coverage varied by socioeconomic characteristics and healthcare access. In multivariate regression analysis, factors that were significantly associated with incomplete vaccination in at least one country included sex of the child, Muslim mothers, lower household wealth index, <4 antenatal visits, home delivery, and distance to health facility vaccination (all p < 0.05). Understanding and addressing modifiable determinants of incomplete vaccination will be essential to help achieve the 2030 viral hepatitis elimination goals.

Understanding COVID-19 Vaccine Uptake and Hesitancy among People with HIV in Freetown, Sierra Leone: A Cross-Sectional Study.

People with HIV (PWH) incur a higher risk of COVID-19-related morbidity and mortality rates, yet less is known about COVID-19 vaccine uptake and hesitancy in this group. We conducted a cross-sectional study in Freetown, Sierra Leone, from April to June 2022, using the VAX scale, a validated instrument, to assess attitudes towards COVID-19 vaccination and calculate the hesitancy (VAX) scores. We used generalized linear models to identify the factors associated with vaccine hesitancy. Overall, 490 PWH were enrolled (71.4% female, median age: 38 years, median CD4 count: 412 cells/mm3). About 17.3% received ≥1 dose of a COVID-19 vaccine. The mean VAX score was 43.14 ± 7.05, corresponding to 59.9% participants being vaccine-hesitant. A preference for natural immunity (65.8%) and concerns about profiteering (64.4%) were the commonest reasons for hesitancy, followed by a mistrust of vaccine benefits (61.4%) and worries about future effects (48.0%). In the adjusted regression analysis, being a Muslim (ß = 2.563, p < 0.001) and having an urban residence (ß = 1.709, p = 0.010) were associated with greater vaccine hesitancy, while testing for COVID-19 was associated with reduced vaccine hesitancy (ß = -3.417, p = 0.027). These findings underscore the importance of addressing vaccine hesitancy as a critical element boosting COVID-19 vaccine uptake among PWH.

Standardised Competency-Based Training of Medical Doctors and Associate Clinicians in Inguinal Repair with Mesh in Sierra Leone.

INTRODUCTION: In low-income settings, there is a high unmet need for hernia surgery, and most procedures are performed with tissue repair techniques. In preparation for a randomized clinical trial, medical doctors and associate clinicians received a short-course competency-based training on inguinal hernia repair with mesh under local anaesthesia. The aim of this study was to evaluate feasibility, safety and effectiveness of the training. METHODS: All trainees received a one-day theoretical module on mesh hernia repair under local anaesthesia followed by hands-on training. Performance was assessed using the American College of Surgeon's Groin Hernia Operative Performance Rating System. Patients were followed up two weeks and one year after surgery. Outcomes of the patients operated on during the training trial were compared to the 229 trial patients operated on after the training. RESULTS: During three surgical camps, seven medical doctors and six associate clinicians were trained. In total, 129 patients were operated on as part of the training. Of the 13 trainees, 11 reached proficiency. Patients in the training group had more wound infections after two weeks (8.5% versus 3.1%; p = 0.041). There was no difference in recurrence and mortality after one year, and none of the deaths were attributed to the surgery. DISCUSSION AND CONCLUSION: Mesh repair is the international standard for inguinal hernia repair worldwide. Nevertheless, this is not widely accessible in low-income settings. This study has demonstrated that short-course intensive hands-on training of MDs and ACs in mesh hernia repair is effective and safe. TRIAL REGISTRATION: International Clinical Trial Registry ISRCTN63478884.

Understanding COVID-19 Vaccine Uptake and Hesitancy Among People With HIV in Freetown, Sierra Leone: A Cross-sectional Study.

Objectives: People living with HIV (PWH) are at increased risk of COVID-19 related morbidity and mortality, yet less is known about COVID-19 vaccination uptake and hesitancy, especially in sub-Saharan Africa. We aimed to evaluate COVID-19 vaccine uptake and hesitancy among PWH in Sierra Leone. Methods: We conducted a cross-sectional study in a convenience sample of PWH in routine care at Connaught Hospital in Freetown, Sierra Leone from April through June 2022. We collected sociodemographic and health-related data. We used the VAX Scale, a validated instrument to assess attitudes towards COVID-19 vaccination. From the responses, we constructed hesitancy (VAX) scores, with higher scores implying negative attitudes towards vaccination. We used generalized linear models to identify factors associated with vaccine hesitancy. Results: A total of 490 PWH were enrolled (71.4% female, median age 38 years, median CD4 count 412 cells/mm3, 83.9% virologically suppressed). About 17.3% had received at least one dose of a COVID-19 vaccine. The mean VAX score was 43.14 ± 7.05, corresponding to 59.9% participants classified as vaccine hesitant. Preference for natural immunity (65.8%) and concerns about commercial profiteering (64.4%) were the commonest reasons for hesitancy, followed by mistrust of vaccine benefits (61.4%) and worries about future side effects (48.0%). In adjusted regression analysis, being Muslim (ß = 2.563, p < 0.001) and residence in urban areas (ß = 1.709, p = 0.010) were associated with greater vaccine hesitancy, while having tested ever for COVID-19 was associated with lesser vaccine hesitancy (ß = -3.417, p = 0.027). Conclusion: We observed a low COVID-19 vaccine uptake and high hesitancy among PWH in Sierra Leone. Our findings underscore the need to address vaccine hesitancy as a critical element of efforts to boost COVID-19 vaccine uptake among this population in Sierra Leone.

Designing a leadership and management training curriculum for undergraduate health professions students: Lessons from the University of Sierra Leone.

Leadership by health professionals is key in any health system, but health leadership training programmes are varied in their conceptualisation, learning objectives, and design. This paper describes an undergraduate leadership and management module for health students at the University of Sierra Leone and provides lessons from the design process. Our methods included an initial scoping review and qualitative study, followed by a co-design process of 10 workshops and 17 consultation meetings. The result was a curriculum with learning outcomes emphasising leadership identity, proactiveness, management of people and of change, and the formation of peer relationships. Learning methods included group teaching, team quality improvement projects, mentoring, and reflective practice. Lessons from the design process included the importance of support from university leadership and extensive consultation. Virtual workshops enabled broader participation but limited relationship building. Integrating doctoral research into the process facilitated inclusion of evidence and theory but risked reducing ownership by faculty. The importance of interprofessionalism and management skills in leadership training emerged during the process, illustrating the effectiveness of a co-design approach. Our programme is broadly aligned with other health leadership frameworks and is distinctive due to its undergraduate focus, offering insights for leadership training design in other settings.

Prevalence of Chronic Hepatitis B Virus Infection in Sierra Leone, 1997-2022: A Systematic Review and Meta-Analysis.

Hepatitis B virus (HBV) infection is a major public health problem in Sierra Leone, yet reliable estimates of cases are lacking. This study aimed to provide an estimate of the national prevalence of chronic HBV infection in the general population and select groups in Sierra Leone. We used the electronic databases PubMed/MEDLINE, Embase, Scopus, ScienceDirect, Web of Science, Google Scholar, and African Journals Online to systematically review articles reporting hepatitis B infection surface antigen seroprevalence estimates in Sierra Leone during 1997-2022. We estimated pooled HBV seroprevalence rates and assessed potential sources of heterogeneity. Of 546 publications screened, 22 studies with a total sample size of 107,186 people were included in the systematic review and meta-analysis. The pooled prevalence of chronic HBV infection was 13.0% (95% CI, 10.0-16.0) (I2 = 99%; Pheterogeneity < 0.01). During the study period, the HBV prevalence rates were as follows: 17.9% (95% CI, 6.7-39.8) before 2015, 13.3% (95% CI, 10.4-16.9) during 2015-2019, and 10.7% (95% CI, 7.5-14.9) during 2020-2022. The use of the 2020-2022 HBV prevalence estimates corresponded to 870,000 cases of chronic HBV infection (uncertainty interval, 610,000-1,213,000), or approximately one in nine people. The highest HBV seroprevalence estimates were among adolescents aged 10-17 years (17.0%; 95% CI, 8.8-30.5), Ebola survivors (36.8%; 95% CI, 26.2-48.8), people living with HIV (15.9%; 95% CI, 10.6-23.0), and those in the Northern Province (19.0%; 95% CI, 6.4-44.7) and Southern Province (19.7%; 95% CI, 10.9-32.8) regions. These findings may help inform national HBV program implementation in Sierra Leone.

Assessment of Knowledge, Stigmatizing Attitudes and Health-Seeking Behaviors Regarding Hepatitis B Virus Infection in a Pharmacy and Community Setting in Sierra Leone: A Cross-Sectional Study.

Hepatitis B virus (HBV) is a major global health challenge. Emerging evidence suggests that poor knowledge and stigma are impacting HBV control efforts in sub-Saharan Africa (SSA), but their role is not well understood. We conducted a cross-sectional study of adults aged ≥18 years in a community and pharmacy setting in Freetown, Sierra Leone. A structured questionnaire was used to assess knowledge, stigmatizing attitudes and health-seeking behaviors regarding HBV. Logistic regression was used to identify predictors of HBV knowledge and related stigma. A total of 306 adult participants were enrolled (50.7% male, 7.5% HBV positive and 11.7% vaccinated). Overall, 52.2% had good HBV knowledge and 49.3% expressed a stigmatizing attitude towards people with HBV. Notwithstanding, 72.2% stated they would receive the HBV vaccine if offered, 80.4% would take anti-HBV medication and 78.8% would be willing to attend clinic regularly. Good HBV knowledge was associated with HBV positive status (aOR 4.41; p = 0.029) and being vaccinated against HBV (aOR 3.30; p = 0.034). HBV-related stigma was associated with secondary or higher level of education (aOR 2.36; p < 0.001), good HBV knowledge (aOR 2.05; p = 0.006) and pharmacy setting (aOR 1.74, p = 0.037). These findings suggest that education and stigma reduction may benefit HBV elimination efforts in SSA.

Exit, voice or neglect: Understanding the choices faced by doctors experiencing barriers to leading health system change through the case of Sierra Leone.

This paper presents a study from Sierra Leone that explored the experiences of doctors as they endeavored to improve the health care systems in which they worked. Twenty-eight interviews were conducted with doctors in Sierra Leone, complemented by long-standing experience of national health provision and research by the authors. Drawing on Hirschman's theory of 'exit, voice and loyalty', the paper's framework analysis elaborates the doctor's career decisions and choices under systematic political and economic constraints, and in particular, the specter of retribution, including posting to undesirable jobs and withholding of salaries. This retribution was considered a driver of exit by doctors from the system, and few examples were given of doctors successfully advocating for change through advocacy ('voice'). We suggest that the relevance of Hirschman's theory to this setting is in drawing attention to the critical themes of retribution, opportunity, loyalties, and partial exits, ones often neglected in efforts to reduce emigration of doctors and strengthen their leadership. Ultimately, this paper critiques the overemphasis of mechanistic 'capacity building' in global health and recommends that health system strengthening must be viewed as a jointly political as well as technical exercise.

High levels of surgical antibiotic prophylaxis: Implications for hospital-based antibiotic stewardship in Sierra Leone.

Objective: Despite the impact of inappropriate prescribing on antibiotic resistance, data on surgical antibiotic prophylaxis in sub-Saharan Africa are limited. In this study, we evaluated antibiotic use and consumption in surgical prophylaxis in 4 hospitals located in 2 geographic regions of Sierra Leone. Methods: We used a prospective cohort design to collect data from surgical patients aged 18 years or older between February and October 2021. Data were analyzed using Stata version 16 software. Results: Of the 753 surgical patients, 439 (58.3%) were females, and 723 (96%) had received at least 1 dose of antibiotics. Only 410 (54.4%) patients had indications for surgical antibiotic prophylaxis consistent with local guidelines. Factors associated with preoperative antibiotic prophylaxis were the type of surgery, wound class, and consistency of surgical antibiotic prophylaxis with local guidelines. Postoperatively, type of surgery, wound class, and consistency of antibiotic use with local guidelines were important factors associated with antibiotic use. Of the 2,482 doses administered, 1,410 (56.8%) were given postoperatively. Preoperative and intraoperative antibiotic use was reported in 645 (26%) and 427 (17.2%) cases, respectively. The most commonly used antibiotic was ceftriaxone 949 (38.2%) with a consumption of 41.6 defined daily doses (DDD) per 100 bed days. Overall, antibiotic consumption was 117.9 DDD per 100 bed days. The Access antibiotics had 72.7 DDD per 100 bed days (61.7%). Conclusions: We report a high rate of antibiotic consumption for surgical prophylaxis, most of which was not based on local guidelines. To address this growing threat, urgent action is needed to reduce irrational antibiotic prescribing for surgical prophylaxis.

Hepatitis B Virus and Tuberculosis Are Associated with Increased Noncommunicable Disease Risk among Treatment-Naïve People with HIV: Opportunities for Prevention, Early Detection and Management of Comorbidities in Sierra Leone.

Noncommunicable diseases (NCDs) are a growing public health concern in low- and middle-income countries and disproportionately affect people living with HIV (PWH). Hepatitis B virus (HBV) and tuberculosis (TB) coinfection are presumed risk factors in endemic settings; however, supporting evidence is conflicting. We analyzed baseline data of newly diagnosed PWH prospectively enrolled in the Sierra Leone HIV Cohort Study in Freetown, Sierra Leone, from March to September 2021. Logistic regression was used to identify associations between NCDs, HBV and TB. A total of 275 PWH aged ≥18 years were studied (55% female, median age 33 years, median CD4 307 cells/mm3, 15.3% HIV/HBV, 8.7% HIV/TB). NCDs were bimodally distributed, with 1 in 4 PWH clustered around liver disease (fibrosis/cirrhosis), diabetes/prediabetes and obesity/preobesity, while 1 in 8 had renal impairment or hypertension (HTN). Overall, 41.5% had ≥1 NCD, while 17.5% were multimorbid (≥2 NCDs). After adjusting for age, sex, sociodemographic factors and CD4 count, liver fibrosis/cirrhosis was strongly associated with HBV (aOR 8.80, 95% CI [2.46−31.45]; p < 0.001) and diabetes/prediabetes (aOR 9.89, 95% CI [1.14−85.67]; p < 0.037). TB independently predicted diabetes/prediabetes (aOR 7.34, 95% CI [1.87−28.74]; p < 0.004), while renal impairment was associated with proteinuria (aOR 9.34, 95% CI [2.01−43.78]; p < 0.004) and HTN (aOR 6.00, 95% CI [1.10−35.39]; p < 0.049). Our findings warrant the implementation of NCD-aware HIV programs for the prevention, early detection and management of comorbidities.

COVID-19 Vaccine Hesitancy among Healthcare Workers and Trainees in Freetown, Sierra Leone: A Cross-Sectional Study.

Despite having safe and efficacious vaccines against COVID-19, vaccine hesitancy is widespread. Although a trusted source of information, vaccine hesitancy has been reported among healthcare professionals, yet few studies have explored this phenomenon in sub-Saharan Africa. We conducted a cross-sectional survey of healthcare professionals in Sierra Leone from January to March 2022. Measures included sociodemographic/health-related information and COVID-19-related concerns. From the responses, we constructed a hesitancy (VAX) score, with higher scores implying negative attitudes or unwillingness to vaccinate. Multivariate linear regression was used to access factors associated with vaccine hesitancy. Overall, 592 participants submitted responses (67.2% female, mean age 29 years, 5.6% physicians/pharmacists, 44.3% medical students, 29.2% nurses, 20.9% nursing students). The mean VAX score was 43.27 ± 8.77, with 60.1% of respondents classified as vaccine hesitant (>50th percentile) and 13.8% as highly hesitant (>75th percentile). Worries about unforeseen future effects (76.3%), a preference for natural immunity (59.5%), and profiteering/mistrust of health authorities (53.1%) were the most common concerns. Being a medical student (ß = 0.105, p = 0.011) and previously refusing a recommended vaccine (ß = 0.177, p < 0.001) were predictors of COVID-19 vaccine hesitancy. Our findings call for addressing vaccine hesitancy among healthcare professionals as an essential component of strategies aimed at increasing COVID-19 vaccine uptake in this setting.

Social and health factors associated with adverse treatment outcomes among people with multidrug-resistant tuberculosis in Sierra Leone: a national, retrospective cohort study.

BACKGROUND: Multidrug-resistant tuberculosis (MDR-TB) is a global health emergency. We aimed to evaluate treatment outcomes among people with MDR-TB in Sierra Leone and investigate social and health factors associated with adverse treatment outcomes. METHODS: This national, retrospective cohort study recruited all people notified with MDR-TB to the Sierra Leone National TB Programme, admitted to Lakka hospital (Lakka, Western Area Rural District, Freetown, Sierra Leone) between April, 2017, and September, 2019. Participants were followed up to May, 2021. People who were eligible but had no social or health data available, or were subsequently found to have been misdiagnosed, were excluded from participation. MDR-TB treatment was with the 2017 WHO-recommended short (9-11 month) or long (18-24 month) aminoglycoside-containing regimens. Multivariable logistic regression models examined associations of programmatic social and health data with WHO-defined adverse treatment outcomes (death, treatment failure, loss to follow-up). FINDINGS: Of 370 notified MDR-TB cases, 365 (99%) were eligible for study participation (five participants were excluded due to lack of social or health data or misdiagnosis). Treatment was started by 341 (93%) of 365 participants (317 received the short regimen, 24 received the long regimen, and 24 received no treatment). Median age was 35 years (IQR 26-45), 263 (72%) of 365 were male and 102 (28%) were female, 71 (19%) were HIV-positive, and 127 (35%) were severely underweight (body-mass index <16·5 kg/m2). Overall, 267 (73%) of 365 participants had treatment success, 95 (26%) had an adverse outcome, and three (1%) were still on treatment in May, 2021. Age 45-64 years (adjusted odds ratio [aOR] 2·4, 95% CI 1·2-5·0), severe underweight (aOR 4·2, 1·9-9·3), untreated HIV (aOR 10, 2·6-40·0), chronic lung disease (aOR 2·0, 1·0-4·2), previously unsuccessful drug-sensitive tuberculosis retreatment (aOR 4·3, 1·0-19), and a long regimen (aOR 6·5, 2·3-18·0) were associated with adverse outcomes. A sensitivity analysis showed that prothionamide resistance (aOR 3·1, 95% CI 1·5-10·0) and aminoglycoside-related complete deafness (aOR 6·6, 1·3-35) were independently associated with adverse outcomes. INTERPRETATION: MDR-TB treatment success in Sierra Leone approached WHO targets and the short regimen was associated with higher success. The social and health factors associated with adverse outcomes in this study suggest a role for integrated tuberculosis, HIV, and non-communicable disease services alongside nutritional and socioeconomic support for people with MDR-TB and emphasise the urgent need to scale up coverage of all-oral aminoglycoside-sparing regimens. FUNDING: Wellcome Trust, Joint Global Health Trials.

Incidence and risk factors of surgical site infections and related antibiotic resistance in Freetown, Sierra Leone: a prospective cohort study.

BACKGROUND: There is limited information on surgical site infections (SSI) and the related antibiotic resistance needed to guide their management and prevention in Sierra Leone. In this study, we aimed to establish the incidence and risk factors of SSI and the related antibiotic resistance among adults attending a tertiary hospital, and a secondary health facility in Freetown, Sierra Leone. METHODS: This is a prospective cohort study designed to collect data from adult (18 years or older) patients who attended elective and emergency surgeries at two hospitals in Freetown between February and July, 2021. Data analysis was done using STATA version 16. RESULTS: Of 338 patients, 245 (72.5%) and 93 (27.5%) had their surgeries at the tertiary and secondary hospitals, respectively. Many were males 192 (56.8%), less than 35 years 164 (48.5%), and 39 (11.5%) developed an SSI. Of the 39 patients who acquired an SSI, 7 (17.9%) and 32 (82.1%) had their surgeries at the secondary and tertiary hospitals, respectively. The incidence of SSI is higher in contaminated 17 (43.6%) than in clean-contaminated 12 (30.8%) and clean 10 (25.6%) wounds. Wound swabs were collected in 29 (74.4%) patients, of which 18 (62.1%) had bacterial growth. In total, 49 isolates of 14 different bacteria including gram-negative 41 (83.7%) and gram-positive 8 (16.3%) isolates were identified. Of these, 32 (65.3%) were Enterobacteriaceae, 9 (18.4%) were Non-fermenting gram-negative bacilli and 10 (12.2%) were Enterococci. The most common isolates were Escherichia coli (12, 24.5%), Klebsiella pneumoniae (10, 20.4%), Acinetobacter baumannii (5, 10.2%), Klebsiella oxytoca (4, 8.2%) and Enterococcus faecalis (4, 8.2%). The Enterobacteriaceae were either resistance to carbapenems (4, 8.2%) or were extended-spectrum beta-lactamase (ESBL) producing organisms (29, 59.2%). Male sex [p = 0.031], an ASA score ≥ 2 [p = 0.020), administration of general anaesthesia [p = 0.018] and elevated fasting glucose [p = 0.033] were predictive of SSI. CONCLUSION: The incidence of SSI in this study is comparable to other low- and middle-income countries, but a substantial proportion of these postoperative wounds have an ESBL-producing Enterobacteriaceae. Therefore, routine surveillance of SSI and related antibiotic resistance is required in resource-limited settings.

Association between oral antimalarial medication administration and mortality among patients with Ebola virus disease: a multisite cohort study.

BACKGROUND: Empiric antimalarial treatment is a component of protocol-based management of Ebola virus disease (EVD), yet this approach has limited clinical evidence for patient-centered benefits. METHODS: This retrospective cohort study evaluated the association between antimalarial treatment and mortality among patients with confirmed EVD. The data was collected from five International Medical Corps operated Ebola Treatment Units (ETUs) in Sierra Leone and Liberia from 2014 through 2015. The standardized protocol used for patient care included empiric oral treatment with combination artemether and lumefantrine, twice daily for three days; however, only a subset of patients received treatment due to resource variability. The outcome of interest was mortality, comparing patients treated with oral antimalarials within 48-h of admission to those not treated. Analysis was conducted with logistic regression to generate adjusted odds ratios (aORs). Multivariable analyses controlled for ETU country, malaria rapid diagnostic test result, age, EVD cycle threshold value, symptoms of bleeding, diarrhea, dysphagia and dyspnea, and additional standard clinical treatments. RESULTS: Among the 424 cases analyzed, 376 (88.7%) received early oral antimalarials. Across all cases, mortality occurred in 57.5% (244). In comparing unadjusted mortality prevalence, early antimalarial treated cases yielded 55.1% mortality versus 77.1% mortality for those untreated (p = 0.005). Multivariable analysis demonstrated evidence of reduced aOR for mortality with early oral antimalarial treatment versus non-treatment (aOR = 0.34, 95% Confidence Interval: 0.12, 0.92, p = 0.039). CONCLUSION: Early oral antimalarial treatment in an EVD outbreak was associated with reduced mortality. Further study is warranted to investigate this association between early oral antimalarial treatment and mortality in EVD patients.

The dynamic change of SARS-CoV-2 variants in Sierra Leone.

Since the beginning of the SARS-CoV-2 pandemic, the emergence of multiple new variants posed an increased risk to global public health. The aim of this study is to investigate SARS-CoV-2 variants and possible transmission of variants of concern (VOCs) in Sierra Leone. A total of 65 nasal swab samples were collected from COVID-19 cases in Sierra Leone, among which 24 samples were collected during the second wave and 41 samples were collected during the third wave. Nanopore sequencing generated 54 SARS-CoV-2 whole genomes. The second COVID-19 wave was mainly caused by R.1 lineage while the third COVID-19 wave was dominated by B.1.617.2 lineage (Delta variant). The phylogenetic analysis suggested multiple introductions of SARS-CoV-2 Delta variant into Sierra Leone and subsequent local transmission in this country. Our findings highlight the importance of genomic surveillance of SARS-CoV-2 variants and the urgent need for implementation of strengthened public health and social measures (PHSM) to control the spread of virus variants.

The Establishment and Application of Mobile Electronic Surveillance System for Infectious Diseases with the Help of China - Sierra Leone, 2016-Present.

INTRODUCTION: Infectious disease surveillance has long been a challenge for low-income countries like Sierra Leone. Traditional approaches based on paper and Short Message Service (SMS) were subject to severe delays in obtaining, transmitting, and analyzing information. METHODS: During the China aid operation for fighting Ebola since the end of 2014, a mobile electronic surveillance system for infectious diseases (MESSID) was developed in collaboration with the Republic of Sierra Leone Armed Forces (RSLAF), which comprised an Android-based reporting system and a complementary web-based program designed by Active Server Page.NET (ASP.NET) with the main functions including surveillance, real-time reporting, and risk assessment of infectious diseases. RESULTS: MESSID was successfully registered in June 2016 and had been used by all medical and health institutions in RSLAF. From June 1, 2016 to July 5, 2021, 34,419 cases were diagnosed with 47 infectious diseases of 5 categories, with a total of 42 clinical symptoms. Compared to traditional approaches based on paper and SMS, the MESSID showed flexibility, high efficiency, convenience, and acceptability. DISCUSSION: MESSID is an accessible tool for surveillance of infectious diseases in Sierra Leone and possibly in other African countries with similar needs, capable of improving timeliness of disease reporting, thus rendering a timely outbreak detection and response.