Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.

We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause of the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomic surveillance.

Predictors of neonatal mortality among neonates admitted to the neonatal intensive care unit at Hawassa University Comprehensive Specialized Hospital, Sidama regional state, Ethiopia.

BACKGROUND: Despite promising efforts, substantial deaths occurred during the neonatal period. According to estimates from the World Health Organization (WHO), Ethiopia is among the top 10 nations with the highest number of neonatal deaths in 2020 alone. This staggering amount makes it difficult to achieve the SDG (Sustainable Development Goals) target that calls for all nations to work hard to meet a neonatal mortality rate target of ≤ 12 deaths per 1,000 live births by 2030. We evaluated neonatal mortality and it's contributing factors among newborns admitted to the Neonatal Intensive Care Unit (NICU) at Hawassa University Comprehensive Specialized Hospital (HUCSH). METHODS: A hospital-based retrospective cross-sectional study on neonates admitted to the NICU from May 2021 to April 2022 was carried out at Hawassa University Comprehensive Specialized Hospital. From the admitted 1044 cases over the study period, 225 babies were sampled using a systematic random sampling procedure. The relationship between variables was determined using bivariate and multivariable analyses, and statistically significant relations were indicated at p-values less than 0.05. RESULTS: The magnitude of neonatal death was 14.2% (95% CI: 0.099-0.195). The most common causes of neonatal death were prematurity 14 (43.8%), sepsis 9 (28.1%), Perinatal asphyxia 6 (18.8%), and congenital malformations 3 (9.4%). The overall neonatal mortality rate was 28 per 1000 neonate days. Neonates who had birth asphyxia were 7.28 times more probable (AOR = 7.28; 95% CI: 2.367, 9.02) to die. Newborns who encountered infection within the NICU were 8.17 times more likely (AOR = 8.17; 95% CI: 1.84, 36.23) to die. CONCLUSION: The prevalence of newborn death is excessively high. The most common causes of mortality identified were prematurity, sepsis, perinatal asphyxia and congenital anomalies. To avert these causes, we demand that antenatal care services be implemented appropriately, delivery care quality be improved, and appropriate neonatal care and treatment be made available.

Building Integrated Testing Programs for Infectious Diseases.

In the past 2 decades, testing services for diseases such as human immunodeficiency virus (HIV), tuberculosis, and malaria have expanded dramatically. Investments in testing capacity and supportive health systems have often been disease specific, resulting in siloed testing programs with suboptimal capacity, reduced efficiency, and limited ability to introduce additional tests or respond to new outbreaks. Emergency demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing overcame these silos and demonstrated the feasibility of integrated testing. Moving forward, an integrated public laboratory infrastructure that services multiple diseases, including SARS-CoV-2, influenza, HIV, tuberculosis, hepatitis, malaria, sexually transmitted diseases, and other infections, will help improve universal healthcare delivery and pandemic preparedness. However, integrated testing faces many barriers including poorly aligned health systems, funding, and policies. Strategies to overcome these include greater implementation of policies that support multidisease testing and treatment systems, diagnostic network optimization, bundled test procurement, and more rapid spread of innovation and best practices across disease programs.

Examining 7 years of implementing quality management systems in medical laboratories in sub-Saharan Africa.

BACKGROUND: Achievement of ISO15189 accreditation demonstrates competency of a laboratory to conduct testing. Three programmes were developed to facilitate achievement of accreditation in low- and middle-income countries: Strengthening Laboratory Management Towards Accreditation (SLMTA), Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA) and Laboratory Quality Stepwise Implementation (LQSI). OBJECTIVE: To determine the level of accreditation and associated barriers and facilitators among medical laboratories in the WHO-AFRO region by 2020. METHODS: A desk review of SLIPTA and SLMTA databases was conducted to identify ISO15189-accredited medical laboratories between January 2013 and December 2020. Data on access to the LQSI tool were extracted from the WHO database. Facility and country characteristics were collected for analysis as possible enablers of accreditation. The chi-square test was used to analyse differences with level of significance set at <0.05. RESULTS: A total of 668 laboratories achieved accreditation by 2020 representing a 75% increase from the number in 2013. Accredited laboratories were mainly in South Africa (n = 396; 55%) and Kenya (n = 106; 16%), two countries with national accreditation bodies. About 16.9% (n = 113) of the accredited laboratories were registered for the SLIPTA programme and 26.6% (n = 178) for SLMTA. Approximately 58,217 LQSI users were registered by December 2020. Countries with a higher UHC index for access to HIV care and treatment, higher WHO JEE scores for laboratory networks, a larger number of registered LQSI users, with national laboratory policy/strategic plans and PEPFAR-priority countries were more likely to have an accredited laboratory. Of the 475 laboratories engaged in the SLIPTA programme, 154 attained ≥4 SLIPTA stars (ready to apply for accreditation) and 113 achieved ISO 15189 accreditation, with 96 enrolled into the SLMTA programme. Lower-tier laboratories were less likely to achieve accreditation than higher-tier laboratories (7.7% vs. 30%) (p < 0.001). The probability of achieving ISO 15189 accreditation (19%) was highest during the first 24 months after enrolment into the SLIPTA programme. CONCLUSION: To sustainably anchor quality improvement initiatives at facility level, national approaches including access to a national accreditation authority, adoption of national quality standards and regulatory frameworks are required.

The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study.

BACKGROUND: Although the first wave of the COVID-19 pandemic progressed more slowly in Africa than the rest of the world, by December, 2020, the second wave appeared to be much more aggressive with many more cases. To date, the pandemic situation in all 55 African Union (AU) Member States has not been comprehensively reviewed. We aimed to evaluate reported COVID-19 epidemiology data to better understand the pandemic's progression in Africa. METHODS: We did a cross-sectional analysis between Feb 14 and Dec 31, 2020, using COVID-19 epidemiological, testing, and mitigation strategy data reported by AU Member States to assess trends and identify the response and mitigation efforts at the country, regional, and continent levels. We did descriptive analyses on the variables of interest including cumulative and weekly incidence rates, case fatality ratios (CFRs), tests per case ratios, growth rates, and public health and social measures in place. FINDINGS: As of Dec 31, 2020, African countries had reported 2 763 421 COVID-19 cases and 65 602 deaths, accounting for 3·4% of the 82 312 150 cases and 3·6% of the 1 798 994 deaths reported globally. Nine of the 55 countries accounted for more than 82·6% (2 283 613) of reported cases. 18 countries reported CFRs greater than the global CFR (2·2%). 17 countries reported test per case ratios less than the recommended ten to 30 tests per case ratio range. At the peak of the first wave in Africa in July, 2020, the mean daily number of new cases was 18 273. As of Dec 31, 2020, 40 (73%) countries had experienced or were experiencing their second wave of cases with the continent reporting a mean of 23 790 daily new cases for epidemiological week 53. 48 (96%) of 50 Member States had five or more stringent public health and social measures in place by April 15, 2020, but this number had decreased to 36 (72%) as of Dec 31, 2020, despite an increase in cases in the preceding month. INTERPRETATION: Our analysis showed that the African continent had a more severe second wave of the COVID-19 pandemic than the first, and highlights the importance of examining multiple epidemiological variables down to the regional and country levels over time. These country-specific and regional results informed the implementation of continent-wide initiatives and supported equitable distribution of supplies and technical assistance. Monitoring and analysis of these data over time are essential for continued situational awareness, especially as Member States attempt to balance controlling COVID-19 transmission with ensuring stable economies and livelihoods. FUNDING: None.

Role of public-private partnerships in achieving UNAIDS HIV treatment targets.

BACKGROUND: Despite progress towards achieving UNAIDS 90-90-90 goals, barriers persist in laboratory systems in sub-Saharan Africa (SSA) restricting scale up of early infant diagnosis (EID) and viral load (VL) test monitoring of patients on antiretroviral therapy. If these facilities and system challenges persist, they may undermine recorded gains and appropriate management of patients. The aim of this review is to identify Public Private Partnerships (PPP) in SSA that have resolved systemic barriers within the VL and EID treatment cascade and demonstrated impact in the scale up of VL and EID. METHODS: We queried five HIV and TB laboratory databases from 2007 to 2017 for studies related to laboratory system strengthening and PPP. We identified, screened and included PPPs that demonstrated evidence in alleviating known system level barriers to scale up national VL and EID testing programs. PPPs that improved associated systems from the point of viral load test request to the use of the test result for patient management were deemed eligible. RESULTS: We identified six PPPs collaborations with multiple activities in select countries that are contributing to address challenges to scale up national viral load programs. One of the six PPPs reached 14.5 million patients in remote communities and transported up to 400,000 specimens in a year. Another PPP enabled an unprecedented 94% of specimens to reach national laboratory through improved sample referral network and enabled a cost savings of 62%. Also PPPs reduced cost of reagents and enabled 300,000 tested infants to be enrolled in care as well as reduced turnaround time of reporting results by 50%. CONCLUSIONS: Our review identified the benefits, enabling factors, and associated challenges for public and private sectors to engage in PPPs. PPP contributions to laboratory systems strengthening are a model and present opportunities that can be leveraged to strengthen systems to achieve the UNAIDS 90-90-90 treatment targets for HIV/AIDS. Despite growing emphasis on engaging the private sector as a critical partner to address global disease burden, PPPs that specifically strengthen laboratories, the cornerstone of public health programs, remain largely untapped.

Combatting Global Infectious Diseases: A Network Effect of Specimen Referral Systems.

The recent Ebola virus outbreak in West Africa clearly demonstrated the critical role of laboratory systems and networks in responding to epidemics. Because of the huge challenges in establishing functional laboratories at all tiers of health systems in developing countries, strengthening specimen referral networks is critical. In this review article, we propose a platform strategy for developing specimen referral networks based on 2 models: centralized and decentralized laboratory specimen referral networks. These models have been shown to be effective in patient management in programs in resource-limited settings. Both models lead to reduced turnaround time and retain flexibility for integrating different specimen types. In Haiti, decentralized specimen referral systems resulted in a 182% increase in patients enrolling in human immunodeficiency virus treatment programs within 6 months. In Uganda, cost savings of up to 62% were observed with a centralized model. A platform strategy will create a network effect that will benefit multiple disease programs.

Improved Specimen-Referral System and Increased Access to Quality Laboratory Services in Ethiopia: The Role of the Public-Private Partnership.

BACKGROUND: Nonstandardized specimen-transport logistics, lack of laboratory personnel to transport specimens, lack of standard specimen containers, and long turnaround time (TAT) hindered access to quality laboratory services. The objective of the Becton, Dickinson, and Company (BD)-US President's Emergency Plan for AIDS Relief (PEPFAR) Public-Private Partnership (PPP) was to support country-specific programs to develop integrated laboratory systems, services, and quality improvement strategies, with an emphasis on strengthening the specimen-referral system (SRS). METHODS: In 2007, through the Centers for Disease Control and Prevention (CDC), the Ethiopian Public Health Institute (EPHI) joined with the BD-PEPFAR PPP to strengthen laboratory systems. A joint planning and assessment committee identified gaps in the SRS for prioritization and intervention and piloted the system in Addis Ababa and Amhara Region. RESULTS: The PPP established standardized, streamlined specimen logistics, using the Ethiopian Postal Service Enterprise to support a laboratory network in which 554 facilities referred specimens to 160 laboratories. The PPP supported procuring 400 standard specimen containers and the training of 586 laboratory personnel and 81 postal workers. The average TAT was reduced from 7 days (range, 2-14 days) to 2 days (range, 1-3 days) in Addis Ababa and from 10 days (range, 6-21 days) to 5 days (range, 2-6 days) in Amhara Region. CONCLUSIONS: This study highlights the feasibility and untapped potential of PPPs to strengthen laboratory systems. This planned and structured approach to improving specimen referral enhanced access to quality laboratory services.

Boosting pathogen genomics and bioinformatics workforce in Africa.

Next-generation sequencing (NGS) of genomic data has established its fundamental value in public health surveillance, research and development, and precision medicine. In Africa, severe shortages of competent experts in genomics and bioinformatics, few opportunities for research, and inadequate genomic infrastructure have had a knock-on effect on the use of NGS technologies for research and public health practice. Several reasons-ranging from poor funding, inadequate infrastructure for training and practice, to brain drain-might partly account for the scarcity of genomics and bioinformatics expertise in the region. In recognition of these shortcomings and the importance of NGS genomic data, which was amplified during the COVID-19 pandemic in mid-2021, the Africa Centres for Disease Control and Prevention (Africa CDC) through the Africa Pathogen Genomics Initiative began building and expanding Africa's workforce in pathogen surveillance. By the end of 2022, the Africa CDC in collaboration with its partners and centres of excellence had trained 413 personnel, mostly from public health institutions, in 53 (96%) of 55 African Union Member States. Although this training has increased genomics, bioinformatics, and genomic epidemiology literacy, and genomic-informed pathogen surveillance, there is still a need for a strategic and sustainable public health workforce development in Africa.

The Looming Threat of Dengue Fever: The Africa Context.

In Africa, compared to 2019, dengue infections have surged ninefold by December 2023, with over 270 000 cases and 753 deaths reported across 18 African Union (AU) Member States. This commentary synthesises the context of dengue outbreaks in Africa and provides recommendations for sustainable control. In 2023, 18 African Union Member States reported outbreaks of dengue, among which seven had ongoing armed conflicts. These countries were amongst the top 15 African countries contributing to the most displaced persons on the continent and accounted for 98% of all dengue cases reported in the continent in 2023. Climate change remains an important driver, both through the displacement of people and global warming. The continent continues to face several challenges in detection, reporting and management, such as the lack of local laboratory capacity, misclassification of dengue cases and lack of medical countermeasures. Solutions targeting the strengthening of cross-border surveillance and early warning systems using a multisectoral one-health approach, local research and development for therapeutics and diagnostics and community engagement empowering communities to protect themselves and understand the gravity of the threat could help curb the spread of the disease in Africa.

Establishing an early warning event management system at Africa CDC.

Africa is home to hotspots of disease emergence and re-emergence. To adequately detect and respond to these health threats, early warning systems inclusive of event-based surveillance (EBS) are needed. However, data systems to manage these events are not readily available. In 2020, Africa Centres for Disease Control and Prevention developed an event management system (EMS) to meet this need. The district health information software (DHIS2), which is free and open-source software was identified as the platform for the EMS because it can support data capture and analysis and monitor and report events. The EMS was created through a collaborative and iterative prototyping process that included modifying key DHIS2 applications like Tracker Capture. Africa CDC started piloting the EMS with both signal and event data entry in June 2020. By December 2022, 416 events were captured and over 140 weekly reports, including 19 COVID-19 specific reports, were generated and distributed to inform continental awareness and response efforts. Most events detected directly impacted humans (69%), were considered moderate (50%) to high (29%) risk level and reflected both emerging and endemic infectious disease outbreaks. Highly pathogenic avian influenza, specifically H5N1, was the most frequently detected animal event and storms and flooding were most frequently detected environmental events. Both data completeness and timeliness improved over time. Country-level interest and utility resulted in four African countries adapting the EMS in 2022 and two more in 2023. This system demonstrates how integrating digital technology into health systems and utilising existing digital platforms like DHIS2 can improve early warning at the continental and country level by improving EBS workflow.

Preservice laboratory education strengthening enhances sustainable laboratory workforce in Ethiopia.

BACKGROUND: There is a severe healthcare workforce shortage in sub Saharan Africa, which threatens achieving the Millennium Development Goals and attaining an AIDS-free generation. The strength of a healthcare system depends on the skills, competencies, values and availability of its workforce. A well-trained and competent laboratory technologist ensures accurate and reliable results for use in prevention, diagnosis, care and treatment of diseases. METHODS: An assessment of existing preservice education of five medical laboratory schools, followed by remedial intervention and monitoring was conducted. The remedial interventions included 1) standardizing curriculum and implementation; 2) training faculty staff on pedagogical methods and quality management systems; 3) providing teaching materials; and 4) procuring equipment for teaching laboratories to provide practical skills to complement didactic education. RESULTS: A total of 2,230 undergraduate students from the five universities benefitted from the standardized curriculum. University of Gondar accounted for 252 of 2,230 (11.3%) of the students, Addis Ababa University for 663 (29.7%), Jimma University for 649 (29.1%), Haramaya University for 429 (19.2%) and Hawassa University for 237 (10.6%) of the students. Together the universities graduated 388 and 312 laboratory technologists in 2010/2011 and 2011/2012 academic year, respectively. Practical hands-on training and experience with well-equipped laboratories enhanced and ensured skilled, confident and competent laboratory technologists upon graduation. CONCLUSIONS: Strengthening preservice laboratory education is feasible in resource-limited settings, and emphasizing its merits (ample local capacity, country ownership and sustainability) provides a valuable source of competent laboratory technologists to relieve an overstretched healthcare system.

Africa CDC's blueprint to enhance early warning surveillance: accelerating implementation of event-based surveillance in Africa.

Event-based surveillance (EBS) is a core component of early warning surveillance. In 2018, Africa CDC developed the first edition of an event-based surveillance framework to guide African Union Member States in implementing EBS. Country experiences during the COVID-19 pandemic demonstrated the value of data from non-traditional sources for real time situational awareness; at the same time revealed the huge gaps in strengthening this arm of surveillance. Learning from these lessons and to begin to close those gaps, Africa CDC convened subject matter experts from African Union Member States and technical partners to develop the second edition of the EBS framework, 2023 and its training materials. The revised version includes additional sections such as, the multi-sectoral one health collaboration in EBS, monitoring and evaluation, cross border EBS, and use of event management systems. The current manuscript provides an overview of the 2023 Africa CDC EBS framework and highlights experience in two countries that have successfully employed this resource in their implementation efforts.

Evaluating event-based surveillance capacity in Africa: Use of the Africa CDC scorecard, 2022-2023.

Introduction: Event-based surveillance (EBS) is a critical component of Early Warning, Alert and Response (EWAR) capacity needed for outbreak prevention and control. To better understand existing EBS and monitor the progress of capacity-building efforts over time, Africa CDC developed an EBS scorecard as part of a revision to the EBS Framework. Methods: We distributed the scorecard to African Union (AU) Member States (MSs). Survey responses from the MSs' human health sector were aggregated, cleaned, and analysed. MS, regional, and continental EBS capacity was assessed. Results: Between 21 July 2022 and 4 April 2023, a total of 63 respondents representing 49 (89%) of 55 MSs completed the survey. Given Africa CDC's public health mandate, we acknowledged the importance of One Health collaboration in MSs but focused on and analysed only the human health sector responses. Thirty-four (71%) MSs stated having EBS in place; hotline was the most common type of EBS implemented (76%). Seventeen (50%) MSs reported multisectoral, One Health collaboration as part of EBS implementation. Scorecard outcomes showed a minimal (score of <60%) to average (score between 60-80%) level of EBS capacity in 29 and five (5) MSs respectively. Discussion: Current EBS capacity levels need to be strengthened in Africa to ensure the continent remains prepared for future public health threats. The Africa CDC EBS scorecard provides a useful way to measure and track this capacity over time. Results can be used to advocate for and target resources for capacity building to foster public health emergency preparedness efforts.

Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance.

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola. Methods: We generated 1210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction. Results: The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South-Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa. Conclusion: A lack of a robust genome surveillance network and strong dependence on out-of-country sequencing limit real-time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola.

Implementation of COVID-19 Laboratory Testing Certification Program (CoLTeP) in African Region.

Objectives: Coronavirus disease 2019 was declared a global pandemic in March 2020 with correct and early detection of cases using laboratory testing central to the response. Hence, the establishment of quality management systems and monitoring their implementation are critical. This study describes the experience of implementing the COVID-19 Laboratory Testing and Certification Program (CoLTeP) in Africa. Methods: Private and public laboratories conducting SARS-CoV-2 testing using polymerase chain reaction were enrolled and assessed for quality and safety using the CoLTeP checklists. Results: A total of 84 laboratories from 7 countries were assessed between April 2021 to December 2021 with 52% of these from the private sector. Among them, 64% attained 5 stars and were certified. Section 4 had the highest average score of 92% and the lowest of 78% in Section 3. Also, 82% of non-conformities (NCs) were related to sample collection, transportation, and risk assessments. Non-availability, inconsistency in performing, recording, instituting corrective actions for failed internal and external quality controls were among major NCs reported. Conclusions: Laboratories identified for SARS-CoV-2 testing by public and private institutions mostly met the requirements for quality and safe testing as measured by the CoLTeP checklist.

Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia: Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up.

Background: Ethiopia is one of the sub-Saharan countries hit hard by the HIV epidemic. Previous studies have shown that subtype C dominates the Ethiopian HIV-1 epidemic, but the evolutionary and temporal dynamics of HIV-1 in Ethiopia have not been closely scrutinized. Understanding the evolutionary and epidemiological pattern of HIV is vital to monitor the spread, evaluate and implement HIV prevention strategies. Methods: We analyzed 1,276 Ethiopian HIV-1 subtype C polymerase (pol sequences), including 144 newly generated sequences, collected from different parts of the country from 1986 to 2017. We employed state-of-art maximum likelihood and Bayesian phylodynamic analyses to comprehensively describe the evolutionary dynamics of the HIV-1 epidemic in Ethiopia. We used Bayesian phylodynamic models to estimate the dynamics of the effective population size (Ne) and reproductive numbers (Re) through time for the HIV epidemic in Ethiopia. Results: Our analysis revealed that the Ethiopian HIV-1 epidemic originated from two independent introductions at the beginning of the 1970s and 1980s from eastern and southern African countries, respectively, followed by epidemic growth reaching its maximum in the early 1990s. We identified three large clusters with a majority of Ethiopian sequences. Phylodynamic analyses revealed that all three clusters were characterized by high transmission rates during the early epidemic, followed by a decline in HIV-1 transmissions after 1990. Re was high (4-6) during the earlier time of the epidemic but dropped significantly and remained low (Re < 1) after the mid-1990. Similarly, with an expected shift in time, the effective population size (Ne) steadily increased until the beginning of 2000, followed by a decline and stabilization until recent years. The phylodynamic analyses corroborated the modeled UNAIDS incidence and prevalence estimates. Conclusion: The rapid decline in the HIV epidemic took place a decade before introducing antiretroviral therapy in Ethiopia and coincided with early behavioral, preventive, and awareness interventions implemented in the country. Our findings highlight the importance of behavioral interventions and antiretroviral therapy scale-up to halt and maintain HIV transmissions at low levels (Re < 1). The phylodynamic analyses provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.

High Level of HIV Drug Resistance and Virologic Nonsuppression Among Female Sex Workers in Ethiopia: A Nationwide Cross-Sectional Study.

OBJECTIVE: To determine viral load (VL) nonsuppression (VLN) rates, HIV drug resistance (HIVDR) prevalence, and associated factors among female sex workers (FSWs) in Ethiopia. METHODS: A cross-sectional biobehavioral survey was conducted among FSWs in 11 cities in Ethiopia in 2014. Whole blood was collected, and HIVDR genotyping was performed. Logistic regression analysis was performed to identify factors associated with VLN and HIVDR. RESULTS: Among 4900 participants, 1172 (23.9%) were HIV-positive and 1154 (98.5%) had a VL result. Participants were categorized into antiretroviral therapy (ART) (n = 239) and ART-naive (n = 915) groups based on self-report. From the 521 specimens (ART, 59; ART-naive, 462) with VL ≥1000 copies/mL, genotyping was successful for 420 (80.6%) and 92 (21.9%) had drug resistance mutations (DRMs). Pretreatment drug resistance (PDR) was detected in 16.5% (63/381) of the ART-naive participants. Nucleoside reverse transcriptase inhibitor (NRTI), non-NRTIs (NNRTIs), and dual-class DRMs were detected in 40 (10.5%), 55 (14.4%), and 35 (9.2%) of the participants, respectively. Among 239 participants on ART, 59 (24.7%) had VLN. Genotyping was successfully performed for 39 (66.1%). DRMs were detected in 29 (74.4%). All 29 had NNRTI, 23 (79.3%) had NRTI or dual-class DRMs. VLN was associated with age 35 years or older, CD4+ T-cell count <350 cells/mm3, and being forced into selling sex. PDR and acquired drug resistance were associated with CD4+ T-cell count <350 cells/mm3 (P < 0.001). CONCLUSIONS: The high VLN and HIVDR rates among FSWs underscore the need for targeted interventions to improve ART access and virologic monitoring to maximize the benefit of ART and limit the spread of HIV and HIVDR.

Genomic-informed pathogen surveillance in Africa: opportunities and challenges.

The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics.

Frequency of isolation and antimicrobial susceptibility pattern of bacterial isolates from blood culture, Gondar University teaching hospital, Northwest Ethiopia.

BACKGROUND: Bacterial bloodstream infections cause substantial morbidity and mortality, with up to one-quarter of affected patients dying as a result of their infection. Up-to-date information on blood culture isolates and their antimicrobial susceptibility pattern is very important as guide for immediate prescription of antimicrobial agents and monitoring of emergence of drug resistant strains. OBJECTIVE: To determine the frequency of blood culture isolation and antimicrobial susceptibility pattern of isolates in Gondar University teaching hospital. METHODS: This was retrospective analysis of records of blood culture results for febrile patients seen at Gondar University teaching hospital, bacteriology section from March 2001 to April 2005. RESULTS: During the four years period, blood cultures were done for a total of 472 febrile patients. Among these, 233 (49.4%) were females and 239 (50.6%) were males. The median age was 20.5 years (age range of 2 hours to 78 years). Out of these, total of 114 bacterial strains were isolated with culture positivity rate of 24.2%. Coagulase-negative Staphylococci (CoNS) were isolated with the highest frequency in 38 (33.3%), followed by Staphylococcus aureus in 34 (29.8%), Salmonella species other than Salmonella typhi in 12 (10.5%), Klebsiella species in 10 (8.8%), Streptococcus pneumoniae in 6 (5.3%), Salmonella typhi in 4 (3.5%), Enterobacter species in 3 (2.6%), Escherichia coli in 2 (1.7%). The gram positive and gram negative bacteria constituted 80 (70.2%) and 34 (29.8%) of the culture isolates, respectively. Culture positivity rates vary as for neonates, 63% (17 out of 27);followed by 25.6% (36 out of 141) in children and 20% (61 out of 304) in adults. The isolates especially gram negative bacteria showed multiple drug resistance, to Ampicillin and penicillin. However, ciprofloxacin is fairly effective against both gram negative and gram positive isolates. CONCLUSION: An effective documented data may serve as a guide for initial empirical treatment of bloodstream infections but in view of these findings the presented data is only imperative to do large-scale prospective and quantitative studies. More importantly, an ongoing surveillance for antimicrobial susceptibility is of the essence to enhance efforts to identify resistance and attempt to limit its spread.