Malaria diagnostic testing in Africa is threatened by Plasmodium falciparum parasites lacking histidine-rich protein 2 (pfhrp2) and 3 (pfhrp3) genes. Among 12,572 subjects enrolled along Ethiopia’s borders with Eritrea, Sudan, and South Sudan and using multiple assays, we estimate HRP2-based rapid diagnostic tests would miss 9.7% (95% CI 8.5-11.1) of falciparum malaria cases due to pfhrp2 deletion. Established and novel genomic tools reveal distinct subtelomeric deletion patterns, well-established pfhrp3 deletions, and recent expansion of pfhrp2 deletion. Current diagnostic strategies need to be urgently reconsidered in Ethiopia, and expanded surveillance is needed throughout the Horn of Africa.Competing Interest StatementJBP reports research support from Gilead Sciences, honoraria from Virology Education for medical education teaching, and non-financial support from Abbott Diagnostics, all outside the scope of the current work. SMF reports research support from AccessBio, outside of the current work.Funding StatementThis work was funded by the Global Fund to Fight AIDS, Tuberculosis, and Malaria through the Ministry of Health-Ethiopia (EPHI5405 to SMF) and the World Health Organization (JAC, JBP). It was also partially supported by MSF Holland, which supported field work in Gambella Region, the Doris Duke Charitable Foundation (JBP), and the US National Institutes of Health (R01AI132547 to JJJ, JAB, OA, and JBP; K24AI134990 to JJJ).Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:Ethical approval was obtained from the Ethiopia Public Health Institute (EPHI) Institutional Review Board (IRB; protocol EPHI-IRB-033-2017) and WHO Research Ethics Review Committee (protocol: ERC.0003174 001). Processing of de-identified samples and data at UNC was determined to constitute non-human subjects research by the UNC IRB (study 17-0155). The study was determined to be non-research by the Centers for Disease Control and Prevention Human Subjects office (0900f3eb81bb60b9).All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesGenomic sequencing data will be available through the Sequence Read Archive (BioSample accession numbers pending). De-identified datasets generated during the current study will be available as supplementary files. Code used during data analysis will be made available on GitHub.

SETTING: Sixty-seven government health facilities providing tuberculosis (TB) and human immunodeficiency virus (HIV) services across Ethiopia. OBJECTIVE: To examine clinician barriers to implementing isoniazid preventive therapy (IPT) among people living with HIV. DESIGN: A cross-sectional study to evaluate the provider-related factors associated with high IPT coverage at the facility level. RESULTS: On bivariate analysis, the odds of high IPT implementation were lower when clinicians felt patients were negatively affected by the side effects of IPT (OR 0.18, 95%CI 0.04-0.81) and perceived that IPT increased multidrug-resistant TB (MDR-TB) rates (OR 0.66, 95%CI 0.44-0.98). The presence of IPT guidelines on site (OR 2.93, 95%CI 1.10-7.77) and TB-HIV training (OR 3.08, 95%CI 1.11-8.53) had a positive relationship with high IPT uptake. In the multivariate model, clinician's perception that active TB was difficult to rule out had a negative association with a high IPT rate (OR 0.93; 95%CI 0.90-0.95). CONCLUSIONS: Clinician impression that ruling out active TB among HIV patients is difficult was found to be a significant barrier to IPT uptake. Continued advancement of IPT relies greatly on improving the ability of providers to determine IPT eligibility and more confidently care for patients on IPT. Improved clinician support and training as well as development of new TB diagnostic technologies could impact IPT utilization among providers.

The coronavirus disease pandemic has highlighted the need to establish and maintain strong infection prevention and control (IPC) practices, not only to prevent healthcare-associated transmission of SARS-CoV-2 to healthcare workers and patients but also to prevent disruptions of essential healthcare services. In East Africa, where basic IPC capacity in healthcare facilities is limited, the US Centers for Disease Control and Prevention (CDC) supported rapid IPC capacity building in healthcare facilities in 4 target countries: Tanzania, Ethiopia, Kenya, and Uganda. CDC supported IPC capacity-building initiatives at the healthcare facility and national levels according to each country's specific needs, priorities, available resources, and existing IPC capacity and systems. In addition, CDC established a multicountry learning network to strengthen hospital level IPC, with an emphasis on peer-to-peer learning. We present an overview of the key strategies used to strengthen IPC in these countries and lessons learned from implementation.

BACKGROUND: Prisoners generally have a higher prevalence of HIV infection compared to the general population from which they come. Whether this higher prevalence reflects a higher HIV prevalence in those entering prisons or intramural transmission of HIV within prisons or both is unclear. Any of these possibilities would increase the prevalence found in resident prisoners above that in the general population. Moreover, comparisons of HIV prevalence in entrants and residents and in men and women in African prisons are not well documented. The purpose of this study was to estimate and compare the prevalence and risk factors for HIV infection amongst both male as well as female and entrant and resident prisoners in a large Ethiopian Federal Prison. METHODS: We studied consenting prisoners cross-sectionally from August 2014 through November 2016. Prison entrants were screened continuously for HIV infection and its associated risk factors and residents were screened in two waves one year apart. HIV was diagnosed at the prison hospital laboratory based on the Ethiopian national HIV rapid antibody testing protocol. An external, internationally-accredited reference laboratory confirmed results. Agreement of results between the laboratories were assessed. RESULTS: A total of 10,778 participants were screened for HIV. Most participants were young (median age of 26 years, IQR: 21-33), male (84%), single (61%), literate (89%), and urban residents (91%) without prior incarceration (96%). Prevalence of HIV was 3.4% overall. Rates of HIV (p = 0.80) were similar in residents and entrants in wave 1 and in entrants in both waves, but were 1.9-fold higher (5.4% vs 2.8%) in residents than entrants in wave 2 (both p<0.001). At entrance to the prison women were more likely to be HIV+ than men (5.5% in women vs 2.5% in men, p< 0.001). In contrast resident women were less likely to be HIV+, but this difference was not statistically significant (3.2% in women vs 4.3% in men, p = 0.125). Other risk factors associated with HIV infection were increasing age (p<0.001), female gender (p<0.001), marital status (never vs other categories, p = 0.016), smaller number of rooms in their houses pre-imprisonment (p = 0.031), TB diagnosis ever (p<0.001), number of lifetime sex partners (especially having 2-10, p<0.001), and genital ulcer (p = 0.037). CONCLUSIONS: Prevalence of HIV in the residents at this large, central Ethiopian prison was higher than that estimated for the general population and lower than in many other studies from other smaller Ethiopian prisons. A higher prevalence in residents than in entrants were found only in our second wave of screening after one year of continuous screening and treatment, possibly representing increased willingness of residents at increased risk of HIV to participate in the second wave. Thus, this findings did not clearly support intramural transmission of HIV or the effectiveness of screening to reduce prevalence. Finally, the higher HIV prevalence in women than men requires that they be similarly screened and treated for HIV infection.

In Africa, most rapid diagnostic tests (RDTs) for falciparum malaria recognize histidine-rich protein 2 antigen. Plasmodium falciparum parasites lacking histidine-rich protein 2 (pfhrp2) and 3 (pfhrp3) genes escape detection by these RDTs, but it is not known whether these deletions confer sufficient selective advantage to drive rapid population expansion. By studying blood samples from a cohort of 12,572 participants enroled in a prospective, cross-sectional survey along Ethiopia's borders with Eritrea, Sudan and South Sudan using RDTs, PCR, an ultrasensitive bead-based immunoassay for antigen detection and next-generation sequencing, we estimate that histidine-rich protein 2-based RDTs would miss 9.7% (95% confidence interval 8.5-11.1) of P. falciparum malaria cases owing to pfhrp2 deletion. We applied a molecular inversion probe-targeted deep sequencing approach to identify distinct subtelomeric deletion patterns and well-established pfhrp3 deletions and to uncover recent expansion of a singular pfhrp2 deletion in all regions sampled. We propose a model in which pfhrp3 deletions have arisen independently multiple times, followed by strong positive selection for pfhrp2 deletion owing to RDT-based test-and-treatment. Existing diagnostic strategies need to be urgently reconsidered in Ethiopia, and improved surveillance for pfhrp2 deletion is needed throughout the Horn of Africa.

BACKGROUND: Pulmonary Tuberculosis (PTB) is a major health problem in prisons. Multiple studies of TB in regional Ethiopian prisons have assessed prevalence and risk factors but have not examined recently implemented screening programs for TB in prisons. This study compares bacteriologically-confirmed PTB (BC-PTB) prevalence in prison entrants versus residents and identifies risk factors for PTB in Kality prison, a large federal Ethiopian prison located in Addis Ababa, through a study of an enhanced TB screening program. METHODS: Participating prisoners (n = 13,803) consisted of 8,228 entrants screened continuously and 5,575 residents screened in two cross-sectional waves for PTB symptoms, demographics, TB risk factors, and medical history. Participants reporting at least one symptom of PTB were asked to produce sputum which was examined by microscopy for acid-fast bacilli, Xpert MTB/RIF assay and MGIT liquid culture. Prevalence of BC-PTB, defined as evidence of Mycobacterium tuberculosis (MTB) in sputum by the above methods, was compared in entrants and residents for the study. Descriptive analysis of prevalence was followed by bivariate and multivariate analyses of risk factors. RESULTS: Prisoners were mainly male (86%), young (median age 26 years) and literate (89%). Prevalence of TB symptoms by screening was 17% (2,334/13,803) with rates in residents >5-fold higher than entrants. Prevalence of BC-PTB detected by screening in participating prisoners was 0.16% (22/13,803). Prevalence in residents increased in the second resident screening compared to the first (R1 = 0.10% and R2 = 0.39%, p = 0.027), but remained higher than in entrants (4.3-fold higher during R1 and 3.1-fold higher during R2). Drug resistance (DR) was found in 38% (5/13) of culture-isolated MTB. Risk factors including being ever diagnosed with TB, history of TB contact and low Body Mass Index (BMI) (<18.5) were significantly associated with BC-PTB (p<0.05). CONCLUSIONS: BC-PTB prevalence was strikingly lower than previously reported from other Ethiopian prisons. PTB appears to be transmitted within this prison based on its higher prevalence in residents than in entrants. Whether a sustained program of PTB screening of entrants and/or residents reduces prevalence of PTB in prisons is not clear from this study, but our findings suggest that resources should be prioritized to resident, rather than entrant, screening due to higher BC-PTB prevalence. Detection of multi- and mono-DR TB in both entrant and resident prisoners warrants regular screening for active TB and adoption of methods to detect drug resistance.

BACKGROUND: Malaria remains a very important public health problem in Ethiopia. Currently, only Plasmodium falciparum and Plasmodium vivax are considered in the malaria diagnostic and treatment policies. However, the existence and prevalence of Plasmodium ovale spp. and Plasmodium malariae in Ethiopia have not been extensively investigated. The objective of this study was to use a multiplex IgG antibody detection assay to evaluate evidence for exposure to any of these four human malaria parasites among asymptomatic individuals. METHODS: Dried blood spots (DBS) were collected from 180 healthy study participants during a 2016 onchocerciasis survey in the Jimma Zone, southwest Ethiopia. IgG antibody reactivity was detected using a multiplex bead assay for seven Plasmodium antigens: P. falciparum circumsporozoite protein (CSP), P. falciparum apical membrane antigen-1 (AMA1), P. falciparum liver stage antigen-1 (LSA1), and homologs of the merozoite surface protein-1 (MSP1)-19kD antigens that are specific for P. falciparum, P. vivax, P. ovale spp. and P. malariae. RESULTS: One hundred six participants (59%) were IgG seropositive for at least one of the Plasmodium antigens tested. The most frequent responses were against P. falciparum AMA1 (59, 33%) and P. vivax (55, 28%). However, IgG antibodies against P. ovale spp. and P. malariae were detected in 19 (11%) and 13 (7%) of the participants, respectively, providing serological evidence that P. malariae and P. ovale spp., which are rarely reported, may also be endemic in Jimma. CONCLUSION: The findings highlight the informative value of multiplex serology and the need to confirm whether P. malariae and P. ovale spp. are aetiologies of malaria in Ethiopia, which is critical for proper diagnosis and treatment.

BACKGROUND: No established strategy for household tuberculosis (TB) contact investigation (HTCI) exists in Ethiopia. We implemented integrated, active HTCI model into two hospitals and surrounding community health services to determine yield of active HTCI of all forms of TB and explore factors associated with active TB diagnosis in household contacts (HHCs). METHODS: Case managers obtained HHC information from index cases at TB/DOTS clinic and liaised with health extension workers (HEWs) who screened HHCs for TB at household and referred contacts under five and presumptive cases for diagnostic investigation. RESULTS: From 363 all forms TB index cases, 1509 (99%) HHCs were screened and 809 (54%) referred, yielding 19 (1.3%) all forms TB cases. HTCI of sputum smear-positive pulmonary TB (SS + PTB) index cases produced yield of 4.3%. HHCs with active TB were more likely to be malnourished (OR: 3.39, 95%CI: 1.19-9.64), live in households with SS + PTB index case (OR: 7.43, 95%CI: 1.64-33.73) or TB history (OR: 4.18, 95%CI: 1.51-11.55). CONCLUSION: Active HTCI of all forms of TB cases produced comparable or higher yield than reported elsewhere. HTCI contributes to improved and timely case detection of Tuberculosis among population who may not seek health care due to minimal symptoms or access issues. Active HTCI can successfully be implemented through integrated approach with existing community TB programs for better coordination and efficiency. Referral criteria should include factors significantly associated with active disease.

Onchocerciasis is a neglected parasitic disease targeted for elimination. Current World Health Organization guidelines for elimination include monitoring antibody responses to the recombinant Onchocerca volvulus antigen OV-16 in children to demonstrate the absence of transmission. We report the performance characteristics of a modified OV-16 enzyme-linked immunosorbent assay (ELISA) and describe anti-OV-16 responses in serum samples from laboratory-inoculated nonhuman primates (NHPs) in relation to microfilariae (mf) in skin snip biopsies. This OV-16 IgG4 ELISA had sensitivity and specificity of 88.2% and 99.7%, respectively, as determined by receiver operator characteristic analysis using a serum panel of 110 positive and 287 negative samples from people infected with other filariae or other parasitic infections. Anti-OV-16 responses in inoculated NHP (N = 9) were evaluated at quarterly intervals for IgM and the four IgG subclasses. Enzyme-linked immunosorbent assay results showed a well-defined IgG4 reactivity pattern and moderate IgG1 antibody responses. Meanwhile, the reactivity by IgG2, IgG3, or IgM did not show a clear pattern. Temporal evolution of IgG4 reactivity was evaluated through monthly testing, showing that NHPs developed anti-OV-16 IgG4 on average at 15 months postinoculation (range: 10-18 months). The average time to detectable mf was also 15 months (range: 11-25). The OV-16 ELISA used in this study was robust and allowed the detection of IgG4 responses, which were observed only among animals with detectable mf (N = 5), four of which showed declines in antibody responses once mf cleared. These findings also confirmed that the most informative antibody subclass responses to OV-16 are IgG4.

Multiplex bead assays (MBAs) may provide a powerful integrated tool for monitoring, evaluation, and post-elimination surveillance of onchocerciasis and co-endemic diseases; however, the specificity and sensitivity of Onchocerca volvulus antigens have not been characterized within this context. An MBA was developed to evaluate three antigens (OV-16, OV-17, and OV-33) for onchocerciasis. Receiver operating characteristics (ROC) analyses were used to characterize antigen performance using a panel of 610 specimens: 109 O. volvulus-positive specimens, 426 non-onchocerciasis controls with filarial and other confirmed parasitic infection, and 75 sera from patients with no other parasitic infection. The IgG and IgG4 assays for OV-16 demonstrated sensitivities of 95.4% and 96.3%, and specificities of 99.4% and 99.8%, respectively. The OV-17 IgG and IgG4 assays had sensitivities of 86.2% and 76.1% and specificities of 79.2% and 82.8%. For OV-33, the IgG and IgG4 assays had sensitivities of 90.8% and 96.3%, and specificities of 96.8% and 98.6%. The OV-16 IgG4-based MBA had the best assay characteristics, followed by OV-33 IgG4. The OV-16 IgG4 assay would be useful for monitoring and evaluation using the MBA platform. Further evaluations are needed to review the potential use of OV-33 as a confirmatory test in the context of program evaluations.

BACKGROUND: IPT with or without concomitant administration of ART is a proven intervention to prevent tuberculosis among PLHIV. However, there are few data on the routine implementation of this intervention and its effectiveness in settings with limited resources. OBJECTIVES: To measure the level of uptake and effectiveness of IPT in reducing tuberculosis incidence in a cohort of PLHIV enrolled into HIV care between 2007 and 2010 in five hospitals in southern Ethiopia. METHODS: A retrospective cohort analysis of electronic patient database was done. The independent effects of no intervention, "IPT-only," "IPT-before-ART," "IPT-and-ART started simultaneously," "ART-only," and "IPT-after-ART" on TB incidence were measured. Cox-proportional hazards regression was used to assess association of treatment categories with TB incidence. RESULTS: Of 7,097 patients, 867 were excluded because they were transferred-in; a further 823 (12%) were excluded from the study because they were either identified to have TB through screening (292 patients) or were on TB treatment (531). Among the remaining 5,407 patients observed, IPT had been initiated for 39% of eligible patients. Children, male sex, advanced disease, and those in Pre-ART were less likely to be initiated on IPT. The overall TB incidence was 2.6 per 100 person-years. As compared to those with no intervention, use of "IPT-only" (aHR = 0.36, 95% CI = 0.19-0.66) and "ART-only" (aHR = 0.32, 95% CI = 0.24-0.43) were associated with significant reduction in TB incidence rate. Combining ART and IPT had a more profound effect. Starting IPT-before-ART (aHR = 0.18, 95% CI = 0.08-0.42) or simultaneously with ART (aHR = 0.20, 95% CI = 0.10-0.42) provided further reduction of TB at approximately 80%. CONCLUSIONS: IPT was found to be effective in reducing TB incidence, independently and with concomitant ART, under programme conditions in resource-limited settings. The level of IPT provision and effectiveness in reducing TB was encouraging in the study setting. Scaling up and strengthening IPT service in addition to ART can have beneficial effect in reducing TB burden among PLHIV in settings with high TB/HIV burden.

In 2008, Ethiopia implemented tuberculosis (TB) treatment registers that included columns for recording human immunodeficiency virus (HIV) test results (integrated registers) to replace the previous system of separate TB and HIV registers (pre-integration registers). We compared the proportion of children with documented HIV rapid test results at eight hospitals before and after adopting the integrated registers. HIV status was more consistently documented in the integrated registers; however, HIV status for infants aged <18 months could not be assessed, as the registers did not capture results from polymerase chain reaction-based testing. Recording procedures should be revised to document age-appropriate HIV diagnostic results and ensure referral for appropriate care.