Risk-adjusted active tuberculosis case finding strategy in central Ethiopia

BACKGROUND: The World Health Organization recommends active case finding for tuberculosis (TB). Our study evaluated the targeted screening of household contacts (HHCs) of patients with contagious pulmonary tuberculosis (PTB) in Central Ethiopia. METHODS: The HHCs of patients with microbiologically confirmed PTB were screened for TB symptoms and risk factors for TB transmission. Symptomatic HHCs were subjected to secondary investigation. Antimicrobial resistance was investigated among study participants. RESULTS: Overall, 112 index patients with TB were included, and 289 HHCs from 89 households were screened. Multidrug-resistant-TB was detected in 2.7% (n=3) of index patients. The routine public health system process did not identify any TB suspects among HHCs. In total, 23.9% (n=69) of HHCs reported ≥1 TB symptom and PTB was confirmed in 2.1% (n=6). Reporting >1 TB symptom (relative risk [RR] 29.4, 95% CI 3.5−245.5, P<0.001) and night sweats (RR 27.1, 95% CI 3.2−226.6, P<0.001) were associated with the greatest relative risk. Regular alcohol consumption was identified as an individual risk factor for TB among HHCs (P=0.022). CONCLUSION: The MDR-TB rate among our patients was higher than recently reported for Ethiopia. Enhanced contact tracing using a risk-adjusted approach seems feasible and increases the case detection rate among HHCs of confirmed TB cases

Prevalence and characterization of antimicrobial resistance among gram-negative bacteria isolated from febrile hospitalized patients in central Ethiopia

BACKGROUND: Infectious diseases are among the leading causes of death in many low-income countries, such as Ethiopia. Without reliable local data concerning causative pathogens and antimicrobial resistance, empiric treatment is suboptimal. The objective of this study was to characterize gram-negative bacteria (GNB) as pathogens and their resistance pattern in hospitalized patients with infections in central Ethiopia. METHODS: Patients ≥ 1 year of age with fever admitted to the Asella Referral and Teaching Hospital from April 2016 to June 2018 were included. Blood and other appropriate clinical specimens were collected and cultured on appropriate media. Antibiotic susceptibility testing (AST) was performed using the Kirby–Bauer method and VITEK® 2. Species identification and detection of resistance genes were conducted using MALDI-ToF MS (VITEK® MS) and PCR, respectively. RESULTS: Among the 684 study participants, 54.2% were male, and the median age was 22.0 (IQR: 14–35) years. Blood cultures were positive in 5.4% (n = 37) of cases. Among other clinical samples, 60.6% (20/33), 20.8% (5/24), and 37.5% (3/8) of swabs/pus, urine and other body fluid cultures, respectively, were positive. Among 66 pathogenic isolates, 57.6% (n = 38) were GNB, 39.4% (n = 26) were gram-positive, and 3.0% (n = 2) were Candida species. Among the isolated GNB, 42.1% (16/38) were Escherichia coli, 23.7% (9/38) Klebsiella pneumoniae and 10.5% (4/38) Pseudomonas aeruginosa. In total, 27/38 gram-negative isolates were available for further analysis. Resistance rates were as follows: ampicillin/sulbactam, 92.6% (n = 25); cefotaxime, 88.9% (n = 24); ceftazidime, 74.1% (n = 20); cefepime, 74.1% (n = 20); gentamicin, 55.6% (n = 15); piperacillin/tazobactam, 48.1% (n = 13); meropenem, 7.4% (n = 2); and amikacin, 3.7% (n = 1). The bla(NDM-1) gene was detected in one K. pneumoniae and one Acinetobacter baumannii isolate, which carried an additional bla(OXA-51) gene. The ESBL enzymes were detected in 81.5% (n = 22) of isolates as follows: TEM, 77.2% (n = 17); CTX-M-1 group, 68.2% (n = 15); SHV group, 27.3% (n = 6); and CTX-M-9 group, 9.1% (n = 2). Based on the in vitro antimicrobial susceptibility results, empiric treatment initiated in 13 of 18 (72.2%) patients was likely ineffective. CONCLUSION: We report a high prevalence of ESBL-producing bacteria (81.5%) and carbapenem resistance (7.4%), with more than half of GNB carrying two or more ESBL enzymes resulting in suboptimal empiric antibiotic therapy. These findings indicate a need for local and national antimicrobial resistance surveillance and the strengthening of antimicrobial stewardship programs

Evidence for Bartonella quintana in Lice Collected from the Clothes of Ethiopian Homeless Individuals

Human lice, Pediculus humanus, can transmit various pathogens, including Bartonella quintana, Borrelia recurrentis, and Rickettsia prowazekii. Xenosurveillance is an epidemiological approach to assessing human infection risks performed by screening vectors of infectious disease agents. In the proof-of-principle study reported herein, the DNA of 23 human lice was collected from the clothes of 30 homeless Ethiopian individuals. These samples were assessed using 16S rRNA gene-specific pan-eubacterial PCR for screening, followed by Bartonella genus 16S-23S internal transcribed spacer (ITS) sequence-specific PCR, Bartonella genus gltA gene-specific PCR, and 16S rRNA gene PCR with specificity for relapsing-fever-associated Borrelia spp. with subsequent sequencing of the amplicons. In one sample, the pan-eubacterial 16S rRNA gene-specific screening PCR, the Bartonella genus 16S-23S ITS sequence-specific PCR, and the Bartonella genus gltA gene-specific PCR allowed for the sequencing of B. quintana-specific amplicons. In two additional samples, Bartonella genus gltA gene-specific PCR also provided sequences showing 100% sequence identity with B. quintana. In total, 3/23 (13.0%) of the assessed lice were found to be positive for B. quintana. Correlating clinical data were not available; however, the assessment confirmed the presence of B. quintana in the local louse population and thus an associated infection pressure. Larger-sized cross-sectional studies seem advisable to more reliably quantify the infection risk of lice-infested local individuals. The need for prevention by providing opportunities to maintain standard hygiene for Ethiopian homeless individuals is stressed by the reported findings, especially in light of the ongoing migration of refugees

Retraction.

This is a retraction of 'Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa' 10.1126/science.add873

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection

Implementation of the WHO multimodal Hand Hygiene Improvement Strategy in a University Hospital in Central Ethiopia

Abstract Background The burden of health-care associated infections in low-income countries is high. Adequate hand hygiene is considered the most effective measure to reduce the transmission of nosocomial pathogens. We aimed to assess compliance with hand hygiene and perception and knowledge about hand hygiene before and after the implementation of a multimodal hand hygiene campaign designed by the World Health Organization. Methods The study was carried out at Asella Teaching Hospital, a university hospital and referral centre for a population of about 3.5 million in Arsi Zone, Central Ethiopia. Compliance with hand hygiene during routine patient care was measured by direct observation before and starting from six weeks after the intervention, which consisted of a four day workshop accompanied by training sessions and the provision of locally produced alcohol-based handrub and posters emphasizing the importance of hand hygiene. A second follow up was conducted three months after handing over project responsibility to the Ethiopian partners. Health-care workers’ perception and knowledge about hand hygiene were assessed before and after the intervention. Results At baseline, first, and second follow up we observed a total of 2888, 2865, and 2244 hand hygiene opportunities, respectively. Compliance with hand hygiene was 1.4% at baseline and increased to 11.7% and 13.1% in the first and second follow up, respectively (p < 0.001). The increase in compliance with hand hygiene was consistent across professional categories and all participating wards and was independently associated with the intervention (adjusted odds ratio, 9.18; 95% confidence interval 6.61-12.76; p < 0.001). After the training, locally produced alcohol-based handrub was used in 98.4% of all hand hygiene actions. The median hand hygiene knowledge score overall was 13 (interquartile range 11–15) at baseline and increased to 17 (15–18) after training (p < 0.001). Health-care workers’ perception surveys revealed high appreciation of the different strategy components. Conclusion Promotion of hand hygiene is feasible and sustainable in a resource-constrained setting using a multimodal improvement strategy. However, absolute compliance remained low. Strong and long-term commitment by hospital management and health-care workers may be needed for further improvement

Variation of vital signs with potential to influence the performance of qSOFA scoring in the Ethiopian general population at different altitudes of residency: A multisite cross-sectional study.

IntroductionThe physiological range of different vital signs is dependent on various environmental and individual factors. There is a strong interdependent relationship between vital signs and health conditions. Deviations of the physiological range are commonly used for risk assessment in clinical scores, e.g. respiratory rate (RR) and systolic blood pressure (BPsys) in patients with infections within the quick sequential organ failure assessment (qSOFA) score. A limited number of studies have evaluated the performance of such scores in resource-limited health care settings, showing inconsistent results with mostly poor discriminative power. Divergent standard values of vital parameters in different populations, e.g. could influence the accuracy of various clinical scores.MethodsThis multisite cross-sectional observational study was performed among Ethiopians residing at various altitudes in the cities of Asella (2400m above sea level (a.s.l.)), Adama (1600m a.s.l.), and Semara (400m a.s.l.). Volunteers from the local general population were asked to complete a brief questionnaire and have vital signs measured. Individuals reporting acute or chronic illness were excluded.ResultsA positive qSOFA score (i.e. ≥2), indicating severe illness in patients with infection, was common among the studied population (n = 612). The proportion of participants with a positive qSOFA score was significantly higher in Asella (28.1%; 55/196), compared with Adama, (8.3%; 19/230; pDiscussionThe high positivity rate of qSOFA score in the studied population without signs of acute infection may be explained by variations of the physiological range of different vital signs, possibly related to the altitude of residence. Adaptation of existing scores using local standard values could be helpful for reliable risk assessment

Access to the World Health Organization-recommended essential diagnostics for invasive fungal infections in critical care and cancer patients in Africa: A diagnostic survey

Background: Invasive fungal infections (IFIs) contribute to significant morbidity and mortality among patients with haemato-oncological conditions, seriously ill hospitalised patients and those in intensive care (ICU). We surveyed for the World Health Organization-recommended essential diagnostic tests for IFIs in these risk groups in Africa. Methods: The Global Action For Fungal Infections (GAFFI) evaluated the different levels of access to both diagnostics for IFIs for populations in Africa, with the aim of building a comparative dataset and a publicly available interactive map. Data was collected through a validated questionnaire administered to a country leader in relevant topics (i.e., HIV, laboratory coordination) and/or Ministry of Health representatives and followed up with 2 rounds of validation by video calls, and later confirmation by email of findings. Results: Initial data was collected from 48 African countries covering 99.65 % of the population. Conventional diagnostics such as blood cultures, direct microscopy and histopathology were often used for diagnosis of IFIs in more than half of the facilities. Bronchoscopy was rarely done or not done in 20 countries (population 649 million). In over 40 African countries (population >850 million), Aspergillus antigen testing was never performed in either the public or private sectors. Computed tomography (CT) imaging is routinely used in 27 (56 %) of countries in the public sector and 21 44 %) in the private sector. However, magnetic resonance imaging remains relatively uncommon in most African countries. Conclusions: There are critical gaps in the availability of essential diagnostics for IFIs in Africa, particularly Aspergillus antigen testing and modern medical imaging modalities. Early diagnosis and commencement of targeted therapy of IFIs are critical for optimal outcomes from complex cancer therapies