Research Articles (Medical Microbiology)

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Post-conflict nutritional status of school-age children in North Wollo zone, Northeast Ethiopia : a multi-center cross-sectional study
(BioMed Central, 2025-08) Dejazmach, Zelalem; Ayal, Birtukan Gizachew; Kassahun, Woldeteklehaymanot; Kumie, Getinet; Kassa, Muluemebet; Yayeh, Berihun Mulu; Ahmed, Seada Seid; Gela, Abebe Worku; Debash, Habtu; Ayalew, Selamawit; Ameshe, Asmamaw; Alamrew, Abebaw; Asfaw, Mulu Shiferaw; Feleke, Sefineh Fenta; Reta, Melese Abate
BACKGROUND : Conflict invariably disrupts food production in affected areas, exacerbates food insecurity, and results in population displacement. In 2021, the invasion of the Amhara region by the Tigrayan armed group led to widespread impoverishment of much of Amhara population. The conflict particularly exacerbated malnutrition rates in the North Wollo Zone. Despite this, studies focusing on undernutrition in conflict-affected areas within the Zone have not yet been documented. Therefore, this study assessed post-conflict nutritional status of school-age children in Northeast Ethiopia. METHODS : Cross-sectional study was conducted from April to May 2022 within the community, involving 584 school-age children. Socio-demographic data was collected through a structured questionnaire, and anthropometric measurements were transformed into indices using the World Health Organization’s Anthro-software. Descriptive and analytical statistical analyses were conducted with a 95% confidence interval. A p-value of less than 0.05 was regarded as statistically significant in the multivariate regression models. RESULTS : Among the 584 participants, 45.7% (95% CI: 42.0–50.0) were found to be stunted, while 33.0% (95% CI: 29.3–37.0) were classified as thin. Stunting was significantly associated with being: age 10–14 years (AOR = 6.16, 95% CI: 3.89–9.78); male (AOR = 1.52, 95% CI: 1.03–2.22); having an employed father (AOR = 3.40, 95% CI: 1.46–7.92); having farmer father (AOR = 4.70, 95% CI: 2.61–8.47). The odds of thinness were significantly higher among children who were male (AOR = 1.93, 95% CI: 1.23–3.03); lived in rural areas (AOR = 2.84, 95% CI: 1.55–5.20); had a mother who was a housewife (AOR = 4.38, 95% CI: 2.09–9.18) or a merchant (AOR = 4.84, 95% CI: 1.72–13.61); had a merchant father (AOR = 14.06, 95% CI: 6.97–28.35) or employed (AOR = 11.41, 95% CI: 4.33–30.07); and lived in a food-insecure household (AOR = 6.17, 95% CI: 3.84–9.90). CONCLUSIONS : Undernutrition is significant public health concern among school-age children in the conflict-affected study area. Stunting and thinness were significantly linked to factors such as the child’s sex, age, parents’ occupational status. These findings underscore the pressing need to implement health and nutrition programs aimed at enhancing the nutritional status of school-age children in the conflict-affected region.
The global prevalence of biofilm-forming Enterococcus faecalis in clinical isolates : a systematic review and meta-analysis
(BioMed Central, 2025-08) Tamrat, Ephrem; Asmare, Zelalem; Geteneh, Alene; Sisay, Assefa; Getachew, Ermias; Kassanew, Brhanu; Dessale, Mesfin; Gashaw, Yalewayker; Jemal, Abdu; Gashaw, Muluken; Bazezew, Alembante; Gedfie, Solomon; Kassahun, Woldeteklehaymanot; Abebe, Wagaw; Dejazmach, Zelalem; Misganaw, Tadesse; Ashagre, Agenagnew; Nigatie, Marye; Damtie, Abebe Adisu; Alemu, Bewuketu Belete; Tefera, Zewdu; Mezgebu, Bahriew; Kumie, Getinet; Kiros, Mulugeta;; Reta, Melese Abate
BACKGROUND : Enterococcus faecalis (E. faecalis) is a major cause of healthcare-associated infections (HAIs). It exhibits a strong biofilm-forming ability, which contributes to treatment resistance and persistence. Despite its clinical relevance, the global prevalence of biofilm-forming E. faecalis remains poorly defined. This study aimed to estimate the pooled prevalence of biofilm-forming E. faecalis in clinical isolates worldwide. METHODS : Following PRISMA 2020 guidelines, we systematically searched PubMed, Scopus, ScienceDirect, Google Scholar, and institutional repositories for studies published between 2015 and 2024. A total of 56 studies involving 3,739 clinical isolates met the inclusion criteria. We used a random-effects model to estimate pooled prevalence and conducted subgroup analyses based on WHO region, continent, publication year, specimen type, and biofilm detection method. Meta-regression and sensitivity analyses assessed heterogeneity and robustness. Publication bias was evaluated using Egger’s test and corrected with trim-and-fill analysis. RESULTS : The global pooled prevalence of biofilm-forming E. faecalis was 68.68% (95% CI: 61.33–76.02%), with significant heterogeneity (I² = 99.30%). By WHO region, prevalence ranged from 57.93% (95% CI: 41.01–71.85%) in South-East Asia to 73.66% (95% CI: 63.40–83.92%) in the Eastern Mediterranean. By continent, South America (all from Brazil) showed the highest prevalence at 89.79% (95% CI: 73.02–106.56%). Studies from 2021 to 2024 reported higher prevalence (76.18%, 95% CI: 66.25–86.11%) than those from 2015 to 2020. Among specimens, urine showed the highest prevalence (80.47%, 95% CI: 61.17–99.77%). Among biofilm-positive isolates, 47.92% (95% CI: 39.34–56.51%) were strong producers. Meta-regression identified WHO region (p = 0.005) and specimen type (p = 0.043) as significant sources of heterogeneity. Egger’s test indicated publication bias (p = 0.0066), but trim-and-fill analysis yielded a consistent adjusted prevalence of 68.08%. CONCLUSION : Biofilm formation is highly prevalent in E. faecalis clinical isolates globally, with substantial regional and specimen-based variation. These findings highlight the urgent need for standardized biofilm detection protocols, improved infection prevention and control, tailored antibiotic stewardship, and the development of anti-biofilm therapies to mitigate biofilm-associated resistance and enhance patient outcomes.
Sputum and tongue swab molecular testing for the in-home diagnosis of tuberculosis in unselected household contacts : a cost and cost-effectiveness analysis
(Oxford University Press, 2025-07) Bezuidenhout, Charl; Long, Lawrence; Nichols, Brooke; Meyer-Rath, Gesine; Fox, Matthew P.; Theron, Grant; Fourie, Bernard P.; Olifant, Sharon; Penn-Nicholson, Adam; Ruhwald, Morten; Medina-Marino, Andrew
BACKGROUND : Delayed and missed diagnoses are a persistent barrier to tuberculosis (TB) control, driven by difficulties collecting sputum and an unmet need for decentralized testing. Household contact investigation with point-of-care (POC) testing of noninvasive specimens may offer a cost-effective solution to strengthen active case finding. METHODS : In-home molecular POC testing was conducted using sputum and tongue specimens collected from household contacts of people with confirmed TB residing in South Africa. A health economic assessment was executed to estimate and compare the cost and cost-effectiveness of different in-home POC testing strategies against centralized sputum testing (standard of care) from a provider's perspective. The primary cost-effectiveness outcome was measured as the incremental cost per additional household contact with TB detected and linked to treatment. Decision analytic modeling was used to estimate and compare incremental cost-effectiveness ratios across strategies. RESULTS : The total implementation cost of delivering the standard of care to 300 households over a 2-year period was $85 188. Strategies that integrated in-home POC testing ranged from $88 672 to $97 271. The cost per test for in-home POC sputum testing was the highest at $20.08. Two strategies, POC sputum testing and POC combined sputum and individual tongue swab testing, were the most cost-effective with incremental cost-effectiveness ratios of $641 and $775, respectively, both below a $2760 willingness-to-pay threshold. CONCLUSIONS : In-home POC molecular TB testing strategies that use combination testing of tongue swabs and sputum specimens can meaningfully improve the number of people tested, diagnosed, and notified during household contact investigation while being cost-effective.
In-home TB testing using geneXpert edge is acceptable, feasible, and improves the proportion of symptomatic household contacts tested for TB : a proof-of-concept study
(Oxford University Press, 2024-06) Medina-Marino, Andrew; Bezuidenhout, Dana; Bezuidenhout, Charl; Facente, Shelley N.; Fourie, Bernard P.; Shin, Sanghyuk S.; Penn-Nicholson, Adam; Theron, Grant
BACKGROUND : Household contact investigations are effective for finding tuberculosis (TB) cases but are hindered by low referral uptake for clinic-based evaluation and testing. We assessed the acceptability and feasibility of in-home testing of household contacts (HHC) using the GeneXpert Edge platform. METHODS : We conducted a 2-arm, randomized study in Eastern Cape, South Africa. HHCs were verbally assessed using the World Health Organization-recommended 4-symptom screen. Households with ≥1 eligible symptomatic contact were randomized. Intervention households received in-home GeneXpert MTB/RIF molecular testing. GeneXpert-positive HHCs were referred for clinic-based treatment. Standard-of-care households were referred for clinic-based sputum collection and testing. We defined acceptability as agreeing to in-home testing and feasibility as generation of valid Xpert MTB/RIF results. The proportion and timeliness of test results received was compared between groups. RESULTS : Eighty-four households were randomized (n = 42 per arm). Of 100 eligible HHCs identified, 98/100 (98%) provided consent. Of 51 HHCs allocated to the intervention arm, all accepted in-home testing; of those, 24/51 (47%) were sputum productive and 23/24 (96%) received their test results. Of 47 HCCs allocated to standard-of-care, 7 (15%) presented for clinic-based TB evaluation, 6/47 (13%) were tested, and 4/6 (67%) returned for their results. The median (interquartile range) number of days from screening to receiving test results was 0 (0) and 16.5 (11-15) in the intervention and standard-of-care arms, respectively. CONCLUSIONS : In-home testing for TB was acceptable, feasible, and increased HHCs with a molecular test result. In-home testing mitigates a major limitation of household contact investigations (dependency on clinic-based referral), revealing new strategies for enhancing early case detection.
A prolonged outbreak of enteric fever associated with illegal miners in the City of Matlosana, South Africa, November 2020–September 2022
(Oxford University Press, 2024-02-28) Sekwadi, Phuti; Smith, Anthony Marius; Maruma, Wellington; Mongologa, Gift; Tsele, Grace; Ngomane, Mimmy; Tau, Nomsa; Williams, Shannon; Disenyeng, Bolele; Sebiloane, Mahlaku; Johnston, Leigh; Erasmus, Linda Kathleen; Thomas, Juno
BACKGROUND : In South Africa, the annual incidence of enteric fever averaged 0.1 per 100 000 persons between 2003 and 2018. During 2021 an increase in the number of enteric fever cases was observed. An outbreak investigation was conducted to determine the magnitude and source of the outbreak. METHODS : We performed a cross-sectional descriptive study. Data were collected through telephonic or face-to-face interviews with cases or proxies via a standardized case investigation form. Whole genome sequencing was performed on all Salmonella Typhi isolates. Drinking water samples were collected, tested, and analyzed. Descriptive analysis was performed with Microsoft Excel. RESULTS : Between January 2020 and September 2022, a cluster of 53 genetically highly related Salmonella Typhi isolates was identified from 5 provinces in South Africa. Isolates associated with the cluster showed ≤5 allelic differences, as determined following core genome multilocus sequence typing analysis. Most cases (60%, 32/53) were in the North West province. Males represented 68% (36/53). Of these, 72% (26/36) were aged 15 to 49 years, with a median age of 31 years. Where occupation was known within this age group, 78% (14/18) were illegal gold miners. Illegal miners reported illness onset while working underground. Five municipal tap water samples were tested and showed no evidence of fecal contamination. CONCLUSIONS : This outbreak predominantly affected illegal gold miners, likely due to the consumption of contaminated groundwater while working in a gold mine shaft. In addition, this investigation highlights the value of whole genome sequencing to detect clusters and support epidemiologic investigation of enteric fever outbreaks.
Business model innovation based on disruptive technologies : a critical success factors categorization
(IADIS, 2024) Edwards, Mikhail David; Smuts, Hanlie
Business model innovation (BMI) holds significant importance in today's digital landscape, empowering enterprises to leverage disruptive technology for value creation and competitive advantage. However, the rapid evolution of these technologies presents various challenges, including uncertain market conditions, potential financial risks during the initial phases, employee resistance, and the risk of distraction from core responsibilities. This research aimed to identify the characteristics essential for the successful implementation of BMI through effective utilization of disruptive technologies. This was accomplished through a thorough review of existing literature, organizing critical success factors into the business model canvas framework, and applying a framework for identifying and classifying digital technologies based on demand. The findings underscored the importance of trust, efficiency, and adaptability across various BMI components. Technologies like Artificial Intelligence enhance objective alignment and personalized client experiences, while blockchain technology fosters trust and transparency. Cloud computing, on the other hand, enhances resource accessibility and flexibility. To achieve optimal BMI in today's digital landscape, it is important for organisations to proactively integrate these technologies into their operations, while fostering adaptability and engaging stakeholders.
Immunogenicity and safety following a homologous booster dose of a SARS-CoV-2 recombinant spike protein vaccine with Matrix-MTM adjuvant (NVX-CoV2373) versus a primary series in people living with and without HIV-1 infection in South Africa : a randomized crossover phase 2a/2b trial
(Taylor and Francis, 2024-12) Shinde, Vivek; Koen, Anthonet Lombard; Hoosain, Zaheer; Archary, Moherndran; Bhorat, Qasim; Fairlie, Lee; Lalloo, Umesh; Masilela, Mduduzi S.L.; Moodley, Dhayendre; Hanley, Sherika; Fouche, Leon Frederik; Louw, Cheryl; Tameris, Michele; Singh, Nishanta; Goga, Ameena; Dheda, Keertan; Grobbelaar, Coert; Joseph, Natasha; Lombaard , Johan J.; Mngqibisa, Rosie; Bhorat, As’ad Ebrahim; Benade, Gabriella; Lalloo, Natasha; Pitsi, Anna; Vollgraaff, Pieter-Louis; Luabeya, Angelique; Esmail, Aliasgar; Petrick, Friedrich G.; Jose, Aylin Oommen; Foulkes, Sharne; Ahmed, Khatija; Thombrayil, Asha; Kalonji, Dishiki; Cloney-Clark, Shane; Zhu, Mingzhu; Bennett, Chijioke; Albert, Gary; Marcheschi, Alex; Plested, Joyce S.; Neal, Susan; Chau, Gordon; Cho, Iksung; Fries, Louis; Glenna, Greg M.; Madhi, Shabir A.
COVID-19 remains a global public health issue and an improved understanding of vaccine performance in immunocompromised individuals, including people living with HIV (PLWH), is needed. Initial data from the present study's pre-crossover/booster phase were previously reported. This phase 2a/b clinical trial in South Africa (2019nCoV-501/NCT04533399) revisits 1:1 randomly assigned HIV-negative adults (18-84 years) and medically stable PLWH (18-64 years) who previously received two NVX-CoV2373 doses (5 μg recombinant Spike protein with 50 μg Matrix-M™ adjuvant) or placebo. During the 6-month blinded crossover/booster phase, NVX-CoV2373 recipients could receive a single NVX-CoV2373 booster dose and placebo recipients a 2-dose NVX-CoV2373 primary series. NVX-CoV2373 safety and immunogenicity were assessed according to prior SARS-CoV-2 infection and HIV status. Post-crossover, 1900/3793 NVX-CoV2373 recipients were assigned another dose, and 1893/3793 placebo recipients were assigned NVX-CoV2373 primary series. Approximately 56% of the participants were SARS-CoV-2-seropositive ("seropositive") at crossover (6% PLWH). In seropositive participants (HIV-negative and PLWH), booster-dose anti-spike IgG, MN50 and hACE2 inhibition responses increased to similar levels, exceeding those in seronegative participants. In primary-series and booster cohorts, seronegative PLWH showed higher neutralizing responses (4.9- to 5.5-fold, respectively) versus peak pre-crossover primary-series responses. The safety profile was similar among the pre-crossover/booster phase groups; solicited and unsolicited adverse events were infrequent in all groups. A single NVX-CoV2373 booster dose substantially increased antibodies. All baseline seropositive participants showed higher immune responses than seronegative participants. These findings support use of NVX-CoV2373, including in immunocompromised individuals.
Molecular epidemiology of carbapenemase‑producing Klebsiella pneumoniae in Gauteng South Africa
(Nature Research, 2024-11-09) Salvador-Oke, Kafilat Taiwo; Pitout, Johann D.D.; Peirano, Gisele; Strydom, Kathy‑Anne; Kingsburgh, Chanel; Ehlers, Marthie Magdaleen; Ismail, Arshad; Takawira, Faustinos T.; Kock, Marleen M.; marleen.kock@up.ac.za
Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient’s urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (blaNDM-1 + blaOXA-48 + blaOXA-181), while all the ST2497 strains co-harboured (blaNDM-1 + blaOXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.
Missed rifampicin and isoniazid resistance by commercial molecular assays
(South African Medical Association, 2024-07) Richards, L.; Ismail, Farzana; Nel, J.; Omar, Shaheed Vally
Drug-resistant tuberculosis (TB) has poor outcomes unless resistance is detected early, ideally by commercially available molecular tests. We present a case of occult multidrug-resistant TB where both rifampicin and isoniazid resistance were missed by molecular testing and were only identified by phenotypic testing.
Innovative timing strategies for tuberculosis household contact investigation : cost-effectiveness analysis from a randomized trial in rural and urban South Africa (Kharituwe Study)
(Elsevier, 2025-06) Young, Neenah; Biché, Patrick; Mohlamonyane, Mbali; Morolo, Matshidiso; Maholwana, Babalwa; Ahmed, Khatija; Martinson, Neil; Hanrahan, Colleen F.; Dowdy, David W.
BACKGROUND : Household contact investigation (HCI) for tuberculosis (TB) is recommended but often limited by resource constraints, particularly for individuals unavailable during business hours. METHODS : We conducted an economic evaluation from January 1, 2022, through December 31, 2022, nested within a randomized trial in South Africa (“Kharituwe”) comparing standard HCI for TB and two novel strategies: HCI during holiday periods in a rural setting and off-peak HCI during weekends and evenings in an urban setting. Costs were derived from 2022 expenditures, and secondary TB cases were defined by positive sputum cultures. As a secondary outcome of the Kharituwe Study, we assessed the incremental cost-effectiveness ratio (ICER) of each strategy against a hypothetical no-HCI scenario from the health system perspective in 2022 US dollars. Cost-effectiveness was assessed using a country-specific willingness-to-pay threshold of US$3015 per disability-adjusted life year (DALY) averted. The trial is registered with clincaltrials.gov (NCT04520113). FINDINGS : Relative to a hypothetical no-HCI approach, standard HCI was estimated to cost US$1400 [95% uncertainty interval (UI): $1000–$2100] per DALY averted in the urban setting and US$3600 [95% UI: $2500–$5400] in the rural setting. Corresponding cost-effectiveness ratios were US$1900 [95% UI: $1300–$2800] for off-peak (urban) and US$6400 [$3900–$10,000] for holiday-based (rural) HCI. Personnel costs, travel costs (in the rural setting), and TB prevalence among contact persons were primary drivers of cost-effectiveness. INTERPRETATION : HCI for TB is likely cost-effective in urban South Africa and may be cost-effective in rural settings, which face barriers including long travel times and lower TB prevalence. Holiday-based HCI was not found to be cost-effective. Integrating HCI for TB into broader home-based interventions may improve cost-effectiveness.
Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa
(Elsevier, 2025-01) Kanzi, Aquillah M.; Smith, Stella I.; Msefula, Chisomo; Mwaba, John; Ajayi, Abraham; Kwenda, Geoffrey; Tanui, Collins K.; Smith, Anthony Marius; Bester, Linda A.; Derra, Firehiwot A.; Yamba, Kaunda; Banda, Daniel L.; Kalule, John B.; Kumburu, Happiness H.; Fakim, Yasmina J.; Sithole, Nyasha; Njage, Patrick M.K.; Chikuse, Francis F.; Ondoa, Pascale; Tessema, Sofonias K.; Foster-Nyarko, Ebenezer
The role of genomics in public health surveillance has been accentuated by its crucial contributions during the COVID-19 pandemic, demonstrating its potential in addressing global disease outbreaks. While Africa has made strides in expanding multi-pathogen genomic surveillance, the integration into foodborne disease (FBD) surveillance remains nascent. Here we highlight the critical components to strengthen and scale-up the integration of whole genome sequencing (WGS) in foodborne disease surveillance across the continent. We discuss priority use-cases for FBD, and strategies for the implementation. We also highlight the major challenges such as data management, policy and regulatory frameworks, stakeholder engagement, the need for multidisciplinary collaborations and the importance of robust monitoring and evaluation, aiming to bolster Africa's preparedness and response to future health threats.
Prevalence of genes encoding carbapenem-resistance in Klebsiella pneumoniae recovered from clinical samples in Africa : systematic review and meta-analysis
(BioMed Central, 2025-04) Sisay, Assefa; Kumie, Getinet; Gashaw, Yalewayker; Nigatie, Marye; Gebray, Habtamu Mesele; Reta, Melese Abate
Please read abstract in the article.
Prevalence of colistin-resistant Enterobacteriaceae isolated from clinical samples in Africa: a systematic review and meta-analysis
(BioMed Central, 2025-03) Gashaw, Yalewayker; Asmare, Zelalem; Tigabie, Mitkie; Sisay, Asefa; Getatachew, Ermias; Tadesse, Selamyhun; Bitew, Getachew; Ashagre, Agenagnew; Misganaw, Tadesse; Gashaw, Muluken; Kassahun, Woldeteklehaymanot; Dejazimach, Zelalem; Jemal, Abdu; Gedfie, Solomon; Kumie, Getinet; Nigatie, Marye; Gelaw, Baye; Abebe, Wagaw; Kidie,Atitegeb Abera; Abate, Biruk Beletew; Reta, Melese Abate; Gelaw, Baye
BACKGROUND : Antimicrobial resistance among Enterobacteriaceae poses a significant global threat, particularly in developing countries. Colistin, a critical last-resort treatment for infections caused by carbapenem-resistant and multidrug-resistant strains, is increasingly facing resistance due to inappropriate use of colistin and the spread of plasmid-mediated resistance genes. Despite the significance of this issue, comprehensive and updated data on colistin resistance in Africa is lacking. Thus, the current study was aimed to determine the pooled prevalence of colistin-resistant Enterobacteriaceae in Africa. METHODS : A systematic search was conducted across PubMed, Scopus, ScienceDirect, and Google Scholar to identify relevant studies. Forty-one studies reporting on the prevalence of colistin resistance in Enterobacteriaceae isolates from clinical specimens in Africa were included in the analysis. Stata 17 software was used to calculate the pooled prevalence of colistin resistance, employing a random-effects model to determine the event rate of resistance. Heterogeneity across studies was assessed using the I2 statistic, and publication bias was evaluated using Egger’s test. Subgroup analyses were performed to address any identified heterogeneity. RESULTS : This systematic review analyzed the colistin resistance profile of 9,636 Enterobacteriaceae isolates. The overall pooled prevalence of colistin resistance was 26.74% (95% CI: 16.68–36.80). Subgroup analysis by country revealed significant variability in resistance rates, ranging from 0.5% in Djibouti to 50.95% in South Africa. Species-specific prevalence of colistin resistance was as follows: K. pneumoniae 28.8% (95% CI: 16.64%-41.05%), E. coli 24.5% (95% CI: 11.68%-37.3%), Proteus spp. 50.0% (95% CI: 6.0%-106.03%), and Enterobacter spp. 1.22% (95% CI: -0.5%-3.03%). Analysis based on AST methods revealed significant differences in colistin resistance rates (p = 0.001). The resistance rates varied between 12.60% for the disk diffusion method and 28.0% for the broth microdilution method. Additionally, a subgroup analysis of clinical specimens showed significant variation (p < 0.001) in colistin resistance. Stool specimen isolates had the highest resistance rate at 42.0%, while blood specimen isolates had a much lower resistance rate of 3.58%. CONCLUSIONS : Colistin resistance in Enterobacteriaceae is notably high in Africa, with significant variation across countries. This underscores the urgent need for effective antimicrobial stewardship, improved surveillance, and the development of new antibiotics.
Antimicrobial resistance pattern of Acinetobacter baumannii clinical isolate in Ethiopia. A systematic review and meta-analysis
(BioMed Central, 2025-04) Asmare, Zelalem; Tamrat, Ephrem; Erkihun, Mulat; Endalamaw, Kirubel; Alelign, Dagninet; Getie, Molla; Sisay, Assefa; Gashaw, Yalewayker; Reta, Melese Abate
BACKGROUND : Antimicrobial resistance (AMR) is a growing global health threat. Acinetobacter baumannii (A. baumannii) emerged as one of the most concerning critical priority pathogens due to its ability to develop resistance to multiple antimicrobial agents. In Ethiopia, the public health impact of AMR is increasingly significant, with A. baumannii responsible for a variety of infections. Although A. baumannii causes a range of infections in Ethiopian patients, the drug resistance status of the clinical isolates has not been thoroughly assessed. Therefore, this systematic review and meta-analysis aimed to determine the country-wide AMR of A. baumannii. METHODS : This systematic review and meta-analysis followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We conducted a search of articles on PubMed, Web of Science, Science Direct, Scopes electronic databases, Google Scholar search engine, and institutional repositories/libraries for studies published between 2015 and 2024. Eligible studies on A. baumannii-related infections and AMR in Ethiopia were assessed for quality using the Joanna Briggs Institute (JBI) criteria. Data on study characteristics were extracted, and statistical analyses, including heterogeneity (Invers of variance), publication bias (Eggers test), and subgroup analyses, were performed using STATA 17.0. A random effect model was used to compute the pooled prevalence of AMR. RESULTS : This systematic review and meta-analysis of 26 Ethiopian studies (26,539 participants) found an A. baumannii prevalence of 3.99% (95% CI: 3.01–4.98%) and 9.13% of all bacterial infections (95% CI: 6.73–11.54%). The most common infections were surgical site infections, urinary tract infections, pneumonia, and sepsis. Pooled resistance to antibiotics varied, with amikacin showing the lowest resistance (20.27%) (95% CI: 11.51–29.03) and cefotaxime the highest (83.18) (95% CI: 71.87–94.48). A pooled multi-drug resistant (MDR) A. baumannii was found in 88.22% (95% CI: 82.28–94.15) of isolates, with regional and infection-type variations, particularly in higher prevalence in Oromia and Amhara regions and sepsis cases. CONCLUSION : This systematic review underscores the alarming rise of antimicrobial resistance in A. baumannii, particularly against carbapenems. The findings highlight a high prevalence of MDR A. baumannii and widespread extended-spectrum beta-lactamase production, with notable regional variations in resistance patterns. These high resistance rates reinforce A. baumannii as a critical global health threat, necessitating urgent interventions such as enhanced antimicrobial stewardship programs, improved infection control measures, and the development of alternative treatment strategies. Healthcare professionals, policymakers, and researchers must collaborate to mitigate the clinical and public health impact of this pathogen. PROTOCOL REGISTRATION : This systematic review and meta-analysis was registered on PROSPERO (Registration ID: CRD42024623927).
Does a waiting room increase same-day treatment for sexually transmitted infections among pregnant women? A quality improvement study at South African primary healthcare facilities
(BioMed Central, 2025-04) Gigi, Ranjana M.S.; Mdingi, Mandisa M.; Butikofer, Lukas; Babalola, Chibuzor M.; Klausner, Jeffrey D.; Medina-Marino, Andrew; Muzny, Christina A.; Taylor, Christopher M.; Van de Wijgert, Janneke H.H.M.; Peters, Remco P.H.; Low, Nicola
BACKGROUND : Same-day testing and treatment of curable sexually transmitted infections (STI) is a strategy to reduce infection duration and onward transmission. South African primary healthcare facilities often lack sufficient waiting spaces. This study aimed to assess the proportion of, and factors influencing, pregnant women waiting for on-site STI test results before and after the installation of clinic-based waiting rooms. METHODS : We conducted an observational quality improvement study at 5 public primary healthcare facilities in South Africa from March 2021 to May 2023. The intervention was the installation of a waiting room in two clinics. Three clinics were used as comparators: two already had a waiting room in an existing building and one had access to a shared waiting area. The outcome was the percentage of women who waited for their STI test results. We conducted univariable and multivariable analyses and report marginal risk differences (with 95% confidence intervals, CI) of the proportions of women who waited for results. A subset of women answered structured questions about factors influencing their decision to wait for results. RESULTS : We analysed data from 624 women across the 5 facilities. Overall, 36% (95% CI 31 to 40) waited for their test results (range 7 to 89%). In the two intervention clinics, 17% (95% CI 11 to 24) waited for results before the introduction of a waiting room and 10% (95% CI 5 to 18) after (crude absolute difference − 7% (95% CI -16 to + 3), adjusted difference, -6% (95% CI -17 to + 5)). The percentages of pregnant women waiting for STI test results were higher throughout the study period in 2 clinics which always had a dedicated waiting room than in 2 clinics where a waiting room was installed, or in 1 clinic, which only had access to a shared waiting area. Most women reported before testing that they did not intend to wait and none of the suggested factors would change their decision. CONCLUSIONS : Introduction of a waiting room did not increase the proportion of women who waited for their results in this observational study. Future studies should investigate infrastructure, individual and test-based factors that affect same-day STI testing and treatment.
Twice-yearly Lenacapavir or daily F/TAF for HIV prevention in cisgender women
(Massachusetts Medical Society, 2024-10) Bekker, Linda-Gail; Das, Moupali; Karim, Quarraisha Abdool; Ahmed, Khatija; Batting, Joanne; Brumskine, William; Gill, Katherine; Harkoo, Ishana; Jaggernath, Manjeetha; Kigozi, Godfrey; Kiwanuka, Noah; Kotze, Philip; Lebina, Limakatso; Louw, Cheryl; Malahleha, Moelo; Manentsa, Mmatsie; Mansoor, Leila E.; Moodley, Dhayendre; Naicker, Vimla; Naidoo, Logashvari; Naidoo, Megeshinee; Nair, Gonasagrie; Ndlovu, Nkosiphile; Palanee-Phillips, Thesla; Panchia, Ravindre; Pillay, Saresha; Potloane, Disebo; Selepe, Pearl; Singh, Nishanta; Singh, Yashna; Spooner, Elizabeth; Ward, Amy M.; Zwane, Zwelethu; Ebrahimi, Ramin; Zhao, Yang; Kintu, Alexander; Deaton, Chris; Carter, Christoph C.; Baeten, Jared M.; Kiweewa, Flavia Matovu
BACKGROUND : There are gaps in uptake of, adherence to, and persistence in the use of preexposure prophylaxis for human immunodeficiency virus (HIV) prevention among cisgender women. METHODS : We conducted a phase 3, double-blind, randomized, controlled trial involving adolescent girls and young women in South Africa and Uganda. Participants were assigned in a 2:2:1 ratio to receive subcutaneous lenacapavir every 26 weeks, daily oral emtricitabine–tenofovir alafenamide (F/TAF), or daily oral emtricitabine–tenofovir disoproxil fumarate (F/TDF; active control); all participants also received the alternate subcutaneous or oral placebo. We assessed the efficacy of lenacapavir and F/TAF by comparing the incidence of HIV infection with the estimated background incidence in the screened population and evaluated relative efficacy as compared with F/TDF. RESULTS : Among 5338 participants who were initially HIV-negative, 55 incident HIV infections were observed: 0 infections among 2134 participants in the lenacapavir group (0 per 100 person-years; 95% confidence interval [CI], 0.00 to 0.19), 39 infections among 2136 participants in the F/TAF group (2.02 per 100 person-years; 95% CI, 1.44 to 2.76), and 16 infections among 1068 participants in the F/TDF group (1.69 per 100 person-years; 95% CI, 0.96 to 2.74). Background HIV incidence in the screened population (8094 participants) was 2.41 per 100 person-years (95% CI, 1.82 to 3.19). HIV incidence with lenacapavir was significantly lower than background HIV incidence (incidence rate ratio, 0.00; 95% CI, 0.00 to 0.04; P<0.001) and than HIV incidence with F/TDF (incidence rate ratio, 0.00; 95% CI, 0.00 to 0.10; P<0.001). HIV incidence with F/TAF did not differ significantly from background HIV incidence (incidence rate ratio, 0.84; 95% CI, 0.55 to 1.28; P=0.21), and no evidence of a meaningful difference in HIV incidence was observed between F/TAF and F/TDF (incidence rate ratio, 1.20; 95% CI, 0.67 to 2.14). Adherence to F/TAF and F/TDF was low. No safety concerns were found. Injection-site reactions were more common in the lenacapavir group (68.8%) than in the placebo injection group (F/TAF and F/TDF combined) (34.9%); 4 participants in the lenacapavir group (0.2%) discontinued the trial regimen owing to injection-site reactions. CONCLUSIONS : No participants receiving twice-yearly lenacapavir acquired HIV infection. HIV incidence with lenacapavir was significantly lower than background HIV incidence and HIV incidence with F/TDF.
Prevalence of antimalaria drug resistance-conferring mutations associated with sulphadoxine-pyrimethamineine-resistant Plasmodium falciparum in East Africa : a systematic review and meta-analysis
(BioMed Central, 2025-04) Abebe, Wagaw; Ashagre, Agenagnew; Misganaw, Tadesse; Dejazmach, Zelalem; Kumie, Getinet; Nigatie, Marye; Jemal, Abdu; Asmare, Zelalem; Kassahun, Woldeteklehaymanot; Gedfie, Solomon; Getachew, Ermias; Gashaw, Muluken; Ayana, Sisay; Gashaw, Yalewayker; Sisay, Assefa; Tadesse, Selamyhun; Eshetu, Tegegne; Awoke, Mulat; Kassanew, Birhanu; Kidie, Atitegeb Abera; Abate, Biruk Beletew; Reta, Melese Abate
BACKGROUND : The emergence and spread of drug resistance to antimalarial drugs pose a severe threat to effective malaria control and treatment. Although sulfadoxine-pyrimethamine resistance is well-documented, it is still the drug of choice for treating intermittent resistance. Molecular markers play a crucial role in tracking and understanding the prevalence of antimalarial drug resistance. Currently, there is insufficient information on the prevalence of molecular markers associated with sulfadoxine-pyrimethamine resistance in P. falciparum. OBJECTIVE : This systematic review and meta-analysis aimed to determine the pooled prevalence of antimalaria drug resistance-conferring markers associated with sulphadoxine-pyrimethamineine in Plasmodium falciparum in East Africa. METHODS : Systematic searches was performed to retrieve articles from PubMed, Scopus, Science Direct databases, and Google Scholar search engine. Sixteen potential studies that provided important data on markers for sulphadoxine-pyrimethamineine resistance in Plasmodium falciparum were systematically reviewed and analyzed. Nine antimalarial drug resistance markers responsible for sulphadoxine-pyrimethamineine resistance in Plasmodium falciparum were extracted separately into Microsoft Excel and analyzed using STATA 17.0. The inverse of variance was done to evaluate heterogeneity across studies. A funnel plot was used to determine the presence of publication bias. A trim-and-fill-meta-analysis was carried out to generate a bias-adjusted effect estimate. A random effect model was used to determine the pooled prevalence of markers responsible for sulphadoxine-pyrimethamineine resistance. Subgroup analysis was performed based on country and year of publication. RESULTS : A total of 16 studies were included for this systematic review and meta-analysis.The molecular markers like dhfr (N51I, C59R, S108N, 108N, 59R, and I164L), and dhps (A437G, K540E, & 540E) were selected for meta-analysis. From this meta-analysis, the pooled prevalence of dhfr N51I, dhfr C59R, dhfr S108N, dhfr 108N, dhfr 59R, and dhfr I164L was 88.6%, 85.3%, 89.6%, 92.2%, 71.5%, and 3.9%, respectively. Likewise, the aggregated prevalence of dhps A437G, dhps K540E, and dhps 540E was 90.2%, 80.9%, and 91.5%, respectively. The subgroup analysis based on year of publication showed that the pooled prevalence of dhfr N51I, dhfr C59R, dhfr S108N, dhps A437G, and dhps K540E, in studies conducted 2014–2018 was 97.11%, 90.57%, 96.45%, 90.89%, and 89.45%, respectively, while it was 82.03%, 81.78%, 85.12%, 89.24%, and 73.98%, respectively, in studies conducted 2019–2023. On the other hand, country-based analysis showed that the pooled prevalence of dhfr N51I, dhfr C59R, dhfr S108N, dhps A437G, and dhps K540E, in Kenya was 85.88%, 84.02%, 86.56%, 90.7%, and 77.55%, respectively. CONCLUSIONS : This systematic review and meta-analysis reveal a high prevalence of drug resistance markers associated with sulphadoxine-pyrimethamine resistance in Plasmodium falciparum across the East African region. This underscores the significant challenges in managing malaria infections caused by Plasmodium falciparum in the region. Therefore, regular monitoring, identification, and limiting of drug-resistance markers and drug-resistant P. falciparum strains must be sustained to ensure the effectiveness of malaria treatment.
Antimicrobial resistance profile of Pseudomonas aeruginosa clinical isolates from healthcare-associated infections in Ethiopia : a systematic review and meta-analysis
(Public Library of Science, 2024-08-13) Asmare, Zelalem; Reta, Melese Abate; Gashaw, Yalewayker; Sisay, Assefa; Gashaw, Muluken; Tamrat, Ephrem; Abebe, Wagaw; Misganaw, Tadesse; Ashagre, Agenagnew; Dejazmach, Zelalem; Kumie, Getinet; Nigatie, Marye; Ayana, Sisay; Jemal, Abdu; Gedfie, Solomon; Kassahun, Woldeteklehaymanot; Kassa, Mulat Awoke; Tadesse, Selamyhun; Abate, Biruk Beletew
BACKGROUND : Antimicrobial-resistant (AMR) bacterial infection is a significant global threat to the healthcare systems. Pseudomonas aeruginosa, the leading infectious agent in the healthcare setting is now one of the major threats due to AMR. A comprehensive understanding of the magnitude of AMR, particularly highly public health important pathogens such as P. aeruginosa, is necessary for the management of infections based on local information. OBJECTIVE : This systematic review and meta-analysis aimed to determine the country-wide AMR of P. aeruginosa. METHODS : Systematic searches were performed to retrieve articles from PubMed, Scopus, Web of Science, ScienceDirect electronic databases, Google Scholar search engine, and repository registrars from 2015 to 31st December 2023. Twenty-three studies that provided important data on AMR in P. aeruginosa were systematically reviewed and analyzed to determine the country-wide magnitude of P. aeruginosa AMR profile from healthcare-associated infections. AMR of P. aeruginosa to 10 different antibiotics were extracted separately into Microsoft Excel and analyzed using STATA 17.0. Cohen’s kappa was computed to determine the agreement between reviewers, the Inverse of variance (I2) was used to evaluate heterogeneity across studies, and Egger’s test to identify publication bias. A random effect model was used to determine the pooled resistance to each antibiotic. Subgroup analysis was performed by infection type and year of publication. RESULTS : This systematic review and meta-analysis revealed that the pooled prevalence of P. aeruginosa in clinical specimens associated with HAI was 4.38%(95%CI: 3.00–5.76). The pooled prevalence of AMR in P. aeruginosa for different antibiotics varies, ranging from 20.9% (95%CI: 6.2–35.8) for amikacin to 98.72% (95%CI: 96.39–101.4) for ceftriaxone. The pooled resistance was higher for ceftriaxone (98.72%), Trimethoprim-sulfamethoxazole (75.41), and amoxicillin-clavulanic acid (91.2). In contrast relatively lower AMR were observed for amikacin (20.9%) and meropenem (28.64%). The pooled multi-drug resistance (MDR) in P. aeruginosa was 80.5% (95%CI: 66.25–93.84). Upon subgroup analysis by infection types and year of publication, P. aeruginosa isolated from healthcare-associated infections exhibited higher resistance to ceftazidime (94.72%) compared to isolates from mixed types of healthcare-associated infections (70.84%) and surgical site infections (57.84%). Antimicrobial resistance in gentamicin was higher during the periods of 2018–2020 (73.96%), while comparatively lower during 2021–2023 (42.69%) and 2015–2017 (29.82%) CONCLUSIONS : Significantly high AMR and MDR were observed from this systematic review and meta-analysis. AMR obtained from this systematic review and meta-analysis urges the need for improved infection control, antimicrobial stewardship practices, and strengthened surveillance systems to control the spread of AMR and ensure effective treatment of P. aeruginosa infections.
Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa
(Public Library of Science, 2024-08-26) Smith, Anthony Marius; Ramudzulu, Masindi; Munk, Patrick; Avot, Baptiste J.P.; Esterhuyse, Kerneels C.M.; Van Blerk, Nico; KwendaI, Stanford; Sekwadi, Phuti
Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.
Prevalence of pulmonary tuberculosis among key and vulnerable populations in hotspot settings of Ethiopia. A systematic review and meta-analysis
(Public Library of Science, 2024-08-29) Reta, Melese Abate; Asmare, Zelalem; Sisay, Assefa; Gashaw, Yalewayker; Getachew, Ermias; Gashaw, Muluken; Dejazmach, Zelalem; Jemal, Abdu; Gedfie, Solomon; Kumie, Getinet; Nigatie, Marye; Abebe, Wagaw; Ashagre, Agenagnew; Misganaw, Tadesse; Kassahun, Woldeteklehaymanot; Tadesse, Selamyhun; Geteneh, Alene; Kidie, Atitegeb Abera; Abate, Biruk Beletew; Maningi, Nontuthuko Excellent; Fourie, Petrus Bernardus
BACKGROUND : Despite the decline in tuberculosis (TB) incidence across many regions worldwide, including Ethiopia, the disease remains highly concentrated among vulnerable or socially marginalized populations and in high-risk settings. This systematic review and meta-analysis aims to estimate the pooled prevalence of pulmonary tuberculosis (PTB) among key and vulnerable populations (KVPs) residing in hotspot settings in Ethiopia. METHODS : Potential papers were searched systematically in PubMed, Scopus, ScienceDirect databases, Google Scholar search engine, and institutional electronic repositories/registrars. A total of 34 potential articles that provide necessary information on the prevalence of PTB were reviewed and data were analyzed to determine the pooled prevalence of PTB among KVPs. The relevant data were recorded and analyzed using STATA 17.0. Cohen’s kappa was computed to determine the agreement between reviewers, the Inverse of variance (I2) to evaluate heterogeneity across studies, and Egger’s test to identify publication bias. A random effect model was used to determine the pooled prevalence of PTB, subgroup analysis was computed by types of hotspot settings and year of publication. RESULTS : This meta-analysis demonstrates that the pooled prevalence of PTB among populations residing in hotspot settings in Ethiopia was 11.7% (95% confidence interval (95CI): 7.97–15.43) with an I2 of 99.91% and a p< 0.001. Furthermore, the subgroup analysis unveiled the pooled prevalence of PTB among KVPs residing in different hotspot settings as follows: Prison inmates 8.8% (95CI: 5.00–12.55%), University students 23.1% (95CI: 15.81–30.37%), Refugees 28.4% (95CI: -1.27–58.15%), Homeless peoples 5.8% (95CI: -0.67–12.35%), Healthcare settings 11.1% (95CI: 0.58–21.63%), Spiritual holy water sites attendees 12.3% (95CI: -6.26–30.80%), and other high-risk settings 4.3% (95CI: 0.47–8.09%). Besides, the subgroup analysis revealed that the pooled prevalence of PTB post-2015 was 10.79% (95CI: 5.94–15.64%), whereas it stood at 14.04% (95CI: 10.27–17.82%) before 2015. CONCLUSION : The prevalence of PTB among KVPs residing in the hotspot settings in Ethiopia remains significant, with a weighted pooled prevalence of 11.7%. Thus, the national TB control programs should give due attention and appropriate control measures should be instituted that include regular systematic TB screening, compulsory TB testing for presumptive TB cases among KVPs, and tightened infection control at hotspot settings.

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