A multi-modal molecular characterization of the Philadelphia translocation featuring long read sequencing

OBJECTIVE

Clinically significant structural variation (SV), notably chromosomal translocation, results in the formation of fusion genes that drive leukaemogenesis. Detection of SVs is vital in clinical diagnosis, prognosis and therapy of haematological malignancies. Current methods for SV identification are low in sensitivity for cryptic cases and time-consuming for complex cases. This study investigated the feasibility of long read sequencing as an approach for SV detection and precise breakpoint characterization.

METHODS

Six archival samples, including 4 bone marrow blood samples (F/66 B-ALL, F/25 B-ALL, M/53 CML, F/34 B-ALL) and 1 cytogenetic cell pellet each in cell culture medium (M/52 CML) or Carnoy's fixative (M/44 CML) with known and previously characterized BCR::ABL1 fusion transcript were selected for study. The genomic DNA was extracted from each case for further breakpoint characterization by long read sequencing (MinION R9.4.1 flow cell, Oxford Nanopore Technologies, UK).

RESULTS

All the genomic breakpoints were concordant with the RNA fusion transcript breakpoints. Three typical (e1a2, e13a2, and e14a2) and 3 variant (e23a2Ins52, e8a2, and e13a2ins74) BCR breakpoints were identified.

CONCLUSION

Using the Ph translocation as an example, long read sequencing is a promising alternative method to detect SV, revolutionizing detection of chromosomal translocation to a higher precision. A more comprehensive spectrum of SV can be resolved along with cytogenetic results, enabling precise diagnosis and personalized monitoring of haematological malignancies.

Cytopathology Practice in Nigeria

Cytopathology is a cost-effective diagnostic method crucial for investigating suspected neoplastic lesions, particularly in Nigeria's healthcare system, where non-communicable diseases, especially with increasing rates of cancer. This review highlights the evolution of cytopathology practice in Nigeria, detailing its historical development, current methodologies, and the challenges faced within the healthcare framework. Despite advancements in diagnostic techniques such as immunocytochemistry and molecular diagnostics globally, conventional methods remain essential due to their affordability and accessibility. Fine needle aspiration cytology (FNAC) has gained acceptance for its diagnostic accuracy; however, significant disparities exist in the availability of cytological services across various regions. The lack of trained personnel and inadequate infrastructure further complicate the effective implementation of cytopathology practices. The findings highlight the urgent need for specialized training programs and improved resource allocation to enhance cytopathology services in Nigeria. We advocate for strategic interventions aimed at optimizing cytopathology's potential to improve cancer diagnosis and patient outcomes in resource-limited settings across the country.

Current access, availability and use of antibiotics in primary care among key low- and middle-income countries and the policy implications

INTRODUCTION

Antimicrobial resistance (AMR) poses a significant threat, particularly in low- and middle-income countries (LMICs), exacerbated by inappropriate antibiotic use, access to quality antibiotics and weak antimicrobial stewardship (AMS). There is a need to review current evidence on antibiotic use, access, and AMR, in primary care across key countries.Areas covered: This narrative review analyses publications from 2018 to 2024 regarding access, availability and use of appropriate antibiotics.

EXPERT OPINION

There were very few studies focussing on a lack of access to antibiotics in primary care. However, there was considerable evidence of high rates of inappropriate antibiotic use, including Watch antibiotics, typically for minor infections, across studied countries exacerbated by patient demand. The high costs of antibiotics in a number of LMICs impacts on their use resulting in short courses and sharing of antibiotics. This can contribute to AMR alongside the use of substandard and falsified antibiotics. Overall, limited implementation of national action plans, insufficient resources, and knowledge gaps, affects sustainable development goals to provide routine access to safe, effective and appropriate antibiotics.

CONCLUSIONS

There is a clear need to focus health policy on the optimal use of essential AWaRe antibiotics in primary care settings to reduce AMR in LMICs.

The Global Health Security Index and Its Role in Shaping National COVID‑19 Response Capacities: A Scoping Review

Introduction: Following the introduction of the Global Health Security Index (GHSI), the coronavirus disease 2019 (COVID‑19) pandemic emerged as an unprecedented global health crisis, underscoring the need for robust health security frameworks and preparedness measures. This study conducts a scoping review to analyze the existing literature on the GHSI and assess national COVID‑19 responses across different countries. Method: A comprehensive search of electronic databases (EBSCO, EMBASE, PubMed, Scopus, and Web of Science) was conducted for articles published from 2020 to 2024. Search terms included "Global Health Security Index" and terms related to COVID‑19. The study followed the Preferred Reporting Items for Systematic Reviews and Meta‑analyses for Scoping Reviews (PRISMA‑ScR) guidelines. The Newcastle-Ottawa Scale (NOS), adjusted for cross‑sectional studies, was used for quality assessment. Results: A total of 3,243 studies were identified, of which 20 were finalized for data synthesis. Specific COVID‑19 parameters were analyzed to provide a comprehensive overview of each country's pandemic response capacity. Among the selected studies, 17 (85%) had a low risk of bias, while 3 (15%) had a medium risk. Countries' response capacities were categorized into five key parameters: detection, mortality, transmission, fatality, and recovery. Findings revealed significant discrepancies between GHSI scores and actual national responses, with some high‑scoring countries struggling to control the pandemic. This raises concerns about the GHSI's predictive reliability. Conclusion: The study highlights that the GHSI does not fully capture a country's capacity to respond effectively to COVID‑19. However, it remains a valuable tool for identifying gaps in pandemic preparedness. To enhance its relevance, the index should integrate a wider range of factors, including political leadership, governance, public health infrastructure, and socio‑cultural elements, which are crucial in managing public health emergencies.

Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia

Rapid and comprehensive drug susceptibility testing (DST) is essential for diagnosing and treating drug-resistant tuberculosis effectively, and next-generation sequencing can be an effective genotypic DST method. We implemented and evaluated the performance of a nanopore targeted sequencing assay, called the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom), which predicts drug resistance to 16 TB drugs, at a South African reference laboratory and a district diagnostic laboratory in Zambia. We compared the sequencing success rates between unprocessed and decontaminated sputum samples and determined the diagnostic accuracy against local DST (Xpert MTB/RIF Ultra, Xpert MTB/XDR, and BD BACTEC MGIT phenotypic DST). We prospectively sequenced 236 samples and have 148 samples with sequencing results from unprocessed and decontaminated sputum. We obtained successful sequencing results from 66.4% (94/148) unprocessed sputum samples and 75% (111/148) decontaminated samples. Sequencing success rates at the two sites differed, with 50.7% (36/71) successful sequencing results from unprocessed sputum in Zambia and 75.3% (58/77) in South Africa. Samples with "low" bacterial load, measured by Xpert MTB/RIF Ultra, tended to produce fewer successful sequencing results. TBDR sequencing predicted resistances in 48 samples, detecting resistance for rifampicin (n = 41) and isoniazid (n = 20), as well as 10 second-line drugs (n = 15). Sensitivity was variable compared to phenotypic DST, ranging from 33 (ethionamide) to 94% (rifampicin), while specificity remained above 90% for all drugs, except clofazimine. The TBDR assay can provide rapid, comprehensive genotypic DST. Technical and operational challenges need to be addressed for its broader implementation in high tuberculosis-burden settings.IMPORTANCEThis study illustrates the use of the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom) as a rapid drug susceptibility testing (DST) approach for diagnosing drug-resistant TB in the high TB-burden countries of South Africa and Zambia. The TBDR assay predicts resistance to 16 TB drugs, including first- and second-line treatments. By implementing the TBDR assay in a national reference laboratory in South Africa and a district diagnostic laboratory in Zambia, we demonstrate how this technology can provide faster diagnostic results (days) compared to traditional phenotypic DST methods (~2 months), with adequate sensitivity. Missed resistances compared to phenotypic DST indicate that technical improvements are needed. Successful sequencing from unprocessed and decontaminated sputum samples at different sites suggests feasibility in diverse settings, though operational challenges remain. Implementing this rapid, comprehensive DST approach could enhance drug-resistant tuberculosis diagnosis and treatment, ultimately improving patient outcomes and helping to combat tuberculosis in high-burden regions.

Field deployment of the mobile suitcase laboratory for rapid detection of Mpox virus in the Democratic Republic of the Congo

The 2022 Mpox outbreak in the DRC highlighted the urgent need for rapid, fielddeployable diagnostic tools in resource-limited LMIC settings. A mobile diagnostic setup was evaluated, demonstrating operational readiness within 20 minutes and safe testing within 50 minutes. This approach proved practical for Mpox detection in remote, rural regions.

Clinical and hematological profile of patients with pancytopenia at a tertiary medical center in Ethiopia

BACKGROUND

Pancytopenia is an important hematological problem encountered in routine clinical practice associated with a multitude of disease states. The possible causes of pancytopenia can be influenced by geography, socioeconomic conditions, and endemic illnesses. Information regarding the underlying clinical conditions and morphologic features of blood cells of pancytopenia is limited and varied across different regions. Thus, this study was designed to assess the peripheral morphologic features of blood cells and the underlying clinical causes of pancytopenia.

METHODS

A facility-based cross-sectional study was conducted at the Jimma Medical Center hematology laboratory from June 13 to November 13, 2022. A total of 3 mL of whole blood was collected from each subject for complete blood count analysis and peripheral blood morphology examination. Data on sociodemographic and clinical conditions were collected from medical records using a checklist. The data were analyzed using Statistical Package for the Social Sciences version 26.

RESULTS

A total of 163 patients with pancytopenia were identified within the 5 months. Hyper-reactive malarial splenomegaly was the most prevalent cause (29.4%), followed by megaloblastic anemia (20.2%), chronic liver disease (10.4%), and acute leukemia (8.6%). Anisocytosis was the predominant peripheral blood morphology finding (82.2%), along with microcytosis (49.7%), ovalocytosis (31.3%), and macrocytosis (30.7%). Severe anemia was observed in 57% of cases, whereas the majority (92%) exhibited moderate leukopenia. A significant proportion (42.3%) had a platelet count below 50,000/μL.

CONCLUSION

Unlike previous studies conducted in other parts of the world, this study showed that hyperreactive malarial splenomegaly was the leading cause of pancytopenia. This emphasizes the necessity of considering this condition as a possible cause for pancytopenia, particularly in malaria-endemic areas. The findings of the hematological profiles and peripheral blood morphology strongly suggest that early identification and prompt management of patients with pancytopenia require collaboration between clinical and laboratory investigations.

Empowering Global AMR Research Community: Interactive GIS dashboards for AMR data analysis and informed decision-making

Background

Antimicrobial Resistance (AMR) poses a global public health challenge, necessitating advanced tools to support data analysis, and visualization. This study introduces interactive Geographic Information System (GIS) dashboards as innovative platforms for AMR data analysis and visualization, offering comprehensive insights into resistance patterns, and geographic distribution across multiple countries, with a specific focus on Africa.

Methods

Three GIS dashboards were developed to address key objectives. The first integrates over 860,000 ATLAS data points from 83 countries, providing an interactive platform. Users can filter data by variables such as country, year, and region, enhancing data accessibility and visualization. The second dashboard focuses on the ATLAS dataset for Kenya and Uganda, incorporating detailed variables such as species, sample sources, and resistance phenotypes. The third involves Kampala, Uganda, to fill data gaps, enabling localized analyses through interactive features like geographic mapping and sample breakdowns by year.

Results

Sub-Saharan Africa faces three major challenges in handling antimicrobial resistance (AMR) data: limited accessibility for non-technical users, inefficiencies in processing large datasets, and insufficient longitudinal data for analysis. The introduction of interactive dashboards significantly improved AMR data visualization and interpretation across different scales. The global AMR dashboard effectively mapped geographical trends, uncovering critical data gaps, particularly the scarcity of AMR records from Africa. The Kenya and Uganda dashboard revealed key resistance patterns, highlighting the ineffectiveness of Ceftriaxone, Erythromycin, Levofloxacin, and Ampicillin against E. coli isolates. Additionally, the Kampala-specific dashboard, developed using simulated data, demonstrated the potential for localized AMR visualization, providing valuable insights where real-world data is limited. Across all platforms, the dashboards' interactive features enhanced data accessibility and streamlined trend identification, making AMR insights more interpretable, especially for researchers in Sub-Saharan Africa.

Conclusions

Interactive GIS dashboards enhance AMR data analysis in Sub-Saharan Africa by improving accessibility, efficiently handling large datasets, and addressing data gaps. Unlike spreadsheets such as Excel, which struggle with large datasets due to computer constraints, dashboards offer dynamic visualization, real-time updates, and intuitive data exploration.

Hidden stories of caregivers with children living with sickle cell disease in Uganda: Experiences, coping strategies and outcomes

BACKGROUND

Sickle Cell Disease (SCD) poses a substantial public health challenge in Uganda, exhibiting distinct regional variations in prevalence. The Uganda Sickle Cell Surveillance Study has estimated an overall SCD prevalence of 13.3%. Notably, this prevalence varies significantly across the country's regions, reaching its highest in the northern region at 22.2% and it's lowest in the central region at 5.3%. This variation reflects the diverse impact of SCD and underscores the need for a comprehensive understanding of its regional implications. SCD places substantial physical, social, and psychological burdens on caregivers, potentially leading to heightened parental stress. However, limited research has focused on the daily challenges and experiences of SCD caregivers, despite evidence showing the detrimental impact on their emotional well-being, personal lives, employability, and socioeconomic status. This study explored the undisclosed struggles of Ugandan caregivers tending to children with SCD, uncovering their coping strategies and subsequent outcomes.

METHODS

In June and July 2023, we conducted in-depth interviews with caregivers at Mulago sickle cell clinic after obtaining their informed consent. An interview guide was used as the primary data collection tool, with interviews lasting 30-45 minutes. Twelve participants were recruited, ensuring comprehensive data collection by following the data saturation principle. We analyzed the collected data using open coding.

RESULTS

Three key themes emerged: caregiver experiences, coping strategies, and outcomes. Initially, caregivers grappled with confusion and uncertainty before a formal diagnosis. Financial strain and inadequate support posed persistent challenges, affecting their emotional well-being. Coping strategies varied, encompassing traditional remedies and modern medical treatments for symptom relief. Coping outcomes were complex, reflecting caregivers' resilience alongside substantial emotional distress and sleep disturbances. The substantial financial burden further exacerbated their overall well-being.

CONCLUSION

Elevating awareness and knowledge about sickle cell disease within communities is essential. Such awareness can empower caregivers of children living with sickle cell disease, promoting emotional resilience and mitigating family disruptions.

Preanalytical Sedimentation Effects on Hematological Tests

INTRODUCTION

Specimens suspected of errors related to low hemoglobin or changes in hemoglobin beyond that of clinically explained variations during hospital stays are frequently redrawn under the auspices that they are contaminated. When lack of an indwelling IV eliminates contamination as a possibility, evaluation of the specimen between the time of collection and testing should occur.

METHODS

As part of a quality improvement project, we investigated the impact of sedimentation on collected blood specimens not immediately transferred to their respective tubes from a syringe. Each syringe of blood was allowed to stand in a vertical position on the transfer device. After 10 min, each syringe was divided into a bottom half and top half into fresh blood tubes, with half of the samples inverted prior to division. Samples were then analyzed for complete blood count.

RESULTS

These results indicate that implementing an inversion of collected specimens prior to transferring will effectively eliminate variations related to sedimentation of blood.

CONCLUSIONS

Results highlight the importance of specimen handling after collection, including appropriate mixing to avoid erroneous results caused by erythrocyte sedimentation. Mixing syringes before transferring blood to collection tubes ensures a uniform sample and accurate result.

Detection of I491F and V170F rpoB mutations associated with misdiagnosis of rifampicin resistance among patients with drug-susceptible tuberculosis treatment failure, Myanmar, 2022

OBJECTIVE

Detecting rifampicin (RIF) resistance is crucial in selecting tuberculosis (TB) treatment. Recently, several studies reported that I491F and V170F rpoB mutations were found with a varying prevalence. This study aimed to find out RIF resistance missed by routine diagnostic assays using next generation genome sequencing tool.

METHODS

Sputum specimens from first-line TB treatment failed patients attending Tuberculosis Centers in Yangon Region during 2022 were cultured in solid media. Phenotypic drug susceptibility testing was conducted using Mycobacterial Growth Indicator Tube method. Whole genome or Deeplex-targeted next-generation sequencing was performed using Illumina Miseq. Mutation analysis was done by PhyResSE and SAM-TB online platforms.

RESULTS

A total of 32 culture-positive isolates with DNA qualified for genome sequencing were included in the study. Those were diagnosed as rifampicin-susceptible by routine GeneXpert and line probe assays. RIF resistance-conferring mutations were found in 17/32 (53.1%) Mycobacterium tuberculosis isolates; 14 (43.7%) had mutations outside the RIF resistance determining region (I491F and V170F), two (6.3%) were S450L, mutation within RIF resistance determining region, and one isolate (3.1%) with interim resistance mutations S428T and S441A.

CONCLUSION

This study highlighted the presence of rifampicin-resistant TB strains missed by current diagnostic strategies, and are circulating as treatment-failed patients. This demonstrates a gap in current World Health Organization-endorsed algorithms for capturing all multidrug-resistant-TB strains.

Burkitt's Lymphoma of the Uterine Cervix in a Woman with Advanced HIV Disease: A Case Report on Challenges with Its Management in a Low Resource Setting

Background

Burkitt's lymphoma (BL) affecting the female genital tract is rare.

Objective

The aim of this paper is to report BL of the cervix in an HIV-positive patient to discuss the fatality of the condition and ways to mitigate it through advocacy for improved health care delivery in resource limited settings.

Methods

The patient was a 29-year-old woman, Para 1, with abnormal vaginal bleeding for a month and living with HIV and had a CD4 of 26 cells/μL. The histological examination of the cervical biopsy confirmed an extra-nodal BL. She had International Federation of Gynecology and Obstetrics (FIGO) stage 3B cervical cancer based on presence of hydronephrosis and pelvic wall involvement. The patient was reviewed at the oncology multidisciplinary meeting and required chemoradiation. There was delay in her management due to a long waiting list for chemoradiation at oncology unit in the referral center and the patient demised 43 days after diagnosis and did not receive the treatment.

Results

This case suggests that women living with HIV who have BL should be fast-tracked for treatment as HIV viremia may worsen the prognosis of the malignancy. Following the encounter with the index patient an advocacy action plan has been made by the oncology multidisciplinary team to prioritize the treatment of women with aggressive histological types of cervical cancer.

Conclusion

A long waiting list for chemoradiation in low resource settings may delay management of advanced BL of the cervix. Inadequate cervical cancer screening and delays in diagnosis are other barriers to the care of women with aggressive cervical cancers in low resource settings. Systemic changes in healthcare delivery are therefore required in many low resource settings. Advocacy for patients particularly those with aggressive diseases using the index case as a point of reference is ideal and should be promoted in resource-limited settings to improve health care delivery.

Surgical prophylaxis in Haydom Lutheran Hospital, Tanzania - learning from a point prevalence survey

Background

Antimicrobial resistance (AMR) is a significant global health concern, with improper antibiotic use contributing to its rise. Tanzania initiated an AMR action plan in 2017, but comprehensive surveillance and stewardship efforts remain limited. This study focused on evaluating antibiotic use, particularly surgical prophylaxis, in a rural Tanzanian hospital.

Methods

The study was conducted at Haydom Lutheran Hospital in Tanzania in May 2023, using a cross-sectional point prevalence survey. Antibiotic use in all patients admitted for >24 h and those undergoing surgery was recorded, including type, dose, indication and duration. Quality indicators for surgical prophylaxis were assessed.

Results

Among 199 inpatients, 55% received antibiotics, with surgical prophylaxis accounting for 23% of prescriptions. Notably, none of the patients who received surgical prophylaxis received a single-dose regimen, and 67% exceeded the recommended 24-h duration. A combination of ampicillin-cloxacillin plus metronidazole was the most commonly prescribed combination for surgical prophylaxis (41% of prescriptions). Thirty-three percent of the antibiotics prescribed for surgical prophylaxis were classified as 'Not recommended' by the World Health Organization. Furthermore, 90% of surgical prophylaxis prescriptions lacked documented rationale, and 83% of prescriptions lacked stop/review dates in medical records.

Conclusion

This study reveals a high prevalence of prolonged antibiotic use for surgical prophylaxis, frequent use of antibiotics classified as 'Not recommended', and a lack of adequate documentation, which deviates from international standards. These practices highlight the urgent need for contextualized national guidelines, large-scale implementation projects of evidence-based interventions, and local initiatives in antibiotic stewardship, particularly in low-resource settings.

Vertical transmission of hepatitis B virus in the WHO African region: a systematic review and meta-analysis

BACKGROUND

More new infections with hepatitis B virus (HBV) occur annually in the WHO African region than in the rest of the world combined. We did a systematic review and meta-analysis to estimate the prevalence of hepatitis B surface antigen (HBsAg) in pregnant women and vertical transmission events in the region.

METHODS

In this systematic review and meta-analysis, we searched PubMed, Embase, Scopus, Africa Index Medicus, and Africa Journals Online for publications between Jan 1, 1992, and Jan 7, 2024, with no language restrictions. HBsAg prevalence and vertical transmission (HBsAg positivity in children aged 6-12 months) were estimated with the use of binomial mixed models with logit links, stratified by infant vaccination status. We estimated HBsAg prevalence for subregions of Africa and for the WHO African region by weighting by estimated livebirths for each subregion. We estimated transmission events using WHO and UNICEF vaccine coverage data and UN population estimates.

FINDINGS

We included 113 studies reporting on HBsAg prevalence from 190 983 pregnant women and 11 studies reporting on vertical transmission. HBsAg prevalence in women receiving antenatal care in the WHO African region (based on 2014-23 data) was 6·2% (95% CI 5·3-7·2). No relationship between risk of bias and HBsAg prevalence was observed. In 2022, an estimated 172 000 vertical transmission events (95% CI 82 000-383 000) occurred (0·4% of livebirths), a fall from a peak of 339 000 (149 000-634 000; 1·2% of all livebirths) in 2001. Increasing birth dose vaccination coverage to the WHO target of 90% could reduce vertical transmission by 43·7% (95% CI 11·6-78·0) to 97 000 events per year (95% CI 58 000-160 000). Adding maternal antiviral prophylaxis with 90% coverage could reduce transmission by 86·3% (95% CI 78·4-94·6) to 24 000 events per year (95% CI 14 000-39 000; 0·06% of livebirths) and achieve WHO elimination targets.

INTERPRETATION

Vertical transmission is an important contributor to HBV transmission in the WHO African region. Scaling up of hepatitis B birth dose vaccination and antiviral prophylaxis is urgently needed, which could achieve elimination of vertical transmission.

FUNDING

Wellcome Trust.

Emerging threats: Antimicrobial resistance in extended-spectrum beta-lactamase and carbapenem-resistant Escherichia coli

Antimicrobial resistance (AMR) in Escherichia coli strains, particularly those producing Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase (CR-Ec), represents a serious global health threat. These resistant strains have been associated with increased morbidity, mortality, and healthcare costs, as they limit the effectiveness of standard antibiotic therapies. The prevalence of ESBL- and CR-Ec-producing strains continues to rise, driven by the overuse and misuse of antibiotics in healthcare and agricultural settings, and facilitated by global interconnectedness through international travel, trade, and food distribution. This review article examines the molecular mechanisms behind ESBL and CR resistance, focusing on the key genes involved in these processes, such as blaCTX-M, blaKPC, and blaNDM, and the clinical challenges posed by these strains. Additionally, the public health impact, including the spread of infections in hospital and community environments, is highlighted. The discussion emphasizes the urgent need for improved diagnostic tools, robust surveillance systems, and innovative therapeutic strategies. Emerging treatments, including phage therapy and novel antibiotic combinations, show promise in addressing these challenges and offer potential breakthroughs in combating resistant strains. Lastly, the review calls for stronger antimicrobial stewardship and policy reforms to mitigate the spread of resistant E. coli strains and protect global public health. Effective intervention at multiple levels, from diagnostics to policy, is critical to controlling the threat posed by AMR.

Performance of molecular tests for diagnosis of bloodstream infections in the clinical setting: a systematic literature review and meta-analysis

BACKGROUND

Rapid identification of bloodstream pathogens and associated antimicrobial resistance (AMR) profiles by molecular tests from positive blood cultures (PBCs) have the potential to improve patient management and clinical outcomes.

OBJECTIVES

A systematic review and meta-analysis were conducted to evaluate diagnostic test accuracy (DTA) of molecular tests from PBCs for detecting pathogens and AMR in the clinical setting.

METHODS

.

DATA SOURCES

Medline, Embase, Cochrane, conference proceedings, and study bibliographies were searched.

STUDY ELIGIBILITY CRITERIA

Studies evaluating DTA of commercially available molecular tests vs. traditional phenotypic identification and susceptibility testing methods in patients with PBCs were eligible.

PARTICIPANTS

Patients with PBCs.

TESTS

Commercially available molecular tests.

REFERENCE STANDARD

Traditional phenotypic identification and susceptibility testing methods (standard of care, SOC).

ASSESSMENT OF RISK OF BIAS

Study quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2.

METHODS OF DATA SYNTHESIS

Summary DTA outcomes were estimated using bivariate random-effects models for gram-negative bacteria (GNB), gram-positive bacteria (GPB), yeast, GNB-AMR, GPB-AMR, and specific targets when reported by ≥ 2 studies (PROSPERO CRD42023488057).

RESULTS

Seventy-four studies including 24 590 samples were analysed, most of which had a low risk of bias. When compared with SOC, molecular tests showed 92-99% sensitivity, 99-100% specificity, 99-100% positive predictive value, and 97-100% negative predictive value for identifying total GNB (43 studies), GPB (38 studies), yeast (24 studies), GNB-AMR (35 studies), and GPB-AMR (39 studies). For individual pathogen targets, 93-100% sensitivity, 98-100% specificity, 86-100% positive predictive value, and 99-100% negative predictive value were estimated. Five of seven AMR genes had 91-99% sensitivity and 99-100% specificity. Sensitivity was lower for IMP (four studies; 62%; 95% CI, 34-83%) and VIM (four studies; 70%; 95% CI, 38-90%) carbapenemases, where genes were not detected or were not harboured in Pseudomonas aeruginosa (i.e. low prevalence). Performance of molecular tests in detecting AMR was generally comparable when grouped by geographical region (Europe, North America, and East Asia).

DISCUSSION

High DTA support the use of molecular tests in identifying a broad panel of pathogens and detecting AMR in GNB and GPB.

Characterization and genome analysis of novel Klebsiella pneumoniae phage vbKpUKJ_2 isolated from hospital sewage water

INTRODUCTION

Multidrug-resistant (MDR) Klebsiella pneumoniae is a critical healthcare challenge due to its extensive resistance to antibiotics and role in causing severe infections. Bacteriophages offer a promising alternative for targeting MDR pathogens. This study characterizes a novel phage, vbKpUKJ_2, isolated from hospital sewage water, against clinical K. pneumoniae isolates.

METHODS

Phage vbKpUKJ_2 was isolated and purified using the double agar overlay method. Host range and sensitivity were tested against 40 clinical K. pneumoniae isolates using growth inhibition assays. Morphological characterization was performed using transmission electron microscopy (TEM). Genomic analysis was conducted to evaluate the absence of antibiotic resistance genes and determine phylogenetic relationships. Stability assays assessed the phage's thermal and pH tolerance.

RESULTS

Phage vbKpUKJ_2 demonstrated broad range activity against clinical K. pneumoniae isolates. TEM revealed it belongs to the Drexlerviridae family. Genomic analysis confirmed the absence of antibiotic resistance genes and identified conserved functional regions shared with related phages. vbKpUKJ_2 exhibited broad pH stability (pH 4-10) and thermal stability between 30 °C and 60 °C. The one-step growth curve indicated rapid lytic activity, with a burst size of 323 phage particles per cell.

CONCLUSION

vbKpUKJ_2 shows promising therapeutic potential against MDR K. pneumoniae. Its stability, absence of resistance genes, and rapid lytic cycle highlight its suitability for inclusion in phage therapy protocols, particularly as part of combination therapies targeting MDR infections.

Building capacity for pediatric hematological diseases in Sub-Saharan Africa

ABSTRACT

The spectrum of hematological diseases in African children includes anemias, bleeding disorders, thromboses, and oncological diseases such as leukemias. Although data are limited, outcomes for these diseases are poorer in Africa. The dearth of specialists, and lack of infrastructure that supports diagnosis and management, have been identified as key barriers to improving outcomes for childhood hematological disorders in Sub-Saharan Africa (SSA). To address these, intentional capacity building efforts addressing education and training, diagnostic capacity, and access to blood products and medicines are needed. This article explores some ongoing efforts in the region aimed at fostering the capacity to identify and treat childhood hematological disorders across a breadth of initiatives targeting the critical themes of education, diagnostic support, and treatment. We also identify existing opportunities through international partnerships, to build sustainable programs that can support children with hematological diseases in SSA.

Pseudomonas aeruginosa Vaccine Development: Lessons, Challenges, and Future Innovations

Pseudomonas aeruginosa is an opportunistic pathogen with a multidrug-resistant profile that has become a critical threat to global public health. It is one of the main causes of severe nosocomial infections, including ventilator-associated pneumonia, chronic infections in patients with cystic fibrosis, and bloodstream infections in immunosuppressed individuals. Development of vaccines against P. aeruginosa is a major challenge owing to the high capacity of this bacterium to form biofilms, its wide arsenal of virulence factors (including secretion systems, lipopolysaccharides, and outer membrane proteins), and its ability to evade the host immune system. This review provides a comprehensive historical overview of vaccine development efforts targeting this pathogen, ranging from early attempts in the 1970s to recent advancements, including vaccines based on novel proteins and emerging technologies such as nanoparticles and synthetic conjugates. Despite numerous promising preclinical developments, very few candidates have progressed to clinical trials, and none have achieved final approval. This panorama highlights the significant scientific efforts undertaken and the inherent complexity of successfully developing an effective vaccine against P. aeruginosa.

Workplace bullying among medical laboratory professionals in Ghana: insights from self-reported experiences, challenges to mitigation structures, and coping strategies

BACKGROUND

Workplace bullying is a major concern in Ghana's healthcare sector, often arising from power imbalances and an excessive emphasis on achieving results at the cost of employee well-being. While bullying among healthcare professionals like doctors and nurses is well-documented, little is known about its prevalence among medical laboratory professionals, who play a vital role in patient care. We assessed bullying in this group to inform strategies for mitigation.

METHODS

We conducted a cross-sectional survey involving 378 medical laboratory professionals. The survey included demographic information, workplace characteristics, the Revised Negative Acts Questionnaire (NAQ-R), and questions about bullying perpetrators, mental health breaks, and anti-bullying policies. Data analysis involved descriptive statistics, the Kruskal-Wallis test, and logistic regression. Results were reported as frequencies, percentages, and odds ratios with 95% confidence intervals (CIs), and statistical significance set at p < 0.05.

RESULTS

44% of the medical laboratory professionals reported experiencing bullying; 29% faced frequent bullying, while 71% encountered it occasionally. Common issues included ignored opinions, unmanageable workloads, gossip, and exclusion. Non-clinical administrative managers were the most frequent perpetrators. Diploma and bachelor's degree holders had higher odds of being bullied compared to master's degree holders (AOR = 6.13, p = 0.013; AOR = 2.56, p = 0.007). Rural professionals had higher odds than urban counterparts (AOR = 2.23, p = 0.007).

CONCLUSION

The high prevalence of workplace bullying among medical laboratory professionals highlights the need for effective policies to enhance workplace conditions and patient care.

Does perceived social support buffer the impact of psychological distress on health-related quality of life among people living with tuberculosis?

People living with tuberculosis have been reported to encounter greater distress than normal population, and this distress is known to impact their quality of life adversely. However, studies examining the mechanisms that could mitigate this adverse impact of distress are sparse, hence this study. We investigated whether perceived social support (including emotional and instrumental support from family, friends, and significant others) plays a buffering role in the link between psychological distress and health-related quality of life (HRQoL) among people living with tuberculosis (PLWTB). We utilized a cross-sectional design to conveniently sample 200 tuberculosis patients drawn from a health facility in South-Eastern Nigeria. These participants completed measures of relevant variables. Results showed that psychological distress was negatively associated with HRQoL. Perceived social support (from family, friends, and significant others) significantly predicted HRQoL. Perceived social support moderated the link between psychological distress and HRQoL, but did not buffer against the association. Management of psychological distress associated with tuberculosis health condition should therefore be a major focus in efforts to improve the health and well-being of TB patients.

Antimicrobial resistance patterns of WHO priority pathogens at general hospital in Southern Ethiopia during the COVID-19 pandemic, with particular reference to ESKAPE-group isolates of surgical site infections

BACKGROUND

Antimicrobial resistance represents a significant public health challenge, resulting in an estimated 4.95 million deaths annually. In response to the global escalation of antimicrobial resistance in prevalent hospital-acquired infections such as surgical site infections (SSIs), the World Health Organization (WHO) has identified critical and priority pathogens necessitating research and development. Nevertheless, there remains a paucity of data from numerous developing nations. Therefore this study was conducted to evaluate the prevalence of SSIs, examine the microbial profile, and identify factors associated with SSIs, with a particular emphasis on WHO-priority pathogens during the COVID-19 pandemic at a general hospital in southern Ethiopia.

METHODS

A cross-sectional study was conducted on 207 adult patients clinically suspected of SSIs from September 1, 2019, to November 2022. Demographic data, clinical characteristics, and surgery-related variables were collected using pre-tested, structured, interviewer-administered questionnaires and patient chart reviews. Wound samples (swabs and/or pus) were collected aseptically from each participant following standard microbiological procedures and processed for isolation and identification of pathogens by conventional culture and biochemical testing. Bacterial isolates subjected to antimicrobial susceptibility testing, including the detection of extended-spectrum beta-lactamase (ESBL) and methicillin-resistant Staphylococcus aureus (MRSA), by the standard Kirby-Bauer disk diffusion method in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. Data were analyzed by Statistical Packages for Social Science (SPSS) version 25, and bivariable and multivariable logistic regression was done to determine the associations between dependent and independent variables. Adjusted odds ratio with 95% confidence interval (CI) was reported, and P-value < 5% was considered statistically significant.

RESULTS

The overall prevalence of culture-confirmed SSIs among adult patients who underwent major surgery was 76.8% (95% CI: 71.0, 82.6). Among the 178 pathogens recovered, 58.5% were Gram-negative, 40.4% were Gram-positive, and 1.1% were Candida spp. The ESKAPE pathogens comprised 65.3% of the isolates, with S. aureus being the most common species, accounting for 43.5%, followed by K. pneumoniae (33.9%). Multidrug resistance (MDR) was observed in 84.37% of ESKAPE pathogens, with ESBL-producing and MRSA-producing isolates accounting for 88% and 76.5%, respectively. A. baumannii showed the highest MDR rate at 100%, followed by MRSA (90%) and K. pneumoniae (88.23%). Amikacin, meropenem, and piperacillin-tazobactam were effective agents against Gram-negatives, while linezolid, clindamycin, and gentamicin were most effective against Gram-positive bacteria. SSIs was significantly associated with emergency surgery (P < 0.001), prolonged surgery waiting time (P = 0.004), and clean-contaminated surgery (P = 0.008).

CONCLUSION

The high prevalence of MDR-ESKAPE pathogens is concerning, highlighting the need for improved infection prevention practices and antimicrobial stewardship programs.

Knowledge, attitude, and practices regarding antibiotic use and antimicrobial resistance among urban slum dwellers in Uganda

BACKGROUND

Antimicrobial resistance (AMR) remains a public health threat especially in low-and-middle-income countries (LMICs). Urban slum dwellers are at higher risk of developing AMR than the general population. The aim of this study was to assess the knowledge, attitude and practices (KAP) regarding antibiotic use and AMR and the associated socio-demographic determinants among urban slum dwellers in Uganda.

METHODS

A cross sectional study was conducted among 371 adults of Bwaise slum in Uganda selected through multi-stage cluster sampling techniques. An interviewer administered questionnaire was used to collect data on participants' socio-demographics, KAP regarding antibiotic use and AMR. The responses to the KAP were aggregated into scores for each participant which were later dichotomized by the mean to form the predictors variables. Analysis was done in STATA 17.0. A modified Poisson regression model was used to determine predictors of each of KAP, while considering a 5% significance level.

RESULTS

The study enrolled 371 participants of which 238(64.2%) were females. The median (IQR) age of the participants was 31 [24, 40] years. Over half of the respondents, 205(55.3%) were married and 157(42.3%) had primary level education. Of all participants, 177 (47.7%), 184 (49.6%) and 205 (55.3%) had good knowledge, a positive attitude and good practices regarding antibiotic use and AMR respectively. Being single (aPR = 0.75, p-value = 0.040) was negatively associated with good knowledge of antibiotic use and resistance, while having acquired tertiary education level (aPR = 1.88, p-value < 0.001) and self-employed (aPR = 1.36, p = 0.017) were associated with good knowledge of antibiotic use and resistance. Male gender (aPR = 1.25, p-value = 0.036) and monthly income < 300,000 UGX (aPR = 1.42, p-value = 0.003) were associated with a positive attitude towards antibiotic use and resistance. Likewise tertiary level of education (aPR = 0.64, p-value = 0.033) was negatively associated with good practices of antibiotic use and resistance.

CONCLUSION AND RECOMMENDATIONS

Residents of urban slums have limited knowledge of antibiotic use and AMR with minimal understanding of AMR concepts. Education level, gender, occupational status are key players in people's understanding and practices of antibiotic use and AMR. There's need for context specific health education programs. Health promotion messaging should emphasize AMR concepts and dangers of drug misuse. Antimicrobial stewardship initiatives should trickle down to the local citizen.

Major blood stream infection-causing bacterial pathogens, antimicrobial resistance patterns and trends: a multisite retrospective study in Asmara, Eritrea (2014-2022)

BACKGROUND

An important knowledge gap exists on the epidemiology of blood stream infections (BSIs) in low-middle-income countries (LMICs). In this retrospective analysis, we evaluated the etiology, antimicrobial resistance (AMR) and trends of BSIs in Eritrea.

METHODS

The study reviewed 9-year records (January 2014- December 2022) of 3153 patients with blood culture results available in the National Health Laboratory (NHL) archives. Relevant data included age, sex, hospital/care center, and year.

RESULT

During the surveillance period, we examined data from 3153 patients (1797 (57.0%) men vs. 1356 (43.0%) females, and 1.2 years (Q1: 0.01 months - Q3: 15 years). Of the samples submitted, 1026 (35.5%) samples were positive for the presence of pathogens (663(64.6%) pathogens vs. 363 (35.4%)) potential contaminants. In decreasing frequency, the most common isolates were: Coagulase-negative Staphylococcus (CoNs), 189 (28.6%); Klebsiella spp., 120 (18.2%); Escherichia coli, 66 (10.0%); Citrobacter spp., 48 (7.3%); Staphylococcus aureus, 47(7.1%); Pseudomonas aeruginosa, 34 (5.1%); and Salmonella spp., 33(5.1). The relative prevalence of BSIs changed somewhat over time (p-value < 0.001) with the isolation of multiple isolates trending upward from 2018 and onwards. Additional findings included the likely presence of extended spectrum beta lactamase (ESBL), high frequency of methicillin resistant Staphylococcus aureus (MRSA) (37(80.4%) and high rate of resistance to gentamicin (363(62.5%) and fluoroquinolones. Furthermore, the multiple antimicrobial resistances (MAR) index was relatively high (mean = 0.55, SD: ±0.23) with wide species-level variation. In a related density cluster analysis, we demonstrated a time-dependent increase in the diversity of resistotypes.

CONCLUSION

This study highlights the considerable health burden of AMR/or MDR in BSIs in Eritrea. Additionally, it underscores the urgent need for enhanced laboratory capacity, surveillance, institutionalisation of antibiotic stewardship programs, and robust infection control programs in hospitals across the country. The need for multidisciplinary research was also highlighted.

Building health research capacity in Africa: the Einstein-Rwanda research and capacity building program

The growing demand for healthcare services and the burden of diseases such as cancer in sub-Saharan Africa (SSA) requires locally-led and setting-relevant evidence that should be driven by local investigators. However, there is a huge gap in the health research capacity to generate such evidence in most of SSA, particularly in Rwanda. With a changing focus and the willingness of investigators and funders from high-income countries (HICs) to support investigators and research from SSA, it is important to build strong, successful, and sustained partnerships. In this perspective, we describe the Einstein-Rwanda Research and Capacity Building Program (ER-RCBP), which represents almost two decades of a fruitful and sustained partnership that has contributed to the development of research physical and human resources in Rwanda. We have established a broad range of health research infrastructure that involves human resources, including training three pathologists, leadership and administrative personnel and structures, clinical research operations, laboratory capacity, and data collection and management systems, and are implementing a long-term plan to transfer most of the leadership to local investigators and the local lead institution. Our experience demonstrates that collaborations between high- and low-income countries can be leveraged to strengthen research capacity in SSA but that such efforts require putting in place structures and systems to ensure success. Building strong partnerships and collaborations, good leadership, empowering local teams, and having buy-in from national governments are key to achieving sustainable research capacity in SSA.

Hemoglobin phenotypes of children attending pediatric clinics in Lomé, Togo, 2022

OBJECTIVE

To provide an up-to-date data, we aim to estimate the frequency of sickle cell disease among children in the pediatric clinics of the Sylvanus Olympio University Hospital, Lome, Togo, in 2022.

RESULTS

A total of 317 children with a median age of 8 years (Interquartile range: 4-12) were included. Both parents knew their Hb phenotype in 7.3% of cases. Nineteen children had sickle cell disease (6.0%) and about 15.6% of the children had sickle cell trait AS. This study found a high frequency of children with sickle cell disease seen in pediatric clinics. We therefore emphasize the need for continued education to improve knowledge of the hemoglobin phenotype at community level and the importance of premarital screening to reduce this burden in the country.

Investigation of methicillin, beta lactam, carbapenem, and multidrug resistant bacteria from blood cultures of septicemia suspected patients in Northwest Ethiopia

The presence of microorganisms in the bloodstream can result in severe, potentially life-threatening conditions, which are a significant cause of morbidity and mortality worldwide. The rise of antimicrobial-resistant strains further exacerbates these outcomes. However, the data concerning bacterial profiles and resistance to antimicrobials, particularly against extended-spectrum beta-lactams and carbapenems, are limited. Aimed to characterize pathogens isolated from positive blood cultures, including bacterial profiles and antibiotic susceptibility patterns, and to identify predictors of blood culture positivity in septicemia-suspected patients at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. A hospital-based cross-sectional study was conducted from February 15 to May 30, 2023. The study involved 341 patients suspected of having septicaemia who were selected consecutively through a convenience sampling technique. Blood samples were collected aseptically from each patient (10 ml from adults, 5 ml from children, and 1 ml from neonates) and inoculated into bottles containing tryptic soy broth in volumes appropriate for the patient's age. The samples were incubated at 35-37 °C for up to 7 days to detect bacterial growth. Positive blood cultures were subcultured onto various media, including chocolate agar, blood agar, modified Thayer-Martin agar, MacConkey agar, and mannitol salt agar, and incubated again at 35-37 °C for 24 h. The suspected bacteria were identified on the basis of colony morphology, Gram staining, and biochemical tests. Antimicrobial susceptibility testing was conducted via both the Kirby-Bauer and modified Kirby-Bauer disk diffusion methods. Resistance to methicillin, extended-spectrum beta-lactams, and carbapenems was determined via the cefoxitin disc test, combined-disk diffusion method, and modified carbapenem inactivation method, respectively. The data were entered into Epi-Data version 4.6 and analysed via SPSS version 25. Binary logistic regression analyses were employed to identify factors associated with bloodstream infections (BSI), with a P value of less than 0.05 considered statistically significant. Out of 341 patients suspected of septicemia, 196 (57.5%) were male and 145 (42.5%) were female, with a mean (± SD) age of 16.5 (± 7.5) years. Bloodstream infection was identified in 87 (25.5%) patients (95% CI: 21.1-30.4). Among these positive cases, 67 (77%) were from ward patients, while 20 (23%) were from those visiting outpatient departments. The primary gram-positive bacteria identified included S. aureus 27 (31.0%), CoNS 14 (16.1%), S. viridans 8 (9.2%), and S. agalactiae 4 (4.6%). The gram-negative isolates were predominantly K. pneumoniae 11 (12.6%), followed by E. coli 9 (10.3%), E. cloacae 6 (6.9%), Acinetobacter spp. 3 (3.5%), N. meningitidis 3 (3.5%), and P. aeruginosa 2 (2.3%). Methicillin resistance was detected in 17/27 (63.0%) S. aureus strains and 2/14 (14.3%) CoNS strains. Multidrug resistance was detected in 63/87 (72.4%, 95% CI: 67.2-84.7%) of the isolates. Extended-spectrum beta-lactamase and carbapenemase production were observed in 12/31 (38.7%) and 5/31 (16.1%) of isolates, respectively. The factors associated with BSI were the presence of wounds and burns (AOR = 2.103, 95% CI: 1.365-3.241, P = 0.041), length of hospital stay (≥ 5) (AOR = 2.209, 95% CI: 1.122-4.347, P = 0.022), and prior medical procedures (AOR = 1.982, 95% CI: 1.125-3.492, P = 0.018). Bloodstream infection was identified in 25.5% of suspected septicemia cases, with multidrug-resistant bacteria present in 72.4% of isolates. Gram-positive bacteria, particularly S. aureus, and gram-negative bacteria like K. pneumoniae and E. coli were predominant. High rates of methicillin, beta-lactam, and carbapenem resistance were observed, emphasizing the magnitude of antimicrobial resistance. Risk factors such as wounds, extended hospital stays, and prior medical procedures significantly increased the likelihood of culture positivity. This suggests the need for regular antimicrobial susceptibility testing to guide antibiotic selection and track resistance trends, proper wound care and medical device usage to reduce the risk of BSI in healthcare settings.

Prevalence and Transfusion Risks of Occult Hepatitis B Infection Among HBcAb-Positive Blood Donors in a High-Endemic Region

Background: Hepatitis B virus (HBV) remains a significant global health concern, particularly in sub-Saharan Africa, where endemicity is high. Occult hepatitis B infection (OBI) presents a unique challenge to transfusion safety, as HBV DNA may persist in HBsAg-negative individuals. This study examines the prevalence of HBcAb positivity among blood donors at Usmanu Danfodiyo University Teaching Hospital (UDUTH), Sokoto, and assesses the risk of HBV transmission. Methods: A cross-sectional study was conducted among 200 blood donors. Samples were screened for HBsAg and HBV serological markers using a rapid assay and ELISA. HBcAb-positive samples were analyzed for HBV DNA using real-time polymerase chain reaction (qRT-PCR). Viral loads were quantified, and socio-demographic characteristics were recorded. Results: HBcAb was detected in 57 (28.5%) of the 200 donors. The most common serological pattern among donors was HBsAg-negative and HBcAb-negative (69%). Among these HBcAb-positive donors, HBV DNA was detected in three cases (1.5%), with viral loads of 753.1, 2.193 × 104, and 4.538 × 104 IU/mL. The presence of HBV DNA in these donors confirms the risk of OBI transmission through transfusion. Socio-demographic analysis revealed that 48.5% of donors were aged 26-35 years, 23.5% were aged 18-25 years, 23% were aged 36-42 years, and 2.5% were either 43-50 or above 50 years of age, of which 99.5% were male. These findings highlight a significant prevalence of HBcAb positivity and OBI, aligning with studies in similar high-endemic settings. Conclusions: HBcAb positivity and OBI represent significant transfusion risks in endemic regions. The presence of HBV DNA in 1.5% of HBcAb-positive donors in the study population highlights the limitations of HBsAg-based screening. Incorporating nucleic acid testing (NAT) into routine blood donor screening protocols is critical to enhancing transfusion safety. Further research is needed to evaluate the feasibility and cost-effectiveness of such interventions in resource-limited settings.

Point Prevalence Survey of Antibiotic Use in Level 1 hospitals in Zambia: Future Prospects for Antimicrobial Stewardship Programs

Introduction

The inappropriate prescribing and use of antibiotics have contributed to the emergence and spread of antimicrobial resistance (AMR). In Zambia, there is a paucity of information on the prescribing patterns and use of antibiotics among hospitalized patients in level 1 hospitals. This study investigated antibiotic use in five level 1 hospitals in Lusaka, Zambia.

Methods

This cross-sectional study utilized the World Health Organization (WHO) Point Prevalence Survey (PPS) methodology among in-patients admitted in level 1 hospitals before 08:00 a.m. on the survey day in August 2024. Data were analysed using IBM SPSS version 23.0.

Results

The prevalence of antibiotic use among inpatients was 59.0%, with ceftriaxone being the most prescribed. Antibiotics were prescribed mainly for paediatrics and male inpatients. This study found that 53.0% of prescribed antibiotics were from the Access group while 38.2% were from the Watch group of the World Health Organization Access, Watch, and Reserve (AWaRe) classification. Adherence to national treatment guidelines was 36.0%, with most antibiotics prescribed empirically without evidence of culture and sensitivity tests.

Conclusion

This study found a high use of antibiotics and low adherence to treatment guidelines in level 1 hospitals in Lusaka, Zambia. The findings of this study demonstrate the need to establish and strengthen antimicrobial stewardship programs and strengthen laboratory capacity to aid clinicians in diagnosing, treating, and managing patients across level 1 hospitals in Zambia.

Challenges of genetics in the diagnosis of sudden cardiac death. Interest for forensic and legal medicine

Sudden cardiac death is the leading cause of death in developed countries and a small but significant number of cases cannot be explained after a thorough autopsy process. Cases of sudden cardiac death in people under 40years of age are mainly due to structural heart disease or cardiomyopathies and arrhythmogenic diseases or channelopathies. In these cases, the search for associated genetic factors through molecular autopsy may help to find the cause of unexplained sudden cardiac death, through genetic diagnosis of previously undiagnosed channelopathies or cardiomyopathies. The finding of genetic variants classified as pathogenic associated with cardiac pathology would conclude the autopsy result and provide the possibility of genetic screening in other family members.

Qualitative assessment of the scale-up of COVID-19 testing network in Armenia: turning adversities into opportunities

BACKGROUND

The COVID-19 pandemic reaffirmed the importance of high-quality laboratory services in the face of elevated demand for timely COVID-19 laboratory diagnosis. We explored the scale-up experience of the laboratory system in Armenia as well as the successes and challenges it brought to the overall laboratory system with the aim to identify lessons that can serve as opportunities for improvement.

METHODS

We conducted a qualitative study to explore the experiences concerning the process of scale-up of the COVID-19 testing network through in-depth interviews with policymakers/experts (n = 6), heads (n = 6) and physicians (n = 3) of private and public laboratories conducting COVID-19 testing. Eight domains of the WHO Laboratory Assessment Tool System (S-LAT) questionnaire guided the study and directed the content analysis.

RESULTS

According to the findings, within the COVID-19 testing network, numerous advancements were documented across all essential elements of the S-LAT as a result of the COVID-19 response. The most vivid improvements were related to the newly established network of public and private laboratories for COVID-19 testing and related coordination mechanisms, new laboratory information management practices, improved compliance with biosafety measures, novel quality assurance mechanisms as well as improved technical and human resources. However, suboptimal coordination of the COVID-19 testing network and the whole laboratory system, the gap between existing and proper biosafety management and quality control practices, and insufficient training of laboratory professionals were mentioned as potential challenges for the laboratory system in the future.

CONCLUSION

The assessment revealed challenges and achievements of the laboratory system during the COVID-19 response. Enhancement of coordination and cooperation mechanisms within and beyond the COVID-19 testing network, continuous improvement of human resources as well as quality and biosafety control practices throughout the whole system are crucial for sustaining the achievements and for strengthening future preparedness of the laboratory system to infectious disease outbreaks.

Beyond Low Prevalence: Exploring Antibiotic Resistance and Virulence Profiles in Sri Lankan Helicobacter pylori with Comparative Genomics

Helicobacter pylori infects at least half the population worldwide, and its highly diverse genomic content correlates with its geographic distribution because of its prolonged relationship with humans. The extremely low infection prevalence alongside low inflammation severity observed in some countries might be caused by strains with low virulence potential. Therefore, this study aimed to investigate whole-genome analysis datasets of Sri Lankan H. pylori strains. H. pylori strains were isolated from biopsy specimens and underwent whole-genome sequencing to investigate their antibiotic resistance and virulence potential. The prevalence of H. pylori infection in Sri Lanka is extremely low (1.7% in a previous study), and only six H. pylori strains were successfully isolated from bacterial culture. Antibiotic resistance analysis showed a high prevalence of metronidazole resistance (83.3%, five out of six strains), and investigation of the related genes showed truncation of the rdxA and frxA genes and single-nucleotide polymorphisms in the rdxA, frxA, ribF, omp11, and fur genes. Most virulence genes of the 144 assessed were present, except for the cag pathogenicity island (cagPAI) (absent in four out of six strains), babA/B/C, and tlpB genes. An incomplete type 4 secretion system (tfs) was found in three strains. A pan-genome analysis with non-Sri Lankan H. pylori strains showed that the htpX gene was found only in Sri Lankan strains (p-corrected = 0.0008). A phylogenetic analysis showed that the Sri Lankan strains clustered with strains from hpAsia2 and hpEurope. This comparative genomic study shows that H. pylori strains with low virulence potential are present in countries with a low prevalence of infection and disease severity, indicating a strain-type geographical pattern. The tailored guidelines for screening and treatment strategy for each region are necessary to obtain effective and efficient eradication.

Genetic variations and carcinogenicity analysis of E6/E7 oncogenes in HPV31 and HPV35 in Taizhou, China

BACKGROUND

The purpose of this study was to investigate the genetic variations in the E6 and E7 oncogenes of HPV31 and HPV35, and to explore their potential role in cervical cancer risk among women in Taizhou, China.

METHODS

Cervical exfoliated cells were collected for HPV genotyping, and only patients with a single infection of either HPV31 or HPV35 were selected for this study. The ABI 3730xl sequencer was utilized to sequence the E6 and E7 genes, followed by subsequent sequence alignment, analysis of genetic heterogeneity, and construction of maximum likelihood phylogenetic trees for the sequences of HPV31 and HPV35 using BioEdit and MEGA softwares.

RESULTS

From 2013 to 2023, 148 HPV31 E6/E7 gene sequences and 121 HPV35 E6/E7 gene sequences were successfully obtained. We identified 16 distinct HPV31 E6/E7 variants and 5 distinct HPV35 E6/E7 variants, which have been deposited in GenBank under accession numbers OR540563-OR540578 and OR540579-OR540583, respectively. Phylogenetic analysis revealed that most of the HPV31 variants belonged to sublineage A2 (57.4%), followed by sublineages C2 (26.4%), C3 (14.2%) and B1 (2.0%). The proportion of CIN2 + patients in sublineage A2 was greater than that in other HPV31 sublineages, but the difference was not statistically significant (69.2% vs. 30.8%, P > 0.05). The most common variant in A2 was 31CNTZ07, which has a greater risk of CIN2 + than other A2 variants (OR = 3.5, 95% CI = 1.31 to 9.36; P < 0.05). In addition, all the HPV35 variants belonged to lineage A, of which 99.2% belonged to sublineage A1. 35CNTZ01 and 35CNTZ03 were the two most common HPV35 variants in our population, but no significant difference in their carcinogenic ability was observed (P < 0.05).

CONCLUSION

These data provides a deeper insight into the distribution of geographic/ethnical HPV31 and HPV35 variants, which contribute to the development of multivalent HPV vaccines and diagnostic assays that are suitable for Chinese women.

Whole genomic analysis uncovers high genetic diversity of rifampicin-resistant Mycobacterium tuberculosis strains in Botswana

Background

The emergence of drug-resistant Mycobacterium tuberculosis (M. tb) strains remains a threat to tuberculosis (TB) prevention and care. Understanding the drug resistance profiles of circulating strains is crucial for effective TB control. This study aimed to describe the genetic diversity of rifampicin-resistant M. tb strains circulating in Botswana using whole genome sequencing (WGS).

Methods

This study included 202 stored M. tb isolates from people diagnosed with rifampicin-resistant TB (RR-TB) between January 2016 and June 2023. Genomic DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method. Library preparation was performed using the Illumina DNA prep kit following the manufacturer's instructions. Sequencing was done on Illumina NextSeq2000. TBProfiler software was used to identify known M. tb lineages and drug resistance profiles. Statistical analyses were performed on STATA version 18.

Results

WGS analysis revealed multidrug resistance (57.9%: 95% CI; 50.7-64.8), Pre-XDR (16.8%, 95% CI: 11.9-22.7), RR-TB (20.2%: 95% CI: 14.98-26.5), and HR-TB (0.5%, 95% CI; 0.01-2.7). We identified a high genetic diversity with three predominant lineages: lineage 4 (60.9%, 95% CI; 53.8-67.7), lineage 1 (22.8%: 95% CI; 17.2-29.2), and lineage 2 (13.9%, 95% CI: 9.4-19.4). The most frequently observed drug resistance mutations for rifampicin, isoniazid, ethambutol, streptomycin, pyrazinamide, and fluoroquinolones were rpoB S450L (28.6%), katG S315T (60.5%), embA_c.-29_-28delCT, embB Q497R (31.7%), rrs_n.517C>T (47.1%), pncA_c.375_389delCGATGAGGTCGATGT (36.0%) and gyrA A90V (79.4%), respectively. No bedaquiline and delamanid resistance-associated mutations were detected.

Conclusions

This study highlights the high genetic diversity of M. tb strains, with a predominance of lineage 4 among people with RR-TB in Botswana. It provides valuable insights into the genetic diversity of rifampicin-resistant M. tb strains circulating in Botswana.

Mapping of regions with low tuberculosis notification and estimation of diagnostic gaps in Cameroon, evidence from OpenStreetMap and WorldPop data

Since 2012, Cameroon has introduced rapid molecular diagnostic tests for tuberculosis (TB). Despite this progress, WHO estimates indicate a TB diagnostic gap of 43% at the national level in 2019. This raises questions about the strategic allocation of available rapid molecular diagnostic tools to areas with lower TB notification. In a cross-sectional study, we combined Cameroon notification data on TB (2019), rifampicin-resistant (RR)-TB (2015-2019), as well as local TB risk factors, availability, intensity of use and accessibility of the Xpert MTB-RIF test with openly available geospatial datasets from OpenStreetMap and WorldPop. A mathematical model estimated TB and RR-TB incidence rates at the regional level. We compared these estimates with the number of reported TB cases to identify diagnostic gaps. Centre, East and Far North regions had the highest estimated TB incidence rates (400, 300 and 200 cases per 100,000 inhabitants, respectively), while South and Adamawa had the highest estimated RR-TB incidence rates (14.9 and 8.9 cases per 100,000 inhabitants, respectively). We report a national diagnostic gap of 53% and 50% for TB and RR-TB, respectively. These findings highlight the need to improve the allocation of diagnostic tools that follows the local disease burden in resource-limited settings to improve health equity.

Feasibility and potential impact of a local proficiency testing program in Accra, Ghana

OBJECTIVES

To implement a pilot proficiency testing (PT) program in Accra, Ghana, using locally produced PT materials and to explore the relationship between laboratory test costs and laboratory quality in Accra, Ghana.

METHODS

Remnant serum samples from a local laboratory were pooled, aliquoted, and distributed to a convenience sample of 23 laboratories in Accra, Ghana, 2 of which had International Organization for Standardization (ISO) accreditation. One of the ISO-accredited laboratories was designated as the reference/target, and the range for passing was based on international criteria. Test cost, test results, and testing instruments used were compiled.

RESULTS

Of the 23 laboratories, 18 submitted results. Total testing costs ranged from 80 to 312 Ghanaian cedi (GH₵) (7-26 USD). Overall accuracy (pass rate) was calculated per laboratory and per analyte. The mean laboratory accuracy was 61% (15%-92%). The pass rate for individual analytes ranged from 18% to 94% (mean, 72%). There was no correlation between test cost and pass rate.

CONCLUSIONS

The pass rates of clinical laboratories in Accra, Ghana, varied from 15% to 92%, and there was no relationship to test cost. A PT program to objectively evaluate each laboratory's performance is needed. Making the PT material locally, as in this study, is a financially sustainable approach.

Antimicrobial Resistance Surveillance of Skin and Soft Tissue Infections: Hospital-Wide Bacterial Species and Antibiograms to Inform Management at a Zonal Tertiary Hospital in Mwanza, Tanzania

Purpose

The National Action Plan on antimicrobial resistance (NAP-AMR) in Tanzania is focused on blood stream infections and urinary tract infections despite skin and soft tissue infections (SSTIs) being common. This study assessed the proportion of laboratory-confirmed SSTIs, identify bacterial species involved, analyze AMR phenotypes, and investigate the risk factors associated with multidrug-resistant (MDR) SSTIs.

Patients and Methods

Analytical cross-sectional study was conducted between January and June 2023, involving 614 patients with SSTIs. Patients' information was collected using standard AMR surveillance tools, and either pus swabs or pus aspirate or necrotic tissues were collected and analyzed using standard microbiological procedures, WHONET and STATA software programs.

Results

The median age (interquartile range) of patients was 34 (14-54) years with males accounting for 54.4%. Laboratory-confirmed SSTIs was 72.5% (445/614), yielding 586 bacterial isolates. The most frequent SSTIs types were surgical site infections (30.0%), chronic wounds (27.9%), and traumatic wounds (19.7%). The commonest pathogens were Staphylococcus aureus (17.1%), Escherichia coli (17.1%), and K. pneumoniae (16.0%). The AMR phenotypes identified were methicillin resistant Staphylococcus aureus, 29.0%; Extended-spectrum beta lactamase producing Gram-negative bacteria, 47.3%; and carbapenem resistant Gram-negative bacteria, 12.9%. The overall MDR SSTIs was 40.9% (251/614) and was significantly higher among inpatients compared to outpatients [OR (95% CI); p-value: 1.86 (1.33-2.59); p-value<0.001].

Conclusion

Approximately three-quarter of patients have laboratory-confirmed SSTIs caused predominantly by MDR pathogens. Revisiting SSTIs treatment guidelines at BMC and inclusion of SSTIs in the on-going AMR surveillance in Tanzania are recommended.

Medical students' knowledge, attitudes, and motivation towards antimicrobial resistance efforts in Eastern Uganda

INTRODUCTION

Learning beyond the classroom is important for holistic engagement in antimicrobial resistance(AMR) mitigation. Extracurricular interventions can catalyze multidisciplinary engagement and inspire innovative solutions. This study aimed to determine the knowledge, attitudes, and motivations influencing medical students' engagement in AMR Club initiatives at Busitema University, Uganda.

METHODOLOGY

This was a descriptive cross-sectional study conducted at Busitema University among undergraduate students pursuing Bachelors of Medicine and Surgery, Bachelor of Science in Nursing, and Bachelor of Science in Anesthesia and Critical care. Data collection was performed using a semi-structured, pre-tested questionnaire and administered to the participants The Bloom's cut-off method was used to analyse the knowledge of the participants, while bivariate analysis was conducted using the chi square test. Multivariable logistic regression analysis was used to identify factors independently associated with students' engagement in AMR club activities.

RESULTS

Of the 193 study participants, 71.5%(n) demonstrated sufficient knowledge about antimicrobial resistance (AMR), as determined using Bloom's cutoff categories (≥60% classified as sufficient, <60% as insufficient), with an average knowledge score of 68.18% (SD ±16.12). Additionally, 90% of participants acknowledged the significance of incorporating AMR topics into their curriculum, while 87.5% emphasized the need for AMR training using a One Health approach. The major motivations for students to engage in extracurricular activities addressing AMR were peer influence (n = 42), university support (n = 35), and inspiration drawn from peer mentors' work (n = 35).

CONCLUSION

The students demonstrated a high level of knowledge and positive attitudes towards AMR but highlighted the need for further in-depth training. Participation in extra-curricular activities such as involvement in an AMR Club, was found to significantly influence students' engagement in AMR related interventions.

Laboratory capacity-building during COVID-19 in Somalia: improving access to essential diagnostics for national health security in a fragile setting

INTRODUCTION

Even before the COVID-19 pandemic, Somalia's national laboratory services had insufficient diagnostic capacities. We describe how the country moved rapidly from no testing capability to molecular testing and genomic sequencing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other pathogens.

METHODS

We reviewed primary sources information as well as data and records from secondary sources from 1 January 2020 to 31 December 2023. We also analyzed laboratory surveillance data of cases of COVID-19 and other epidemic diseases reported during the same period and the number of laboratory tests performed during the same period. We used this information to demonstrate improvements in laboratory diagnostic capacity in Somalia before, during and after the COVID-19 pandemic.

RESULTS

The country was able to rapidly scale up testing for SARS-CoV-2 using reverse-transcriptase polymerase chain reaction assays. At the same time, other innovative solutions were used for testing, such as repurposing tuberculosis GeneXpert diagnostic platforms to increase access to testing at points-of-care and introducing antigen rapid diagnostic tests for hard-to-reach communities. Somalia also acquired new generation sequencing capability for detection and characterization of circulating SARS-CoV-2. These laboratory and testing enhancements have enabled Somalia to participate in surveillance for priority diseases and detection of outbreaks caused by emerging pathogens.

CONCLUSION

Somalia's strategic approach to COVID-19 is an inspiring example of resilience and adaptability. Utilizing resources, technology and lessons from COVID-19 enabled the country to increase and improve laboratory services, expand testing capacity, and strengthen workforce capability. As such, Somalia can now better respond to other infectious disease threats and has significantly improved national health security.

External quality assurance (EQA) network in South and South-East Asia: experience and results from an international EQA programme in One Health sector reference laboratories

OBJECTIVES

External quality assurance (EQA) is an objective tool to assess laboratories' diagnostic performance and their adherence to recognized international standards. External Quality Assessment in Asia (EQASIA) is an EQA network in South and South-East Asia established in 2020 with the aim of improving the quality of bacteriology diagnostics across all One Health sectors in the region. The aim of this paper is to provide a comprehensive overview of the EQA results collected from the EQASIA network and to assess improvements among the participating laboratories.

METHODS

Six EQA rounds were conducted between 2021 and 2023, each composed of different panels of WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) and The Food and Agriculture Organization of the United Nations (FAO) priority pathogens of interest to both the human and animal health sector.

RESULTS

Between 24 and 32 laboratories signed up for six EQA rounds (EQA1-6). Participating laboratories were able to isolate and correctly identify most of the isolates across the EQA panels except for the Campylobacter spp. and Enterococcus spp. panels. The overall performance of laboratories across the six EQAs was between 75% and 100% (average 93.3% and median 93.6%). The obtained results showed a significant improvement in laboratories' performance over time.

CONCLUSIONS

Laboratory capacity development and quality assurance in a microbiology laboratory are of particular importance especially in the context of antimicrobial resistance (AMR) and One Health surveillance. The EQASIA programme has the potential to validate laboratories' performance in detecting important One Health pathogens, generating reliable data for effective surveillance to curb AMR.

Detection of hepatitis B virus surface antigen, IgM and IgG antibodies to hepatitis B virus core antigen in the clinical classification and epidemiological surveillance of HBV infection

Hepatitis B virus surface antigen (HBsAg), IgM and IgG antibodies to hepatitis B virus core antigen (anti-HBcIgM and anti-HBcIgG) comprise serological markers of hepatitis B virus (HBV) infection of great importance in the epidemiological surveillance of hepatitis B, since they have been routinely considered for classifying the acute and chronic clinical forms of HBV infection. This classification is established according to the expression and dynamics of these markers in the infected person's bloodstream, which serves as the basis for the differential diagnosis between the two clinical entities. However, in certain circumstances, both acute and chronic infection, the detection of these markers may not occur in the bloodstream, favoring the occurrence of atypical serological profiles of infection, and compromising the correct infection clinical classification. In addition, the complex and varied nature of hepatitis B serological profiles may compromise the health professional's ability to analyze the case and, thus, correctly classify the infection's clinical form. Since the expression of these markers in the bloodstream occurs dynamically, with consequent changes in the patient's serological profile as he progresses towards recovery or chronicity, the diagnosis of acute or chronic infection may also be compromised, if it is established based on the collection of a single sample and without knowing the patient's clinical history and their epidemiological antecedents. This manuscript addresses the sensitivity and specificity of HBsAg, anti-HBcIgM, and anti-HBcIgG serological markers detection in the clinical classification of HBV infection and in the epidemiological surveillance of hepatitis B. This review is covering the clinical and epidemiological interpretations of the markers in and of themselves, not in reference to any specific assays.

One Health distribution of beta-lactamases in Enterobacterales in the United States: A systematic review and meta-analysis

BACKGROUND

The study aimed to review the beta-lactamase resistance genes detected in Enterobacterales from humans, animals, and the environment in the United States.

METHODS

We conducted a comprehensive search on PubMed, Web of Science, and Google Scholar for articles reporting beta-lactamase genes in the United States from 1981 to 22 April 2022, following the PRISMA protocol. Studies were evaluated based on predefined eligibility criteria, and both qualitative and quantitative analyses were conducted on the selected studies.

RESULTS

Of the 335 articles, a total of 169 different beta-lactamase genes, including narrow-spectrum, extended-spectrum, AmpC, and carbapenemase have been detected and reported in the United States, with human (137), animal (53), and environment (47). 22 genes (blaCMY-2, blaCTX-M-(1, 2, 9, 14, 15, 27, 32, 65), blaFOX-5, blaIMP-27, blaKPC-2, blaNDM-(1, 5), blaOXA-(1, 48), blaPSE-1, blaSHV-(1, 12), blaTEM-(1, 1A, 1B)) have been reported across animals, humans, and environment. Notably, blaCTX-M-15 was prevalent in E. coli isolates, with an overall pooled proportion of 10.7 %, varying between animals (8.6 %), humans (13.1 %), and the environment (0.8 %). Similarly, blaCMY-2 in E. coli isolates had an overall pooled proportion of 10.6 %, with distinctions in proportion among animals (1.6 %), humans (41.3 %), and the environment (16.2 %). The sequence type (ST131) was detected as the predominant, mainly associated with the blaCTX-M-15, with a pooled proportion of 56.9 %, varying from 14.3 % to 90 % across studies.

CONCLUSION

This study highlights the distribution of beta-lactamases in the United States, essential for understanding One Health and the molecular epidemiology of key beta-lactamases, especially extended-spectrum beta-lactamases and carbapenemases.

Effectiveness and Cost-effectiveness of Artificial Intelligence-assisted Pathology for Prostate Cancer Diagnosis in Sweden: A Microsimulation Study

BACKGROUND AND OBJECTIVE

Image-based artificial intelligence (AI) methods have shown high accuracy in prostate cancer (PCa) detection. Their impact on patient outcomes and cost effectiveness in comparison to human pathologists remains unknown. Our aim was to evaluate the effectiveness and cost-effectiveness of AI-assisted pathology for PCa diagnosis in Sweden.

METHODS

We modeled quadrennial prostate-specific antigen (PSA) screening for men between the ages of 50 and 74 yr over a lifetime horizon using a health care perspective. Men with PSA ≥3 ng/ml were referred for standard biopsy (SBx), for which cores were either examined via AI followed by a pathologist for AI-labeled positive cores, or a pathologist alone. The AI performance characteristics were estimated using an internal STHLM3 validation data set. Outcome measures included the number of tests, PCa incidence and mortality, overdiagnosis, quality-adjusted life years (QALYs), and the potential reduction in pathologist-evaluated biopsy cores if AI were used. Cost-effectiveness was assessed using the incremental cost-effectiveness ratio.

KEY FINDINGS AND LIMITATIONS

In comparison to a pathologist alone, the AI-assisted workflow increased the number of PSA tests, SBx procedures, and PCa deaths by ≤0.03%, and slightly reduced PCa incidence and overdiagnosis. AI would reduce the proportion of biopsy cores evaluated by a pathologist by 80%. At a cost of €10 per case, the AI-assisted workflow would cost less and result in <0.001% lower QALYs in comparison to a pathologist alone. The results were sensitive to the AI cost.

CONCLUSIONS AND CLINICAL IMPLICATIONS

According to our model, AI-assisted pathology would significantly decrease the workload of pathologists, would not affect patient quality of life, and would yield cost savings in Sweden when compared to a human pathologist alone.

PATIENT SUMMARY

We compared outcomes for prostate cancer patients and relevant costs for two methods of assessing prostate biopsies in Sweden: (1) artificial intelligence (AI) technology and review of positive biopsies by a human pathologist; and (2) a human pathologist alone for all biopsies. We found that addition of AI would reduce the pathology workload and save money, and would not affect patient outcomes when compared to a human pathologist alone. The results suggest that adding AI to prostate pathology in Sweden would save costs.

Seroprevalence of Typhoid Fever and Its Associated Risk Factors Among Clinically Diagnosed Febrile Patients Visiting the Outpatient Department at Debark Hospital and Drug Susceptibility Patterns of Isolates

Typhoid fever is caused by the bacterium Salmonella Typhi, which poses major health problems in developing countries, including Ethiopia. However, there is limited information regarding typhoid fever, contributing factors with it, and its drug susceptibility pattern in the research area. The aim of this study was to determine the seroprevalence of typhoid fever and its associated risk factors among clinically diagnosed febrile patients at Debark Hospital and evaluate the drug susceptibility patterns of the isolates. A hospital-based cross-sectional study was conducted among 158 febrile patients from December 2022 to April 2023. Blood and stool samples were collected from each febrile patient. The Widal test was used to test Salmonella Typhi O and H antigens sera from blood, and bacteria were cultured from the stool. Gram staining and biochemical analyses were carried out for each isolate. Antibiotic susceptibility testing was performed for the isolates using Kirby-Bauer disk diffusion techniques. Descriptive statistics and logistic regression were used for analysis. In this study, the seroprevalence of typhoid fever among febrile patients at Debark Hospital was 22.8%. Gender (adjusted odds ratio (AOR): 95% confidence interval (CI): 0.02, 0.31, p ≤ 0.001), marital status (AOR: 95% CI: 2.63, 4.66, p ≤ 0.001), family size (AOR: 95% CI: 0.01, 0.31, p ≤ 0.001), residence (AOR: 95% CI: 0.09, 0.83, p = 0.021), practice of using toilet (AOR: 95% CI: 0.08, 0.086, p = 0.027), washing fruits and vegetables before eating (AOR: 95% CI: 0.12, 0.87, p = 0.025), and awareness of typhoid fever transmission and prevention (AOR: 95% CI: 0.12, 0.91, p = 0.032) are the associated risk factors for typhoid fever. Fifty percent of the isolates showed multidrug resistance to two or more antibiotics. It was suggested that improving personal hygiene, providing safe drinking water, and careful use of antibiotics could considerably reduce the prevalence of typhoid fever in the study area.

Genetic background of neonatal hypokalemia

Neonatal hypokalemia (defined as a serum potassium level <3.5 mEq/L) is the most common electrolyte disorder encountered in clinical practice. In addition to common secondary causes, primary genetic etiologies are also closely associated with hypokalemia. Currently, a systematic characterization of these genetic disorders is lacking, making early recognition challenging and clinical management uncertain. This review will aid clinicians by summarizing the genetic background of neonatal hypokalemia from two aspects: (1) increased excretion of K+, whereby genetic factors primarily lead to increased renal Na+ influx, decreased H+ efflux, or reduced Cl- influx, ultimately resulting in increased K+ efflux; and (2) decreased extracellular distribution of K+, whereby genetic factors result in abnormalities in transmembrane ion channels, reducing outward potassium currents or generating inward cation leak currents. We describe over ten genetic diseases associated with neonatal hypokalemia, which involve pathogenic variants in dozens of genes and affect multiple target organs, including the kidneys, intestines, and skeletal muscle. For example, in the renal tubules, pathogenic variants in the SLC12A1 gene encoding the Na+-K+-2Cl- cotransporter lead to renal K+ loss, causing Bartter syndrome type I; in intestinal epithelial cells, pathogenic variants in the SLC26A3 gene result in a defective Cl⁻-HCO₃⁻ exchanger, causing congenital chloride diarrhea; and in skeletal muscle, pathogenic variants in the CACNA1S gene impact membrane calcium ion channels resulting in hypokalemic periodic paralysis. Given the wide variety of organs and genetic alterations that can contribute to neonatal hypokalemia, we believe this review will provide valuable insights for clinical diagnosis and treatment.

Characterization of the Phenotypic and Genotypic Antibiotic Resistance Markers in Escherichia coli (E. coli) Associated With Diabetes and Nondiabetic Patients

Introduction: Individuals with diabetes are more susceptible to urinary tract infections (UTIs) than those without the disease. This study aimed to determine the phenotypic and genotypic antibiotic resistance profiles of Escherichia coli in diabetic and nondiabetic patients. Methodology: A total of 374 clean-catch midstream urine specimens were screened for uropathogens, and antibiogram analysis was done on E. coli isolates by the Kirby-Bauer disc diffusion method, followed by phenotypic confirmation of extended spectrum beta-lactamase (ESBL) production. In addition, polymerase chain reaction (PCR) assays were carried out to determine ESBL genotypes. Result: Overall, we observed UTIs prevalence of 19.8% and 10.7% in diabetic and nondiabetic patients. Females exhibited higher UTI prevalence than males in both groups ([71.8% and 28.2%] vs. [85% and 15%]) (p < 0.0001). Among women with and without diabetes, the age groups of 55-64 and 25-34 years showed the highest prevalence of UTIs (25.6% vs. 40%). The most prevalent uropathogen was E. coli (62.2% vs. 75%); multidrug-resistant (MDR) E. coli was (61% vs. 33.3%) and ESBL-E. coli was (34.8% and 20%) in diabetic and nondiabetic patients, respectively. The most common ESBL-mediated gene was blaCTX-M (64.3%) with multiple ESBL genes in some E. coli isolates. High-level resistance was observed for ampicillin (91.2%), cefuroxime (96.7%), ciprofloxacin (44.9%), and trimethoprim (59.4%), and low-level resistance was observed for gentamicin (18.7%), ceftriaxone (20.9%), and nitrofurantoin (19.8%). There was no significant difference between antibiotic resistance in diabetic and nondiabetic patients (p > 0.05). Conclusion: We observed blaCTX-M as the most common ESBL genotype, in combination with other ESBL genes present in some E. coli isolates. Nitrofurantoin and ceftriaxone antibiotics were efficacious. Appropriate prescription of antibiotic therapy, and the prevention of transmission of resistant genes in the context of public health can be facilitated by routine monitoring of the resistance profiles and ESBL markers in patients with and without diabetes.

New Option for Antibiotic Susceptibility Testing in Clinical Practice: Performance Evaluation of AutoMic-i600 Automatic System Based on Broth Microdilution Method

Background

The emergence of multidrug-resistant bacteria limits antibiotic efficacy, making accurate antimicrobial susceptibility testing (AST) essential for clinical decisions. Broth microdilution (BMD) is the gold standard but is impractical for routine application. Current automated AST systems improve efficiency but face accuracy or operational challenges, highlighting the need for reliable and user-friendly solutions.

Objective

This study aims to evaluate the performance of a novel automated AST system (AutoMic-i600) based on the BMD method for AST of common clinical bacteria.

Methods

A total of 229 clinical isolates (150 Gram-negative and 79 Gram-positive) were prospectively collected from microbiology laboratory between June 2023 and August 2023. We reported the comparison of the AutoMic-i600 and Vitek 2 systems for routine antibiotics, and also validated the detection performance of AutoMic-i600 for novel antibiotics, based on the BMD method.

Results

The overall essential agreement (EA) and categorical agreement (CA) between AutoMic-i600 and BMD were 93.2% and 93.5% for Gram-negative bacteria and 98.5% and 97.8% for Gram-positive bacteria, respectively. The overall EA and CA between Vitek 2 and BMD were 92.6% and 93.5% for Gram-negative bacteria and 97.9% and 97.4% for Gram-positive bacteria. Importantly, for drug-resistant bacteria, AutoMic-i600 demonstrated a higher overall agreement than Vitek 2 (EA: 98.1% vs 94.8%, CA: 97.5% vs 92.0%), especially in Gram-negative bacteria (EA: 97.7% vs 93.5%, CA: 97.7% vs 89.3%). The VME rate for Gram-negative bacteria using AutoMic-i600 was significantly lower than that of Vitek 2 (1.0% vs 2.9%). Novel antibiotics detected by AutoMic-i600 exhibited EA and CA rates exceeding 90.0%.

Conclusion

Based on these findings, we recommend that the AutoMic-i600 system could be a new option for routine AST testing in a clinical setting. Particularly for drug-resistant bacteria and novel antibiotics, detection with AutoMic-i600 may be more reliable, which could further contribute to the prevention and treatment of drug-resistant bacteria.

Pretreatment attrition after rifampicin-resistant tuberculosis diagnosis with Xpert MTB/RIF or ultra in high TB burden countries: a systematic review and meta-analysis

INTRODUCTION

The WHO endorsed the Xpert MTB/RIF (Xpert) technique since 2011 as initial test to diagnose rifampicin-resistant tuberculosis (RR-TB). No systematic review has quantified the proportion of pretreatment attrition in RR-TB patients diagnosed with Xpert in high TB burden countries.Pretreatment attrition for RR-TB represents the gap between patients diagnosed and those who effectively started anti-TB treatment regardless of the reasons (which include pretreatment mortality (death of a diagnosed RR-TB patient before starting adequate treatment) and/or pretreatment loss to follow-up (PTLFU) (drop-out of a diagnosed RR-TB patient before initiation of anti-TB treatment).

METHODS

In this systematic review and meta-analysis, we queried EMBASE, PubMed and Web of science to retrieve studies published between 2011 and 22 July 2024, that described pretreatment attrition for RR-TB using Xpert in high TB burden countries. Data on RR-TB patients who did not start treatment after diagnosis and reasons for not starting were extracted in an Excel table. A modified version of the Newcastle-Ottawa scale was used to evaluate the risk of bias among all included studies. The pooled proportion of pretreatment attrition and reasons were assessed using random-effects meta-analysis. Forest plots were generated using R software.

RESULTS

Thirty eligible studies from 21 countries were identified after full-text screening and included in the meta-analysis. Most studies used routine programme data. The pooled proportion of pretreatment attrition in included studies was 18% (95% CI: 12 to 25). PTLFU and pretreatment mortality were, respectively, reported in 10 and nine studies and explained 78% (95% CI: 51% to 92%) and 30% (95% CI: 15% to 52%) of attrition.

CONCLUSION

Pretreatment attrition was widespread, with significant heterogeneity between included studies. National TB programmes should ensure accurate data collection and reporting of pretreatment attrition to enable reliable overall control strategies.

PROSPERO REGISTRATION NUMBER

CRD42022321509.

Implementation of a Laboratory Information Management System (LIMS) for microbiology in Timor-Leste: challenges, mitigation strategies, and end-user experiences

BACKGROUND

Effective diagnostic capacity is crucial for clinical decision-making, with up to 70% of decisions in high-resource settings based on laboratory test results. However, in low- and middle-income countries (LMIC) access to diagnostic services is often limited due to the absence of Laboratory Information Management Systems (LIMS). LIMS streamline laboratory operations by automating sample handling, analysis, and reporting, leading to improved quality and faster results. Despite these benefits, sustainably implementing LIMS in LMIC is challenging due to high costs, inadequate infrastructure, and limited technical expertise.

METHODS

This study evaluated the implementation of a customised microbiology LIMS at the National Health Laboratory (NHL) in Timor-Leste. The LIMS was deployed in November 2020, with an accompanying online results portal introduced in early 2021. The implementation was assessed via a checklist based on key challenges and requirements for LIMS in LMIC, alongside a post-implementation survey of scientists and clinicians.

RESULTS

The assessment revealed significant improvements in laboratory processes, including enhanced sample throughput, data management, and result reporting. The LIMS reduced transcription errors and standardised reporting of antimicrobial susceptibility testing (AST), improving data quality and accessibility. However, challenges such as unreliable internet connectivity and the need for ongoing funding and technical support persist. The user satisfaction survey, with responses from 19 laboratory scientists and 15 clinicians, revealed positive feedback on workflow improvements and result accessibility, although concerns about internet speed, sustainability, and the need for further training were noted.

CONCLUSION

This study highlights the importance of careful planning, customisation, and stakeholder engagement in LIMS implementation in LMIC. The success in Timor-Leste demonstrates the potential for improved laboratory quality and patient outcomes, but also underscores the need for ongoing investment in infrastructure, technical expertise, and sustainability planning.

Pooling the complex survey data across the 64 lower and middle-income countries: A study on antibiotic usage in under-five children

Background

Antibiotic exposure for fever/cough has been rising alarmingly, especially among children under five in low- and middle-income countries (LMICs). This excessive use could result in higher healthcare costs, and antibiotic resistance is an alarming trend in developing countries. As a result, it's crucial to look at the variables that affect antibiotic exposure and highlight the subgroups among whom antibiotic abuse is the most prevalent.

Methods

We used the most recent standard Demographic and Health Survey (DHS) data for 64 LMICs. Sample weights were employed in studies to ensure exact standard errors and estimate p-values. To analyze antibiotic exposures across countries, continents, economic levels, and the top and bottom ten countries with fever/cough, we conducted descriptive statistics. Additionally, we provided accompanying bar diagrams for each descriptive finding to enhance visual understanding. For geospatial analysis, we utilized ArcGIS, a powerful tool for mapping and spatial analysis.

Findings

We used data from 141,018 children under five who were reported to have had fever/cough recently in 64 LMICs. Among them, 30.4 % were exposed to antibiotics for fever/cough. Congo (68.7 %), Egypt (65.5 %), and Tajikistan (61.8 %) had the highest prevalence of antibiotic consumption across LMICs. On the other hand, Cameroon (0.3 %), Armenia (4.0 %), and Mauritania (6.1 %) had the lowest. In the final binary logistic regression, mothers that had any formal education (Primary: OR = 1.28, 95 % CI:1.07-1.53, Secondary: OR = 1.38, 95 % CI:1.14-1.67, Higher Education: OR = 1.69, 95 % CI:1.23-2.33) were more likely to expose their children to antibiotics for fever/cough than illiterate ones. Additionally, children in richer households (Richer: OR = 1.38, 95 % CI:1.15-1.66, Richest: OR = 1.46, 95 % CI:1.19-1.80) were more likely to receive antibiotics than those in poorer households.

Conclusions

Antibiotic exposure for fever/cough in children under five was relatively moderate across 64 LMICs. However, the rate was incredibly high in some LMICs and incredibly low in others. The researchers recommend that the countries with high and low percentages of antibiotic exposure investigate either any possibility of antibiotic abuse or proper healthcare service at the national level.