African Journal of Laboratory Medicine最新文献

Background: HIV testing remains an entry point into HIV care and treatment services. In 2007, Nigeria adopted and implemented a two-test rapid HIV testing algorithm of three HIV rapid test kits, following the sequence: Alere Determine (first test), Unigold^TM (second test), and STAT-PAK^® as the tie-breaker. Sub-analysis of the 2018 Nigeria HIV/AIDS Indicator and Impact Survey data showed significant discordance between the first and second tests, necessitating an evaluation of the algorithm. This manuscript highlights lessons learnt from that evaluation.

Intervention: A two-phased evaluation method was employed, including abstraction and analysis of retrospective HIV testing data from January 2017 to December 2019 from 24 selected sites supported by the United States President's Emergency Plan for AIDS Relief programme. A prospective evaluation of HIV testing was done among 2895 consecutively enrolled and consented adults, aged 15-64 years, accessing HIV testing services from three selected sites per state across the six geopolitical zones of Nigeria between July 2020 and September 2020. The prospective evaluation was performed both in the field and at the National Reference Laboratory under controlled laboratory conditions. Stakeholder engagements, strategic selection and training of study personnel, and integrated supportive supervision were employed to assure the quality of evaluation procedures and outcomes.

Lessons learnt: The algorithm showed higher sensitivity and specificity in the National Reference Laboratory compared with the field. The approaches to quality assurance were integral to the high-quality study outcomes.

Recommendations: We recommend comparison of testing algorithms under evaluation against a gold standard.

What this study adds: This study provides context-specific considerations in using World Health Organization recommendations to evaluate the Nigerian national HIV rapid testing algorithm.

Background: The clinical presentations of coronavirus disease 2019 (COVID-19) exhibit significant variation, ranging from asymptomatic cases to mortality resulting from severe pneumonia. Host genetics can partially explain this variation.

Objective: This study evaluated possible associations between severity and outcome of COVID-19 and single nucleotide polymorphism (SNP) rs2285666 in the ACE2 gene and SNP rs2070788 in the TMPRSS2 gene.

Methods: The study included a sample of 100 consecutive adult patients admitted to the COVID-19 Isolation and Intensive Care Units of the Zagazig University Hospitals, Zagazig, Egypt from July 2021 to November 2021. For rs2285666, polymerase chain reaction-restriction fragment length polymorphism was carried out. For rs2070788, real-time polymerase chain reaction was performed.

Results: For rs2285666, the GA genotype was the most frequent among female patients (39% [16/41]) and the A genotype was more prevalent among male patients (54.2% [32/59]). For rs2070788, the AA genotype was the most frequent among all patients (46% [46/100]). No rs2285666 or rs2070788 genotypes or allele frequencies had significant associations with either severity or outcomes of patients.

Conclusion: This study found no significant associations of COVID-19 severity or outcomes of patients with genotypes or allele frequencies of the rs2285666 SNP in the ACE2 gene or the rs2070788 SNP of the TMPRSS2 gene. The search for other genetic associations with COVID-19 infection is still required.

What this study adds: The study reveals that host genetics explain the variation observed in the disease. Specific genetic variants can confer either increased susceptibility or resistance to the disease.

Background: The impact of antimicrobial resistance on children living in resource-limited countries has been underreported, despite its established global threat.

Objective: This retrospective study aimed to describe the trend of antibiotic susceptibility in the paediatric age group.

Methods: Sensitivity test report data consisting of 300 paediatric patients aged 18 hours to 192 months were retrieved from the microbiology laboratory records at a state-owned children's hospital in Nigeria over a period of 4 months starting from December 2021 to March 2022. Five genera (Escherichia coli, Klebsiella spp., Pseudomonas spp., Staphylococcus aureus and Streptococcus spp.) were cultured as recommended by the Clinical Laboratory Standard Institute, using the Kirby Bauer disc diffusion method. Antimicrobial susceptibility testing was carried out on isolates using 15 different antibiotics.

Results: Staphylococcus aureus was the most frequent pathogen isolated 32.1% (50/156) and Pseudomonas spp. was the least frequent pathogen isolated 7.1% (11/156) in all samples. The isolates with the highest rate of resistance to the tested antibiotics were S. aureus 32.1% (50/156), E. coli 28.2% (44/156) and Klebsiella spp. 20.5% (32/156). Isolates in all age groups were more resistant to ampicillin, amoxicillin + clavulanic acid, cefuroxime and cefepime.

Conclusion: Antibiotic resistance is high, especially the younger Nigerian children. Strict antibiotic protocols should be adhered to especially in the use of empirical antibiotic therapy in hospitals.

What this study adds: Our study reveals a higher trend of antibiotic resistance, especially in younger children. It further shows that the pathogens are most resistant to the most available empirical antibiotics in Nigeria.

Background: Respiratory infections are a major contributor to hospital admissions. Identification of respiratory pathogens by means of conventional culture and serology methods remains challenging. Multiplex molecular assays are an appealing alternative that endeavours to be rapid, more accurate and less arduous.

Objective: The study aimed to compare the clinical performance of three commercial multiplex molecular assays for respiratory viruses.

Methods: Forty-eight respiratory specimens obtained from patients at Tygerberg Hospital in the Western Cape province of South Africa were studied. These specimens were collected between May 2020 and August 2020. The results of the Seegene Anyplex™ II RV16, FilmArray^® Respiratory 2.1 plus Panel (FARP), and QIAstat-Dx^® Respiratory SARS-CoV-2 Panel (QRP) were analysed based on the overlapping targets. A composite reference standard was applied to provide a standard reference for comparison.

Results: The overall sensitivity of the Seegene Anyplex™ II RV16 was 96.6% (57/59), the FARP 98.2% (56/57) and the QRP 80.7% (46/57). The overall specificities were 99.8% (660/661), 99.0% (704/711) and 99.7% (709/711), respectively. The QRP failed to detect coronaviruses and parainfluenza viruses in 41.7% (5/12) and 28.6% (4/14) of positive specimens, respectively, while the FARP produced the lowest target specificity of 88.4% (38/43) for rhinovirus/enterovirus.

Conclusion: The overall specificity of all three platforms was comparable; however, the sensitivity of the QRP was inferior to that of the ARV and FARP.

What this study adds: This study adds to the body of performance characteristics described for respiratory multiplex panels, especially in the African context where molecular diagnostics for infectious diseases are gaining momentum.

Background: The 2013-2016 West Africa Ebola outbreak highlighted the importance of laboratory capacity to outbreak response while also revealing its long-standing neglect. The outbreak prompted massive international investment into strengthening laboratory services across multiple healthcare settings.

Objective: In this article, we explore hospital-based clinical laboratory workers' experiences and perceptions of their everyday working environment in Sierra Leone, and how recent investments in laboratory strengthening have shaped these.

Methods: This qualitative study draws on in-depth interviews with eight laboratory workers and participant observation of laboratory practices at a tertiary referral hospital in Freetown between April 2019 and December 2019. Interview and observational data were coded and analysed using a reflexive thematic approach.

Results: The Ebola outbreak prompted international investments in automated devices, biosafety training, and a new dedicated infectious diseases laboratory. However, little investment was made in the infrastructure and supply systems needed to sustain routine laboratory work or keep machines functioning. Laboratory workers perceived their work to be under-recognised and undervalued by the government, hospital managers and clinical staff, a perception compounded by under-use of the hospital's laboratory services by clinicians.

Conclusion: Understanding laboratory technicians' views, experiences, and priorities is essential to any sustainable laboratory-strengthening effort. Investments in personnel should match investments in technologies and infrastructure for outbreak response.

What this study adds: This study contributes to an understanding of how clinical laboratory personnel in Sierra Leone view and experience their work, and introduces the concept of social invisibility to explain these experiences.

Introduction: Maternally inherited diabetes and deafness (MIDD) is caused by the m.3243A>G pathogenic variant in maternally inherited mitochondrial DNA. Diabetes is prevalent in our setting; however, MIDD is rarely diagnosed. This study, undertaken in Pretoria, South Africa, highlights the variable presentation of MIDD in different patients within the same family.

Case presentation: A 45-year-old man (proband) with hearing impairment was referred to the endocrine unit in July 2015 due to poor glycaemic control (HbA1c = 13%). His clinical and biochemical features were in keeping with MIDD. A genetic study of accessible maternal relatives was pursued. His mother had difficulty hearing and reportedly died from an unspecified cardiovascular cause. Two sisters with diabetes and deafness died of cardiac-related conditions. One nephew had diabetes (HbA1c = 7.7%), hearing loss and tested positive for m.3243A>G. A third sister tested positive for m3243A>G, but aside from bilateral mild hearing loss in higher frequencies, showed no other signs of target organ damage. Her daughter developed end-stage kidney failure necessitating a transplant, while her son had no biochemical abnormalities and was negative for m.3243A>G.

Management and outcome: A multidisciplinary team managed and screened for complications of the patient and his maternal relatives. Proband died prior to genetic testing.

Conclusion: Most MIDD patients initially present with symptoms of diabetes only, and it is probable that many cases remain undiagnosed. A high index of suspicion is necessary when encountering a family history of both diabetes and impaired hearing, and screening should be offered to the patient's maternal relatives.

What the study adds: This study demonstrates the importance of proper assessment when evaluating a patient with diabetes and a family history of hearing loss.

Background: Understanding factors that impact HIV viral load (VL) accuracy in resource-limited settings is key to quality improvement.

Objective: We evaluated whether testing delay and specimen storage between 25 °C and 30 °C before testing affected results.

Methods: Between November 2019 and June 2023, 249 individuals on antiretroviral therapy, or with newly diagnosed HIV, were recruited from clinics in Cape Town and Gqeberha, South Africa, and three plasma preparation tubes were collected. One tube was tested within 24 h, while the others were stored uncentrifuged at ambient temperatures before testing. Centrifugation and testing of matched samples were performed on Day 4 and Day 7 after collection.

Results: Time delay and ambient storage had minimal impact in specimens with a Day 1 VL of > 100 copies/mL. When grouped by Day 1 VL range, 96% - 100% of specimens at Day 4 and 93% - 100% at Day 7 had VLs within 0.5 log copies/mL of the first result. The greatest variability at Days 4 and 7 was observed when the Day 1 VL was < 100 copies/mL. However, there was no trend of increasing difference over time. Of Day 1 specimens with undetectable VL, or VL < 50 copies/mL, 80% had concordant results at Day 4 and 78% at Day 7.

Conclusion: These results show that VL is stable in plasma preparation tubes for 7 days when stored at room temperature. There is significant variability in specimens with low VL, but variability is not affected by testing delay.

What this study adds: Ideal HIV VL testing conditions are frequently unachievable in resource-limited settings. Data are needed on whether this impacts on the validity of test results. Our results provide reassurance that storage at ambient temperature for up to 7 days before testing does not substantially affect the VL result.

Background: Standardising procedures is the best way to harmonise and strengthen the quality of laboratory-based antimicrobial resistance surveillance. Since 2018, Burkina Faso has developed and disseminated the national manual of procedures for performing antibiotic susceptibility tests in sentinel laboratories within its national antimicrobial resistance surveillance network.

Objective: Our study aimed to assess these sentinel laboratories' compliance with good practices for antibiotics susceptibility tests.

Methods: Four teams evaluated the antimicrobial resistance sentinel sites laboratories throughout Burkina Faso from 19 to 28 September 2022. Eighteen out of 19 sentinel laboratories were evaluated. A four-member technical committee designed and validated the evaluation tool composed of three Microsoft Excel sheets. The evaluation emphasised quality controls for culture media, antibiotic discs and compliance with antimicrobial susceptibility testing procedures by the laboratories. Excel software was used for data recording and graphs and table design. The free R software version 4.2.0 was used for descriptive statistics. An overall score below 80% was considered noncompliance.

Results: Most (83.33%) of the sentinel laboratories conducted at least one quality control activity for culture media, and 66.67% conducted at least one quality control activity for antibiotic discs. Over three-quarters (76.47%) of the laboratories were more than 80% compliant with the modified Kirby Bauer antimicrobial susceptibility testing method.

Conclusion: The evaluation revealed the noncompliance of sentinel laboratories with the national procedure manual, particularly in the quality control component.

What this study adds: This study has provided baseline data on the sentinel laboratories' compliance with the national antimicrobial susceptibility testing procedures manual, particularly in areas performing quality control checks or meeting quality indicators for culture media and antibiotic discs.