Assessment of three medical and research laboratories using WHO AFRO_SLIPTA Quality Standards in Southwestern Uganda: a long way to go

Patterns of Non-influenza Respiratory Viruses Among Severe Acute Respiratory Infection Cases in Burkina Faso: A Surveillance Study

BACKGROUND

Although influenza viruses cause only one-fifth of severe acute respiratory infections (SARI) in Burkina Faso, the other viral causes of SARI remain poorly investigated to inform clinical and preventive decision making.

METHODS

Between 2016 and 2019, we prospectively enrolled inpatients meeting the World Health Organization (WHO) case definition of SARI in Burkina Faso. Results of viral etiologies among inpatients tested negative for influenza using the Fast Track Diagnostics Respiratory Kits (FTD-33) were reported.

RESULTS

Of 1541 specimens tested, at least one respiratory virus was detected in 76.1% of the 1231 specimens negative for influenza virus. Human rhinoviruses (hRVs) were the most detected pathogens (476; 38.7%), followed by human adenoviruses (hAdV) (17.1%, 210/1231), human respiratory syncytial virus (hRSV) (15.4%, 189/1231), enterovirus (EnV) (11.2%, 138/1231), human bocavirus (hBoV) (7.9%, 97/1231), parainfluenza 3 (hPIV3) (6.1%, 75/1231), human metapneumovirus (hMPV) (6.0%,74/1321), parainfluenza 4 (hPIV4) (4.1%, 51/1231), human coronavirus OC43 (hCoV-OC43) (3.4%, 42/1231), human coronavirus HKU1(hCoV-HKU1) (2.7%, 33/1231), human coronavirus NL63 (hCoV-NL63) (2.5%, 31/1231), parainfluenza 1 (hPIV1) (2.0%, 25/1231), parainfluenza 2 (hPIV2) (1.8%, 22/1231), human parechovirus (PeV) (1.1%, 14/1231), and human coronavirus 229E (hCoV-229E) (0.9%, 11/1231). Among SARI cases, infants aged 1-4 years were mostly affected (50.7%; 622/1231), followed by those <1 year of age (35.7%; 438/1231). Most detected pathogens had year-long circulation patterns, with seasonal peaks mainly observed during the cold and dry seasons.

CONCLUSION

Several non-influenza viruses are cause of SARI in Burkina Faso. The integration of the most common pathogens into the routine influenza surveillance system might be beneficial.

Evaluating Quality Management and Diagnostics Microbiology Performance Within an International External Quality Assessment (EQA) Program Serving National One Health Sector Reference Laboratories Across Asia: Experience Amid the Coronavirus Disease 2019 (COVID-19) Pandemic

BACKGROUND

Strengthening external quality assessment (EQA) services across the One Health sector supports implementation of effective antimicrobial resistance (AMR) control strategies. Here we describe and compare 2 different approaches for conducting virtual laboratory follow-up assessments within an EQA program to evaluate quality management system (QMS) and procedures for pathogen identification and antimicrobial susceptibility testing (AST).

METHODS

During the coronavirus disease 2019 (COVID-19) pandemic in 2021 and 2022, 2 laboratory assessment approaches were introduced: virtual-based and survey-based methodologies. The evaluation of 2 underperforming Animal Health laboratories through a virtual-based approach occurred between May and August 2021. This evaluation encompassed the utilization of 3 online meetings and document reviews, performed subsequent to the execution of EQA procedures. Within a distinct group of laboratories, the survey-based assessment was implemented from December 2021 to February 2022, also following EQA procedures. This phase encompassed the dissemination of an online survey to 31 participating laboratories, alongside a sole online consultation meeting involving 4 specific underperforming laboratories.

RESULTS

The virtual-based assessment post-EQA aimed to identify gaps and areas for improvement in the laboratory's practices for pathogen identification and AST. This approach was, however, time-intensive, and, hence, only 2 laboratories were assessed. In addition, limited interactions in virtual platforms compromised the assessment quality. The survey-based post-EQA assessment enabled evaluation of 31 laboratories. Despite limitations for in-depth analysis of each procedure, gaps in QMS across multiple laboratories were identified and tailored laboratory-specific recommendations were provided.

CONCLUSIONS

Reliable internet and plans for efficient time management, post-EQA virtual laboratory follow-up assessments are an effective alternative when conducting onsite evaluation is infeasible as observed during the COVID-19 pandemic, although the successful implementation of remediation plans will likely require in person assessments. We advocate application of hybrid approaches (both onsite and virtual) for targeted capacity building of AMR procedures with the ability to implement and oversee the process.

Assessment of laboratory capacity in conflict-affected low-resource settings using two World Health Organization laboratory assessment tools

OBJECTIVES

Laboratory diagnostic services are essential to drive evidence-based treatment decisions, manage outbreaks, and provide population-level data. Many low- and middle-income countries (LMICs) lack sufficient diagnostic capacity, often further exacerbated in conflict-affected areas. This project assessed laboratory services in conflict-affected LMICs to understand gaps and opportunities for improving laboratory capacity.

METHODS

The World Health Organization Laboratory Assessment Tool Facility Questionnaire (WHO Laboratory Tool) and Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA) checklist were used to assess five laboratories in Eastern Democratic Republic of the Congo (DRC) and five in Gaza, Palestine. Total scores and percentage outcomes by indicator were calculated.

RESULTS

Average WHO Laboratory Tool score across all facilities was 41% (range 32-50%) in DRC and 78% (range 72-84%) in Gaza. Lowest scoring indicators in DRC were Biorisk management (13%, range 8-21%), Documentation (14%, range 6-21%), and in Gaza, were Facilities (59%, range 46-75%) and Documentation (60%, range 44-76%). Highest scoring indicators in DRC were Facilities (70%, range 45-83%) and Data and Information Management (61%, range 38-80%), and in Gaza were Data Information and Management (96%) and Public Health Function (91%, range 88-94%). In DRC, no laboratory achieved a SLIPTA star rating. In Gaza, two laboratories had a 3-star SLIPTA rating, one had a 2-star rating and two had a 1-star rating.

CONCLUSIONS

Laboratory systems in conflict-affected LMICs have significant gaps. Implementating improvement strategies in such settings may be especially challenging.

Prevalence of antibiotic-resistant bacteria among patients in two tertiary hospitals in Eastern Uganda

OBJECTIVE

The aim of this study was to determine the prevalence and antibiotic resistance patterns of bacterial isolates from inpatients and outpatients in Mbale and Soroti regional referral hospitals in Eastern Uganda.

METHODS

A retrospective analysis of culture and antibiotic sensitivity test results from the microbiology laboratories of the two tertiary hospitals was conducted for a 3-year period (January 2016-December 2018).

RESULTS

Microbiology records of 3092 patients were reviewed and analysed, with 1305 (42.1%) samples yielding clinical isolates. The most prevalent isolates were Escherichia coli (n = 442; 33.9%), Staphylococcus aureus (n = 376; 28.8%), Klebsiella pneumoniae (n = 237; 18.2%), and Streptococcus pneumoniae (n = 76; 5.8%). High rates of antimicrobial resistance were detected across both Gram-negative and Gram-positive bacteria. Escherichia coli and K. pneumoniae were resistant to several agents such as amoxicillin/clavulanate (83.5%; 64.6%), cefotaxime (74.2%; 52.7%), ciprofloxacin (92.1%; 27.8%), gentamicin (51.8%; 76%), imipenem (3.2%; 10.5%), tetracycline (98%; 74.5%), and trimethoprim-sulfamethoxazole (74.1%; 74.3%), respectively. Staphylococcus aureus and S. pneumoniae exhibited the following resistance profile: cefoxitin (44.4%; 40.9%), chloramphenicol (69.1%; 27.6%) clindamycin (21.5%; 24.4%), gentamicin (83.2%; 66.9%), penicillin (46.5%; -) tetracycline (85.6%; 97.6%), trimethoprim-sulfamethoxazole (88%; 91.3%), and vancomycin (41.2%; -).

CONCLUSION

We observed high resistance rates to antibiotics among the majority of microorganisms that were isolated from the samples collected from patients in Eastern Uganda. Furthermore, measures should be undertaken locally to improve microbiology diagnostics and to prevent the spread of antibiotic-resistant strains as this impedes the optimal treatment of bacterial infections and narrows the choice of effective therapeutic options.

Review of the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) version 2:2015

Background

In 2011 the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) was launched, aimed at strengthening the quality and competence of African clinical, public health and reference laboratories. We reviewed the first version of the SLIPTA checklist in 2011. The continued development and publication of a new version of the International Organization for Standardization (ISO) 15189 standard demands a renewed review.

Objective

This study aimed to determine the suitability of SLIPTA in guiding laboratories towards ISO 15189:2012 compliance and accreditation and provide recommendations for further SLIPTA improvement.

Methods

The study was conducted between September 2018 and April 2019. Coverage of ISO 15189:2012 by SLIPTA checklist version 2:2015 was determined and the point distribution of the scoring system over the different sections of the SLIPTA checklist was re-investigated. These findings were compared with the review of the first version of the SLIPTA checklist (based on ISO 15189:2007) and with findings published on SLIPTA implementation and roll-out.

Results

The coverage of ISO 15189 by the SLIPTA checklist has increased, even though ISO 15189:012 is more extensive than ISO 15189:2007. The point distribution is still skewed towards sections related to quality planning rather than quality control and improvement. Although to date 314 laboratories have been assessed, barriers for laboratories to participate in SLIPTA are high. Sustainability of SLIPTA results is insufficiently studied.

Conclusion

SLIPTA checklist version 2:2015 has improved compared to earlier versions. We recommend increasing accessibility for laboratories to participate and increasing guidance for ISO-based quality management system implementation.