Challenges of Maintaining Good Clinical Laboratory Practices in Low-Resource Settings: A Health Program Evaluation Framework Case Study From East Africa

Building genomic capacity for precision health in Africa

The African continent is poised to have a pivotal role in the global population landscape, with the United Nations projecting a population of 2.5 billion (more than 25% of the global population) by 2050. Amid this demographic shift, Africa faces a unique healthcare challenge-navigating a complex landscape of infectious and non-communicable diseases. This necessitates a departure from the conventional 'one-size-fits-all' medical model toward precision approaches that are efficient and sustainable. Genomic capacity is a pillar of precision health; however, access to up-to-date genetic testing in African countries is limited, compounded by a startling lack of representation of data from populations of African descent in gene discovery studies. In this Review, we delve into the challenges impeding the development of genomic capacity in Africa, such as the lack of electronic clinical and epidemiological records, infrastructural challenges, high supply chain costs and the 'dependency trap' that jeopardizes long-term sustainability. We emphasize the need for strategies hinged on true partnerships, robust infrastructure, workforce development and well-crafted policies. Finally, we outline recent progress and existing initiatives that should be considered as role models for future capacity-building initiatives.

Evaluation of Laboratories Supporting Invasive Bacterial Vaccine-Preventable Disease (IB-VPD) Surveillance in the World Health Organization African Region, through the Performance of Coordinated External Quality Assessment

(1) Background: Laboratories supporting the invasive bacteria preventable disease (IB-VPD) network are expected to demonstrate the capacity to identify the main etiological agents of pediatric bacterial meningitis (PBM) (Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae) on Gram stains and in phenotypic identification. Individual reports of sentinel site (SSL), national (NL) and regional reference (RRL) laboratories participating in the World Health Organization (WHO)-coordinated external quality assessment, distributed by the United Kingdom National External Quality Assessment (EQA) Services (UK NEQAS) for Microbiology between 2014 and 2019 were analyzed. (2) Methods: The panels consisted of (1) unstained bacterial smears for Gram staining, (2) viable isolates for identification and serotyping/serogrouping (ST/SG) and (3) simulated cerebral spinal fluid (CSF) samples for species detection and ST/SG using polymerase chain reaction (PCR). SSLs and NLs tested for Gram staining and species identification (partial panel). RRLs, plus any SSLs and NLs (optionally) also analyzed the simulated CSF samples (full panel). The passing score was ≥75% for NLs and SSLs, and ≥90% for RRLs and NLs/SSLs testing the full panel. (3) Results: Overall, 63% (5/8) of the SSLs and NLs were able to correctly identify the targeted pathogens, in 2019; but there were challenges to identify Haemophilus influenzae either on Gram stains (35% of the labs failed 2014), or in culture. Individual performance showed inconsistent capacity, with only 39% (13/33) of the SSLs/NLs passing the EQA exercise throughout all surveys in which they participated. RRLs performed well over the study period, but one of the two failed to reach the minimal passing score in 2016 and 2018; while the SSLs/NLs that optionally tested the full panel scored between 75% and 90% (intermediate pass category). (4) Conclusions: We identified a need for implementing a robust quality management system for timely identification of the gaps and then implementing corrective and preventive actions, in addition to continuous refresher training in the SSLs and NLs supporting the IB-VPD surveillance in the World Health Organization, Regional Office for Africa (WHO AFRO).

Biocatalytic synthesis of 2'-deoxynucleotide 5'-triphosphates from bacterial genomic DNA: Proof of principle

2'-deoxynucleoside 5'-triphosphates (dNTPs) are the building blocks of DNA and are key reagents which are incorporated by polymerase enzymes during nucleic acid amplification techniques, such as polymerase chain reaction (PCR). These techniques are of high importance, not only in molecular biology research, but also in molecular diagnostics. dNTPs are generally produced by a bottom-up technique which relies on synthesis or isolation of purified small molecules like deoxynucleosides. However, the disproportionately high cost of dNTPs in low- and middle-income countries (LMICs) and the requirement for cold chain storage during international shipping makes an adequate supply of these molecules challenging. To reduce supply chain dependency and promote domestic manufacturing in LMICs, a unique top-down biocatalytic synthesis method is described to produce dNTPs. Readily available bacterial genomic DNA provides a crude source material to generate dNTPs and is extracted directly from Escherichia coli (step 1). Nuclease enzymes are then used to digest the genomic DNA creating monophosphorylated deoxynucleotides (dNMPs) (step 2). Design and recombinant production and characterization of E. coli nucleotide kinases is presented to further phosphorylate the monophosphorylated products to generate dNTPs (step 3). Direct use of the in-house produced dNTPs in nucleic acid amplification is shown (step 4) and their successful use as reagents in the application of PCR, thereby providing proof of principle for the future development of recombinant nucleases and design of a recombinant solid-state bioreactor for on-demand dNTP production.

Laboratory service relocation: experience and lessons learned from relocating a biosafety level-3 clinical mycobacteriology service to a new facility

Objectives

We recount our experiences of relocating an active mycobacteriology reference level service in Karachi, Pakistan, from an older accredited biosafety level-3 facility to a newly constructed and environmentally validated facility.

Methods

The service relocation planning, execution, and verification stages are described in detail.

Results

Lessons learned from our experience include establishing a service transfer plan, including relevant service staff, obtaining their buy-in on the plan, arranging backup service facilities or liaisons for the execution phase, and ensuring viable backup arrangements for troubleshooting during the verification phase of services in the new facility. Careful planning and inclusion of all stakeholders are critical to avoid service interruptions.

Conclusions

This narrative is expected to support other laboratorians, scientists, and clinicians providing laboratory services to large population sectors who are looking to move their services to a new location while continuing to offer said services in a proficient and reliable manner.

Preparedness of district clinical laboratories towards ISO 15189: 2012 accreditation scheme in Lake Zone, Tanzania (a descriptive cross-sectional study)

Introduction

diagnosis, prevention, and surveillance of diseases relies on high quality laboratory services. However, accessibility and availability of the quality laboratory services among healthcare facilities remains a serious challenge among sub-Saharan African countries. This study investigated the preparedness of district clinical laboratories for ISO 15189: 2012 accreditation scheme using Stepwise Laboratory Quality Improvement Process towards Accreditation (SLIPTA) checklistin Lake Zone, Tanzania.

Methods

this descriptive cross-sectional study was conducted from September 2018 to August 2019 among clinical laboratories at district hospitals and council designated hospitals in Lake Zone regions of Tanzania. Data were collected using the verified WHO-SLIPTA checklist. In each laboratory, either the laboratory manager, quality officer or safety officer was interviewed.

Results

a total of 10 health laboratories affiliated to 6 districts and 4 councils designated hospitals were enrolled. Six laboratory managers and four quality officers were interviewed. Six (60%) and 4 (40%) laboratories were under government ownership and private ownership, respectively. The majority (70%, n=7) of medical district laboratories in Lake Zone-Tanzania were not registered for WHO-SLIPTA.

Conclusion

about two third of district and council designated hospital laboratories in Lake zone are not registered for WHO-SLIPTA indicating unpreparedness towards ISO 15189: 2012 accreditation.

Recent advancements and future submissions of silica core-shell nanoparticles

The core-shell silica-based nanoparticles (CSNPs) possess outstanding properties for developing next-generation therapeutics. CSNPs provide greater surface area owing to their mesoporous structure, which offers a high opportunity for surface modification. This review highlights the potential of core-shell silica-based nanoparticle (CSNP) based injectable nanotherapeutics (INT); its role in drug delivery, biomedical imaging, light-triggered phototherapy, Plasmonic enhancers, gene delivery, magnetic hyperthermia, immunotherapy, and potential as next-generation theragnostic. Specifically, the conceptual crosstalk on modern synthetic strategies, biodistribution profiles with a mechanistic view on the therapeutics loading and release modeling are dealt in detail. The manuscript also converses the challenges associated with CSNPs, regulatory hurdles, and their current market position.

Setting up a molecular diagnostic laboratory for SARS-CoV-2 testing: Experience of a single centre in a resource-constrained setting

Background

Molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is at the forefront of the global response to the coronavirus disease 2019 (COVID-19) pandemic. However, molecular diagnostic capabilities are poorly developed in many African countries. Efforts by the Nigeria Centre for Disease Control and other public health agencies to scale up facilities for molecular testing across the continent are well documented, but there are few accounts from the laboratories at the frontline.

Intervention

As part of an institutional response to the COVID-19 pandemic, the University of Benin Teaching Hospital, Benin City, Nigeria, signed a memorandum of understanding with a World Bank-supported institution to obtain a non-proprietary testing platform, renovated an existing molecular virology laboratory and validated the test process to make SARS-CoV-2 testing readily available for decision-making by frontline health workers. These efforts resulted in the University of Benin Teaching Hospital’s inclusion in the Nigeria Centre for Disease Control COVID-19 molecular laboratory network. The laboratory achieved a turnover of 12 123 tests within 7 months of operation. Challenges faced and dealt with include incompatible equipment, limited skilled manpower, unstable (unreliable) electric power supply, disrupted procurement and supply chain, and significant overhead costs.

Lessons learnt

Molecular diagnostic capability is essential in laboratory preparedness for pandemic response and can be achieved by establishing collaborative networks in low-resource settings.

Recommendations

Molecular diagnostic capabilities attained during the COVID-19 pandemic should be maintained by governmental support of the local biotechnology sector, collaboration with partners and stakeholders and the expansion of diagnostics to include other diseases of public health importance.

Clinical diagnosis in paediatric patients at urban primary health care facilities in southern Malawi: a longitudinal observational study

Background

Despite health centres being the first point of contact of care, there are challenges faced in providing care to patients at this level. In Malawi, service provision barriers reported at this level included long waiting times, high numbers of patients and erratic consultation systems which lead to mis-diagnosis and delayed referrals. Proper case management at this level of care is critical to prevent severe disease and deaths in children. We aimed to adopt Emergency, Triage, Assessment and Treatment algorithm (ETAT) to improve ability to identify severe illness in children at primary health centre (PHC) through comparison with secondary level diagnoses.

Methods

We implemented ETAT mobile Health (mHealth) at eight urban PHCs in Blantyre, Malawi between April 2017 and September 2018. Health workers and support staff were trained in mHealth ETAT. Stabilisation rooms were established and equipped with emergency equipment. All PHCs used an electronic tracking system to triage and track sick children on referral to secondary care, facilitated by a unique barcode. Support staff at PHC triaged sick children using ETAT Emergency (E), Priority (P) and Queue (Q) symptoms and clinician gave clinical diagnosis. The secondary level diagnosis was considered as a gold standard. We used statistical computing software R (v3.5.1) and used exact 95% binomial confidence intervals when estimating diagnosis agreement proportions.

Results

Eight-five percentage of all cases where assigned to E (9.0%) and P (75.5%) groups. Pneumonia was the most common PHC level diagnosis across all three triage groups (E, P, Q). The PHC level diagnosis of trauma was the most commonly confirmed diagnosis at secondary level facility (85.0%), while a PHC diagnosis of pneumonia was least likely to be confirmed at secondary level (39.6%). The secondary level diagnosis least likely to have been identified at PHC level was bronchiolitis 3 (5.2%). The majority of bronchiolitis cases (n = 50; (86.2%) were classified as pneumonia at the PHC level facility.

Conclusions

Implementing a sustainable and consistent ETAT approach with stabilisation and treatment capacity at PHC level reinforce staff capacity to diagnose and has the potential to reduce other health system costs through fewer, timely and appropriate referrals.

Africa Centres for Disease Control and Prevention Is Closing Gaps in Disease Detection

In 2017, the African Union established a new continent-wide public health agency, the Africa Centres for Disease Control and Prevention (Africa CDC). Many outbreaks are never detected in Africa, and among outbreaks that are detected, countries often respond slowly and ineffectively. To address these problems, Africa CDC is working to increase early detection and reporting, improve access to diagnostic tests, promote novel laboratory approaches, help establish national public health institutes, improve information exchange between health agencies, and enhance recording and reporting of acute public health events and vital statistics. The health security of Africa will be strengthened by this new public health agency's ability to build comprehensive, timely disease surveillance that rapidly detects and contains health threats.

Gross national income and antibiotic resistance in invasive isolates: analysis of the top-ranked antibiotic-resistant bacteria on the 2017 WHO priority list

OBJECTIVES

To assess the association between country income status and national prevalence of invasive infections caused by the top-ranked bacteria on the WHO priority list: carbapenem-resistant (CR) Acinetobacter spp., Klebsiella spp. and Pseudomonas aeruginosa; third-generation cephalosporin-resistant (3GCR) Escherichia coli and Klebsiella spp.; and MRSA and vancomycin-resistant Enterococcus faecium (VR E. faecium).

METHODS

Active surveillance systems providing yearly prevalence data from 2012 onwards for the selected bacteria were included. The gross national income (GNI) per capita was used as the indicator for income status of each country and was log transformed to account for non-linearity. The association between antibiotic prevalence data and GNI per capita was investigated individually for each bacterium through linear regression.

RESULTS

Surveillance data were available from 67 countries: 38 (57%) were high income, 16 (24%) upper-middle income, 11 (16%) lower-middle income and two (3%) low income countries. The regression showed significant inverse association (P<0.0001) between resistance prevalence of invasive infections and GNI per capita. The highest rate of increase per unit decrease in log GNI per capita was observed in 3GCR Klebsiella spp. (22.5%, 95% CI 18.2%-26.7%), CR Acinetobacter spp. (19.2% 95% CI 11.3%-27.1%) and 3GCR E. coli (15.3%, 95% CI 11.6%-19.1%). The rate of increase per unit decrease in log GNI per capita was lower in MRSA (9.5%, 95% CI 5.2%-13.7%).

CONCLUSIONS

The prevalence of invasive infections caused by the WHO top-ranked antibiotic-resistant bacteria is inversely associated with GNI per capita at the global level. Public health interventions designed to limit the burden of antimicrobial resistance should also consider determinants of poverty and inequality, especially in lower-middle income and low income countries.

Hematological malignancies in East Africa-Which cancers to expect and how to provide services

BACKGROUND

Sub-Saharan Africa (SSA) has an increasing non-communicable disease burden. Tanzania has an incidence of more than 35,000 cancer cases per year with an 80% mortality rate. Hematological malignancies account for 10% of these cases. The numbers will double within the next 10 years due to demographic changes, better diagnostic capabilities and life style changes. Kilimanjaro Christian Medical Centre established a Cancer Care Centre (CCC) in December 2016 for a catchment area of 15 million people in Northern Tanzania. This article aims to display the hematological diagnosis and characteristics of the patients as well as to describe the advancements of hematologic services in a low resource setting.

METHODS

A cross-sectional analysis of all hematological malignancies at CCC from December 2016 to May 2019 was performed and a narrative report provides information about diagnostic means, treatment and the use of synergies.

RESULTS

A total of 209 cases have been documented, the most common malignancies were NHL and MM with 44% and 20%. 36% of NHL cases, 16% of MM cases and 63% of CML cases were seen in patients under the age of 45. When subcategorized, CLL/SLL cases had a median age was 56.5, 51 years for those with other entities of NHL. Sexes were almost equally balanced in all NHL groups while clear male predominance was found in HL and CML.

DISCUSSION

Malignancies occur at a younger age and higher stages than in Western countries. It can be assumed that infections play a key role herein. Closing the gap of hematologic services in SSA can be achieved by adapting and reshaping existing infrastructure and partnering with international organizations.

DNA amplification with in situ nucleoside to dNTP synthesis, using a single recombinant cell lysate of E. coli

Nucleic acid amplification (NAA) is a cornerstone of modern molecular and synthetic biology. Routine application by non-specialists, however, is hampered by difficulties with storing and handling the requisite labile and expensive reagents, such as deoxynucleoside triphosphates (dNTPs) and polymerases, and the complexity of protocols for their use. Here, a recombinant E. coli extract is reported that provides all the enzymes to support high-fidelity DNA amplification, and with labile dNTPs generated in situ from cheap and stable deoxynucleosides. Importantly, this is obtained from a single, engineered cell strain, through minimal processing, as a lysate capable of replacing the cold-stored commercial reagents in a typical PCR. This inexpensive preparation is highly active, as 1 L of bacterial culture is enough to supply ~10⁶ NAA reactions. Lyophilized lysate can be used after a single-step reconstitution, resulting overall in a greatly simplified workflow and a promising synthetic biology tool, in particular for applications such as diagnostics.

Toward Improving Accessibility of Point-of-Care Diagnostic Services for Maternal and Child Health in Low- and Middle-Income Countries

Point-of-care (POC) testing can improve health care provision in settings with limited access to health care services. Access to POC diagnostic services has shown potential to alleviate some diagnostic challenges and delays associated with laboratory-based methods in low- and middle-income countries. Improving accessibility to POC testing (POCT) services during antenatal and perinatal care is among the global health priorities to improve maternal and child health. This review provides insights on the availability of POC testing designed for diagnosing HIV, syphilis, and malaria in pregnancy to improve maternal and child health. In addition, factors such as accessibility of POC testing, training of health work force, and the efficiency of POC testing services delivery in low- and middle-income countries are discussed. A framework to help increase access to POC diagnostic services and improve maternal and child health outcomes in low- and middle-income countries is proposed.

Cellular reagents for diagnostics and synthetic biology

We have found that the overproduction of enzymes in bacteria followed by their lyophilization leads to 'cellular reagents' that can be directly used to carry out numerous molecular biology reactions. We demonstrate the use of cellular reagents in a variety of molecular diagnostics, such as TaqMan qPCR with no diminution in sensitivity, and in synthetic biology cornerstones such as the Gibson assembly of DNA fragments, where new plasmids can be constructed solely based on adding cellular reagents. Cellular reagents have significantly reduced complexity and cost of production, storage and implementation, features that should facilitate accessibility and use in resource-poor conditions.

Clinical bacteriology in low-resource settings: today's solutions

Low-resource settings are disproportionately burdened by infectious diseases and antimicrobial resistance. Good quality clinical bacteriology through a well functioning reference laboratory network is necessary for effective resistance control, but low-resource settings face infrastructural, technical, and behavioural challenges in the implementation of clinical bacteriology. In this Personal View, we explore what constitutes successful implementation of clinical bacteriology in low-resource settings and describe a framework for implementation that is suitable for general referral hospitals in low-income and middle-income countries with a moderate infrastructure. Most microbiological techniques and equipment are not developed for the specific needs of such settings. Pending the arrival of a new generation diagnostics for these settings, we suggest focus on improving, adapting, and implementing conventional, culture-based techniques. Priorities in low-resource settings include harmonised, quality assured, and tropicalised equipment, consumables, and techniques, and rationalised bacterial identification and testing for antimicrobial resistance. Diagnostics should be integrated into clinical care and patient management; clinically relevant specimens must be appropriately selected and prioritised. Open-access training materials and information management tools should be developed. Also important is the need for onsite validation and field adoption of diagnostics in low-resource settings, with considerable shortening of the time between development and implementation of diagnostics. We argue that the implementation of clinical bacteriology in low-resource settings improves patient management, provides valuable surveillance for local antibiotic treatment guidelines and national policies, and supports containment of antimicrobial resistance and the prevention and control of hospital-acquired infections.

Design and Implementation of the Retinoblastoma Collaborative Laboratory

PURPOSE

The purpose of this work was to describe the design and implementation of a digital pathology laboratory, the Retinoblastoma Collaborative Laboratory (RbCoLab) in Kenya.

METHOD

The RbCoLab is a central lab in Nairobi that receives retinoblastoma specimens from all over Kenya. Specimens were processed using evidence-based standard operating procedures. Images were produced by a digital scanner, and pathology reports were disseminated online.

RESULTS

The lab implemented standard operating procedures aimed at improving the accuracy, completeness, and timeliness of pathology reports, enhancing the care of Kenyan retinoblastoma patients. Integration of digital technology to support pathology services supported knowledge transfer and skills transfer. A bidirectional educational network of local pathologists and other clinicians in the circle of care of the patients emerged and served to emphasize the clinical importance of cancer pathology at multiple levels of care. A 'Robin Hood' business model of health care service delivery was developed to support sustainability and scale-up of cancer pathology services.

DISCUSSION

The application of evidence-based protocols, comprehensive training, and collaboration were essential to bring improvements to the care of retinoblastoma patients in Kenya. When embraced as an integrated component of retinoblastoma care, digital pathology offers the opportunity for frequent connection and consultation for development of expertise over time.