External quality assessment of national public health laboratories in Africa, 2002-2009

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.

Blood culture versus antibiotic use for neonatal inpatients in 61 hospitals implementing with the NEST360 Alliance in Kenya, Malawi, Nigeria, and Tanzania: a cross-sectional study

BACKGROUND

Thirty million small and sick newborns worldwide require inpatient care each year. Many receive antibiotics for clinically diagnosed infections without blood cultures, the current 'gold standard' for neonatal infection detection. Low neonatal blood culture use hampers appropriate antibiotic use, fuelling antimicrobial resistance (AMR) which threatens newborn survival. This study analysed the gap between blood culture use and antibiotic prescribing in hospitals implementing with Newborn Essential Solutions and Technologies (NEST360) in Kenya, Malawi, Nigeria, and Tanzania.

METHODS

Inpatient data from every newborn admission record (July 2019-August 2022) were included to describe hospital-level blood culture use and antibiotic prescription. Health Facility Assessment data informed performance categorisation of hospitals into four tiers: (Tier 1) no laboratory, (Tier 2) laboratory but no microbiology, (Tier 3) neonatal blood culture use < 50% of newborns receiving antibiotics, and (Tier 4) neonatal blood culture use > 50%.

RESULTS

A total of 144,146 newborn records from 61 hospitals were analysed. Mean hospital antibiotic prescription was 70% (range = 25-100%), with 6% mean blood culture use (range = 0-56%). Of the 10,575 blood cultures performed, only 24% (95%CI 23-25) had results, with 10% (10-11) positivity. Overall, 40% (24/61) of hospitals performed no blood cultures for newborns. No hospitals were categorised as Tier 1 because all had laboratories. Of Tier 2 hospitals, 87% (20/23) were District hospitals. Most hospitals could do blood cultures (38/61), yet the majority were categorised as Tier 3 (36/61). Only two hospitals performed > 50% blood cultures for newborns on antibiotics (Tier 4).

CONCLUSIONS

The two Tier 4 hospitals, with higher use of blood cultures for newborns, underline potential for higher blood culture coverage in other similar hospitals. Understanding why these hospitals are positive outliers requires more research into local barriers and enablers to performing blood cultures. Tier 3 facilities are missing opportunities for infection detection, and quality improvement strategies in neonatal units could increase coverage rapidly. Tier 2 facilities could close coverage gaps, but further laboratory strengthening is required. Closing this culture gap is doable and a priority for advancing locally-driven antibiotic stewardship programmes, preventing AMR, and reducing infection-related newborn deaths.

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).

Comparative performance evaluation of blood film microscopy for the diagnosis of bovine trypanosomosis by some laboratories in North-central Nigeria

Background

Due to its affordability in disease-affected communities and suitability for field application, microscopy has historically been considered the gold standard for field diagnosis of trypanosomosis in rural settings.

Aim

This works aims to compare the performance of microscopists on bovine trypanosome microscopy by organizing the first comparative assessment on a correct reading of slides by laboratory professionals using the read slide results and a structured interviewer-administered questionnaire in North-central Nigeria.

Methods

Ten participants were addressed, as they were sent a panel of two slides (Slide 1: No Trypanosome present; Slide 2: Trypanosome present) and a questionnaire.

Results

All participants greater than 41 years old reported correctly the presence and absence of parasites on slides. Only 3/8 of microscopists from routine diagnostic laboratories reported correctly the presence of the parasite.

Conclusion

Our study confirmed errors in reading slides. Therefore, training of microscopists besides a nationwide quality assessment is recommended.

Evaluation of the World Health Organization Global Invasive Bacterial Vaccine-Preventable Disease (IB-VPD) Surveillance Network's Laboratory External Quality Assessment Programme, 2014-2019

Introduction. In 2009, the World Health Organization (WHO) established the Global Invasive Bacterial Vaccine Preventable Disease (IB-VPD) Surveillance Network (GISN) to monitor the global burden and aetiology of bacterial meningitis, pneumonia and sepsis caused by Haemophilus influenzae (Hi), Neisseria meningitidis (Nm) and Streptococcus pneumoniae (Sp).Hypothesis/Gap Statement. The GISN established an external quality assessment (EQA) programme for the characterization of Hi, Nm and Sp by culture and diagnostic PCR.Aim. To assess the performance of sentinel site laboratories (SSLs), national laboratories (NLs) and regional reference laboratories (RRLs) between 2014 and 2019 in the EQA programme.Methodology. Test samples consisted of bacterial smears for Gram-staining, viable isolates for identification and serotyping or serogrouping (ST/SG), plus simulated cerebrospinal fluid (CSF) samples for species detection and ST/SG by PCR. SSLs and NLs were only required to analyse the slides for Gram staining and identify the species of the live isolates. RRLs, and any SLs and NLs that had the additional laboratory capacity, were also required to ST/SG the viable isolates and analyse the simulated CSF samples.Results. Across the period, 69-112 SS/NL labs and eight or nine RRLs participated in the EQA exercise. Most participants correctly identified Nm and Sp in Gram-stained smears but were less successful with Hi and other species. SSLs/NLs identified the Hi, Nm and Sp cultures well and also submitted up to 56 % of Hi, 62 % of Nm and 33 % of Sp optional ST/SG results each year. There was an increasing trend in the proportion of correct results submitted over the 6 years for Nm and Sp. Some SSLs/NLs also performed the optional detection and ST/SG of the three organisms by PCR in simulated CSF from 2015 onwards; 89-100 % of the CSF samples were correctly identified and 76-93 % of Hi-, 90-100 % of Nm- and 75-100 % of Sp-positive samples were also correctly ST/SG across the distributions. The RRLs performed all parts of the EQA to a very high standard, with very few errors across all aspects of the EQA.Conclusion. The EQA has been an important tool in maintaining high standards of laboratory testing and building of laboratory capacity in the GISN.

Laboratory-based surveillance of antimicrobial resistance in regions of Kenya: An assessment of capacities, practices, and barriers by means of multi-facility survey

Background

Adequate laboratory capacity is critical in the implementation of coherent surveillance for antimicrobial resistance (AMR). We describe capacities and deficiencies in laboratory infrastructure and AMR surveillance practices among health facilities in Kenya to support progress toward broader sustainable laboratory-based AMR surveillance.

Methods

A convenience sample of health facilities from both public and private sectors across the country were selected. Information was obtained cross-sectionally between 5th October and 8th December 2020 through online surveys of laboratory managers. The assessment covered quality assurance, management and dissemination of AMR data, material and equipment, staffing, microbiology competency, biosafety and certification. A scoring scheme was developed for the evaluation and interpreted as (80% and above) facility is adequate (60-79%) requires some strengthening and (<60%) needing significant strengthening. Average scores were compared across facilities in public and private sectors, rural and urban settings, as well as national, county, and community levels.

Results

Among the participating facilities (n = 219), the majority (n = 135, 61.6%) did not offer bacterial culture testing, 47 (21.5%) offered culture services only and 37 (16.9%) performed antimicrobial susceptibility testing (AST). The major gaps identified among AST facilities were poor access to laboratory information management technology (LIMT) (score: 45.9%) and low uptake of external quality assessment (EQA) programs for cultures (score 67.7%). Access to laboratory technology was more than two-fold higher in facilities in urban (58.6%) relative to rural (25.0%) areas. Whilst laboratories that lacked culture services were found to have significant infrastructural gaps (average score 59.4%), facilities that performed cultures only (average score: 83.6%) and AST (average score: 82.9%) recorded significantly high scores that were very similar across areas assessed. Lack of equipment was identified as the leading challenge to the implementation of susceptibility testing among 46.8% of laboratories.

Conclusions

We identified key gaps in laboratory information management technology, external quality assurance and material and equipment among the surveyed health facilities in Kenya. Our findings suggest that by investing in equipment, facilities performing cultures can be successfully upgraded to provide additional antimicrobial susceptibility testing, presenting a chance for a major leap toward improved AMR diagnostics and surveillance in the country.

Microbiology laboratories involved in disease and antimicrobial resistance surveillance: Strengths and challenges of the central African states

Laboratory systems have been largely neglected on the margins of health systems in Africa. However, since the 2000s, many African countries have benefited from massive investments to strengthen laboratory capacities through projects fighting priority diseases (HIV/AIDS, tuberculosis, malaria). This review examined the laboratory capacities of the Economic Community of Central African States (ECCAS). Online research using specific terms was carried out. Studies published between 2000 and 2021 on the role of the laboratory in disease and antimicrobial resistance surveillance in the 11 ECCAS countries were considered. The number of human and animal health laboratories meeting international standards was very low in the sub-region. There were only seven International Organization for Standardization (ISO) 15189-accredited human health laboratories, with five in Cameroon and two in Rwanda. There were five high biosafety level (BSL) laboratories (one BSL3 laboratory each in Cameroon, the Central African Republic, Democratic Republic of Congo and the Republic of Congo, and one BSL4 laboratory in Gabon) and three ISO 17025-accredited laboratories in the ECCAS sub-region. Only six countries currently have whole-genome sequencing devices, which is insufficient for a sub-region as large and populous as ECCAS. Yet, a plethora of pathogens, particularly haemorrhagic viruses, are endemic in these countries. The need for laboratory capacity strengthening following a One Health approach is imperative. Since emerging and re-emerging zoonotic infectious diseases are projected to triple in frequency over the next 50 years and given the inextricable link between human and animal health, actors in the two health sectors must collaborate to preserve world health.

Improving the quality of malaria diagnosis in southern Africa through the development of a regional malaria slide bank

Background

A malaria slide bank (MSB) is a useful asset for any malaria microscopy testing laboratory to have access to. However, it is not feasible for every country to have its own MSB. If countries are able to pool their resources, a regional MSB is a viable solution. This paper describes the methodology, costing and lessons learnt of establishing and maintaining an MSB over a 3-year period, for a Southern Africa Development Community region.

Methods

A national reference laboratory in South Africa was granted funding for setting up the MSB; it possessed experienced staff and suitable resources. Two additional full-time personnel were employed to carry out the activities of this project. Strict protocols for donor/patient blood sample screening, smear preparation, mass staining, quality control and slide validation were followed. Slides from the MSB were used for training and proficiency testing purposes. The initial and recurrent yearly costs to set up and maintain the MSB were calculated.

Results

Over 35 months, 154 batches (26,623 slides) were prepared; the majority were Plasmodium falciparum. Ninety-two percent (141/154) of batches passed internal quality control, and 89% (93/104) passed external validation. From these slides, two training slide sets and six proficiency testing slide sets were sent out. The initial year’s cost to establish an MSB was calculated at approximately $165,000, and the recurrent year-on-year cost was $130,000.

Conclusions

The key components for maintaining a high-quality MSB are consistent funding, competent staff and adherence to standardized protocols. Travel to malaria-endemic areas for access to non-falciparum malaria species, and dilution of P. falciparum blood to desired parasite densities, are extremely useful to ensure variety. The MSB created here supported multiple laboratories in eight countries, and has the potential to expand.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-021-03899-5.

High Levels of Antibiotic Resistance Patterns in Two Referral Hospitals during the Post-Ebola Era in Free-Town, Sierra Leone: 2017-2019

The Post-Ebola era (2017–2019) presented an opportunity for laboratory investments in Sierra Leone. US CDC supported the Ministry of Health and Sanitation to establish a microbiological unit for routine antimicrobial sensitivity testing in two referral (pediatric and maternity) hospitals in Freetown. This study describes resistance patterns among patients’ laboratory samples from 2017 to 2019 using routine data. Samples included urine, stool, cerebrospinal fluid, pus-wound, pleural fluid, and high vaginal swabs. Selected Gram-positive and Gram-negative bacterial isolates were tested for antimicrobial susceptibility. Of 200 samples received by the laboratory, 89 returned positive bacterial isolates with urine and pus-wound swabs accounting for 75% of positive isolates. The number of positive isolates increased annually from one in 2017 to 42 in 2018 and 46 in 2019. Resistance of the cultures to at least one antibiotic was high (91%), and even higher in the pediatric hospital (94%). Resistance was highest with penicillin (81%) for Gram-positive bacteria and lowest with nitrofurantoin (13%). Gram-negative bacteria were most resistant to ampicillin, gentamycin, streptomycin, tetracycline, cephalothin and penicillin (100%) and least resistant to novobiocin (0%). Antibiotic resistance for commonly prescribed antibiotics was high in two referral hospitals, highlighting the urgent need for antimicrobial stewardship and access to reserve antibiotics.

Surveillance of antimicrobial resistance in low- and middle-income countries: a scattered picture

Data on comprehensive population-based surveillance of antimicrobial resistance is lacking. In low- and middle-income countries, the challenges are high due to weak laboratory capacity, poor health systems governance, lack of health information systems, and limited resources. Developing countries struggle with political and social dilemma, and bear a high health and economic burden of communicable diseases. Available data are fragmented and lack representativeness which limits their use to advice health policy makers and orientate the efficient allocation of funding and financial resources on programs to mitigate resistance. Low-quality data means soaring rates of antimicrobial resistance and the inability to track and map the spread of resistance, detect early outbreaks, and set national health policy to tackle resistance. Here, we review the barriers and limitations of conducting effective antimicrobial resistance surveillance, and we highlight multiple incremental approaches that may offer opportunities to strengthen population-based surveillance if tailored to the context of each country.

A novel deep learning-based point-of-care diagnostic method for detecting Plasmodium falciparum with fluorescence digital microscopy

BACKGROUND

Malaria remains a major global health problem with a need for improved field-usable diagnostic tests. We have developed a portable, low-cost digital microscope scanner, capable of both brightfield and fluorescence imaging. Here, we used the instrument to digitize blood smears, and applied deep learning (DL) algorithms to detect Plasmodium falciparum parasites.

METHODS

Thin blood smears (n = 125) were collected from patients with microscopy-confirmed P. falciparum infections in rural Tanzania, prior to and after initiation of artemisinin-based combination therapy. The samples were stained using the 4',6-diamidino-2-phenylindole fluorogen and digitized using the prototype microscope scanner. Two DL algorithms were trained to detect malaria parasites in the samples, and results compared to the visual assessment of both the digitized samples, and the Giemsa-stained thick smears.

RESULTS

Detection of P. falciparum parasites in the digitized thin blood smears was possible both by visual assessment and by DL-based analysis with a strong correlation in results (r = 0.99, p < 0.01). A moderately strong correlation was observed between the DL-based thin smear analysis and the visual thick smear-analysis (r = 0.74, p < 0.01). Low levels of parasites were detected by DL-based analysis on day three following treatment initiation, but a small number of fluorescent signals were detected also in microscopy-negative samples.

CONCLUSION

Quantification of P. falciparum parasites in DAPI-stained thin smears is feasible using DL-supported, point-of-care digital microscopy, with a high correlation to visual assessment of samples. Fluorescent signals from artefacts in samples with low infection levels represented the main challenge for the digital analysis, thus highlighting the importance of minimizing sample contaminations. The proposed method could support malaria diagnostics and monitoring of treatment response through automated quantification of parasitaemia and is likely to be applicable also for diagnostics of other Plasmodium species and other infectious diseases.

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.

Plasmodium spp. mixed infection leading to severe malaria: a systematic review and meta-analysis

Mixed Plasmodium malaria infections can lead to severe malaria. This systematic review and meta-analysis aimed to explore the prevalence of severe mixed Plasmodium malaria infection and to compare it with the prevalence of severe P. falciparum malaria mono-infection across the included studies. Original English-language research articles from PubMed, Scopus, and ISI Web of Science were identified and screened. Articles reporting the number of mixed infections and the number of severe mixed infections were used to determine the main outcome of this study, while the number of P. falciparum infections and the number of severe P. falciparum infections were used to determine the secondary outcome of this study. For the main outcome, the pooled prevalence and 95% confidence interval (CI) of severe mixed infections was analysed using STATA software version 15.0 (Stata Corp, College Station, TX, USA). For the secondary outcome, the rate of severe mixed infections compared to severe P. falciparum infections was analysed using the meta-analysis approach, and summary odds ratios (ORs) and 95% CIs were calculated. Random-effects models were used to produce the summary ORs. The Mantel–Haenszel method and calculated I² were also reported to test whether there was heterogeneity among the included studies. Publication bias was also assessed using funnel plots. The meta-analysis of secondary outcomes was conducted using Review Manager 5.3 software (Cochrane Community). A total of 894,561 malaria patients were reported in all 16 included studies. Overall, a pooled analysis showed that 9% (2,006/35,768, 95% CI 7.0–12.0%) of patients with mixed Plasmodium infection had severe mixed infection. A meta-analysis of 14 studies demonstrated that patients with mixed Plasmodium infection (1,999/35,755) and patients with P. falciparum malaria (9,249/294,397) had an equal risk of developing severe malaria (OR 0.93, 95% CI 0.59–1.44). Both mixed infection and P. falciparum mono-infection showed a similar trend of complications in which severe anaemia, pulmonary failure, and renal impairment were the three most common complications found. However, patients with mixed infection had a higher proportion of severe anaemia and pulmonary complications than those with P. falciparum infection. Moreover, patients with mixed infection had a higher proportion of multiple organ failure than those with P. falciparum mono-infection. Mixed Plasmodium spp. infections were common but often unrecognized or underestimated, leading to severe complications among these malaria patients. Therefore, in routine clinical laboratories, using an accurate combination of diagnostic procedures to identify suspected patients with mixed infections is crucial for therapeutic decisions, prompt treatment, and effective patient management.

Molecular epidemiology and mechanisms of antibiotic resistance in Enterococcus spp., Staphylococcus spp., and Streptococcus spp. in Africa: a systematic review from a One Health perspective

A systematic review of antibiotic-resistant Gram-positive bacteria in Africa from a One Health perspective is lacking. Here, we report result from a search for English-language articles on the resistance mechanisms and clonality of Gram-positive bacteria in Africa between 2007 and 2019 reported in PubMed, Web of Science, ScienceDirect, and African Journals OnLine; 172 studies from 22 different African countries were identified. Resistance genes, such as mecA, erm(B), erm(C), tet(M), tet(K), tet(L), vanB, vanA, vanC, and tet(O), were found to be common. Staphylococcus spp., Enterococcus spp., and Streptococcus spp. were the main species reported by the studies, with clones such as Staphylococcus aureus ST5 (n = 218 isolates), ST8 (n = 127 isolates), ST80 (n = 133 isolates), and ST88 (n = 117 isolates), and mobile genetic elements such as IS16 (n = 28 isolates), IS256 (n = 96), Tn916 (n = 107 isolates), and SCCmec (n = 4437 isolates) identified. SCCmec IV (n = 747 isolates) was predominant, followed by SCCmec III (n = 305 isolates), SCCmec II (n = 163 isolates), SCCmec V (n = 135 isolates), and SCCmec I (n = 79 isolates). Resistance to penicillin (n = 5926 isolates), tetracycline (n = 5300 isolates), erythromycin (n = 5151 isolates), rifampicin (n = 3823 isolates), gentamycin (n = 3494 isolates), sulfamethoxazole/trimethoprim (n = 3089 isolates), and ciprofloxacin (n = 2746 isolates) was common in most reports from 22 countries. Clonal dissemination of resistance across countries and between humans, animals, and the environment was observed. Resistance rates ranged from 1.4% to 100% for 15 of the studies; 10 were One Health-related studies. Strict infection control measures, antimicrobial stewardship, and periodic One Health epidemiological surveillance studies are needed to monitor and contain the threat of increasing antibiotic resistance in Africa.

Impact of Antibiotic Resistance on Treatment of Pneumococcal Disease in Ethiopia: An Agent-Based Modeling Simulation

Antimicrobial resistance (AMR) is a growing threat to global health. Although AMR endangers continued effectiveness of antibiotics, the impact of AMR has been poorly estimated in low-income countries. This study sought to quantify the effect of AMR on treatments for pediatric pneumococcal disease in Ethiopia. We developed the DREAMR (Dynamic Representation of the Economics of AMR) model that simulate children younger than 5 years who acquire pneumococcal disease (pneumonia, meningitis, and acute otitis media) and seek treatment from various health facilities in Ethiopia over a year. We examined the AMR levels of three antibiotics (penicillin, amoxicillin, and ceftriaxone), treatment failures, and attributable deaths. We used the cost-of-illness method to assess the resulting economic impact of AMR from a societal perspective by estimating the direct and indirect treatment costs and productivity losses. Findings showed that AMR against antibiotics that were used to treat pneumococcal disease led to 195,763 treatment failures per year, which contributed to 2,925 child deaths annually in Ethiopia. Antimicrobial resistance resulted in a first-line treatment failure rate of 29.4%. In 1 year, the proportion of nonsusceptible Streptococcus pneumoniae bacteria increased by 2.1% and 0.5% for amoxicillin and penicillin, and reduced by 0.3% for less commonly used ceftriaxone. Annual costs of AMR to treat pneumococcal disease were around US$15.8 million, including US$3.3 million for ineffective first-line treatments, US$3.7 million for second-line treatments, and US$8.9 million for long-term productivity losses. Antibiotic stewardship to reduce misuse and overuse of antibiotics is essential to maintain the effectiveness of antibiotics, and lessen the health and economic burden of AMR.

External Quality Assessment of Bacterial Identification and Antimicrobial Susceptibility Testing in African National Public Health Laboratories, 2011-2016

Background: In 2002, the World Health Organization (WHO) launched a regional microbiology external quality assessment (EQA) programme for national public health laboratories in the African region, initially targeting priority epidemic-prone bacterial diseases, and later including other common bacterial pathogens. Objectives: The aim of this study was to analyse the efficacy of an EQA programme as a laboratory quality system evaluation tool. Methods: We analysed the proficiency of laboratories’ performance of bacterial identification and antimicrobial susceptibility testing (AST) for the period 2011–2016. The National Institute for Communicable Diseases of South Africa provided technical coordination following an agreement with WHO, and supplied EQA samples of selected bacterial organisms for microscopy (Gram stain), identification, and antimicrobial susceptibility testing (AST). National public health laboratories, as well as laboratories involved in the Invasive Bacterial Diseases Surveillance Network, were enrolled by the WHO Regional Office for Africa to participate in the EQA programme. We analysed participants’ results of 41 surveys, which included the following organisms sent as challenges: Streptococcus pneumonia, Haemophilus influenzae, Neisseria meningitidis, Salmonella Typhi, Salmonella Enteritidis, Shigella flexneri, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus anginosus, Enterococcus faecium, Serratia marcescens, Acinetobacter baumannii, and Enterobacter cloacae. Results: Eighty-one laboratories from 45 countries participated. Overall, 76% of participants obtained acceptable scores for identification, but a substantial proportion of AST scores were not in the acceptable range. Of 663 assessed AST responses, only 42% had acceptable scores. Conclusion: In the African Region, implementation of diagnostic stewardship in clinical bacteriology is generally suboptimal. This report illustrates that AST is poorly done compared to microscopy and identification. It is critically important to make the case for implementation of quality assurance in AST, as it is the cornerstone of antimicrobial resistance surveillance reporting and implementation of the Global Antimicrobial Resistance Surveillance System.

Clinical Referral Laboratory Personnel's Perception of Challenges and Strategies for Sustaining the Laboratory Quality Management System

OBJECTIVES

To explore challenges explaining the decrease in quality performance and suggest strategies to improve and sustain laboratory quality services.

METHODS

Twenty key informants' interviews from laboratory personnel were conducted in five laboratories. Four had previously shown a decrease in quality performance. Interviews were transcribed verbatim and analyzed using inductive thematic analysis.

RESULTS

Two themes emerged: (1) insufficient coordination and follow-up system towards accreditation, where lack of coordination, follow-up, and audits explained the decrease in performance; (2) inadequate resource optimization, where insufficient knowledge in Laboratory Quality Management System (LQMS), ownership by laboratory workforce, and insufficient stakeholders' communication contributed to low-quality performance.

CONCLUSIONS

The coordination, follow-up, and assessments of LQMS, in conjunction with training of laboratory workforce, would establish an institutional culture of continuous quality improvement (CQI) towards accreditation and sustainment of quality health care. To achieve CQI culture, routine gap checking and planning for improvement using a system approach is required.

Diagnostic Bacteriology in District Hospitals in Sub-Saharan Africa: At the Forefront of the Containment of Antimicrobial Resistance

This review provides an update on the factors fuelling antimicrobial resistance and shows the impact of these factors in low-resource settings. We detail the challenges and barriers to integrating clinical bacteriology in hospitals in low-resource settings, as well as the opportunities provided by the recent capacity building efforts of national laboratory networks focused on vertical single-disease programmes. The programmes for HIV, tuberculosis and malaria have considerably improved laboratory medicine in Sub-Saharan Africa, paving the way for clinical bacteriology. Furthermore, special attention is paid to topics that are less familiar to the general medical community, such as the crucial role of regulatory frameworks for diagnostics and the educational profile required for a productive laboratory workforce in low-resource settings. Traditionally, clinical bacteriology laboratories have been a part of higher levels of care, and, as a result, they were poorly linked to clinical practices and thus underused. By establishing and consolidating clinical bacteriology laboratories at the hospital referral level in low-resource settings, routine patient care data can be collected for surveillance, antibiotic stewardship and infection prevention and control. Together, these activities form a synergistic tripartite effort at the frontline of the emergence and spread of multi-drug resistant bacteria. If challenges related to staff, funding, scale, and the specific nature of clinical bacteriology are prioritized, a major leap forward in the containment of antimicrobial resistance can be achieved. The mobilization of resources coordinated by national laboratory plans and interventions tailored by a good understanding of the hospital microcosm will be crucial to success, and further contributions will be made by market interventions and business models for diagnostic laboratories. The future clinical bacteriology laboratory in a low-resource setting will not be an "entry-level version" of its counterparts in high-resource settings, but a purpose-built, well-conceived, cost-effective and efficient diagnostic facility at the forefront of antimicrobial resistance containment.

Experience of Indian association of medical microbiology external quality assurance scheme centre, New Delhi: Challenges and quality assessment of clinical microbiology laboratories

Introduction

EQAS program at New Delhi under IAMM was started in January 2014 across North and North east regions of India with 217 participants, which grew up to 540 by 2018.

Materials and Methods

In 2014, 4 analytes per year were sent for 3 exercises, i.e. smear culture and serology. 2018 onwards PT analytes were increased from 4 to 12 and comparative performance of techniques analysed.

Results

Out of the 22 smears sent for gram staining, ZN staining, Kinyoun staining and Albert staining, completely correct results ranged between 29.55% - 79.9%, 94.3% - 99.2%, 35.5% & 93.8%, respectively. Correct results for culture isolate identification & susceptibility testing and serology exercises varied between 70 & 92.4% and 73.1 & 98.59%, respectively. In the year 2018, 470 responses were received for bacterial culture identification & antibiotic susceptibility testing out of which manual and automated systems were used by 54% & 46% and 52.5% & 47.5% participants, respectively. Techniques used in BBV assays for HBsAg, HCV & HIV found all methods like ELISA, ELFA, CLIA and Card Test performing similarly. The major challenges in running the EQA program included requirement of large amount of specimens for PT item preparation, stability in hot and humid conditions and timely delivery of PT challenges in remote parts of the country.

Conclusion

A large number of the participating laboratories (77%) had an overall score of >80% for all exercises, demonstrating acceptable baseline performance of EQAS registered laboratories. However, continued EQAS participation could further improve the quality of results.

An overview of antimicrobial resistance surveillance among healthcare-associated pathogens in South Africa

Healthcare-associated infections are a serious public health concern resulting in morbidity and mortality particularly in developing countries. The lack of information from Africa, the increasing rates of antimicrobial resistance and the emergence of new resistance mechanisms intensifies this concern warranting the need for vigorous standardised surveillance platforms that produce reliable and accurate data which can be used for addressing these concerns. The implementation of national treatment guidelines, policies, antimicrobial stewardship programmes and infection prevention and control practices within healthcare institutions require a platform from which it can draw information and direct its approach. In this review, the importance of standardised surveillance systems, the challenges faced in the application of a surveillance system and the condition (existence and nonexistence) of such systems in African countries is discussed. This review also reports on some South African data.

Development of IgY-Based Sandwich ELISA as a Robust Tool for Rapid Detection and Discrimination of Toxigenic Vibrio cholerae

Background

The conventional methods for diagnosis of Vibrio cholerae are time consuming, complicated, and expensive. Development of rapid detection tests is critical for prevention and management of cholera. This study aimed to introduce two sensitive sandwich ELISAs based on avian antibodies (IgY) targeting outer membrane protein W (OmpW) and cytotoxin B (CtxB) antigens of V. cholerae.

Methods

The sequences of ompW and ctxB genes were cloned into pET28a vector. Escherichia coli BL21 (DE3) was transformed with the recombinant vectors, and gene expression was induced by IPTG. The expressed proteins were purified by affinity chromatography using Ni-NTA resins. Two groups of white Leghorn chickens were immunized by recombinant proteins, and the generated antibodies were purified from egg yolks of chickens by PEG precipitation. The antibodies were used for the development of α-OmpW and α-CtxB ELISAs.

Results

The expression and purification yielded 59 and 38 mg of recombinant OmpW and CtxB, respectively, per one liter of bacterial culture. PEG precipitation and purification of egg yolk antibodies yielded on average (±SD) 66.5 ± 1.80 and 50.9 ± 2.23 mg of purified α-OmpW and α-CtxB per egg, respectively. The analytical sensitivity of α-OmpW ELISA was 103 cfu/mL of V. cholerae and that of α-CtxB ELISA was 33 pg/mL of recombinant cytotoxin B. The two developed ELISAs did not show any cross-reactivity to any tested bacteria grown in common conditions.

Discussion

The current study is the first report on using IgY for detection of V. cholerae. The developed ELISAs were shown to have considerable analytical sensitivity and specificity. Therefore, the assays can be one of the convenient methods for sensitive and specific detection of toxigenic V. cholerae strains in clinical and environmental samples.

External quality assessment of malaria microscopy diagnosis in selected health facilities in Western Oromia, Ethiopia

Background

Accurate early diagnosis and prompt treatment are one of the key strategies to control and prevent malaria disease. External quality assessment is the most effective method for evaluation of the quality of malaria microscopy diagnosis. The aim of this study was to assess the quality of malaria microscopy diagnosis and its associated factors in selected public health facility laboratories in East Wollega Zone, Western Ethiopia.

Methods

Facility-based cross-sectional study design was conducted in 30 randomly selected public health facility laboratories from November 2014 to January 2015 in East Wollega Zone, Western Ethiopia. Ten validated stained malaria panel slides with known Plasmodium species, developmental stage and parasite density were distributed. Data were captured; cleaned and analyzed using SPSS version 20 statistical software-multivariate logistic regressions and the agreement in reading between the peripheral diagnostic centers and the reference laboratory were done using kappa statistics.

Results

A total of 30 health facility laboratories were involved in the study and the overall quality of malaria microscopy diagnosis was poor (62.3%). The associated predictors of quality in this diagnosis were in-service training [(AOR = 16, 95% CI (1.3, 1.96)], smearing quality [(AOR = 24, 95% CI (1.8, 3.13)], staining quality [(AOR = 15, 95% CI (2.35, 8.61), parasite detection [(AOR = 9, 95% CI (1.1, 8.52)] and identification skills [(AOR = 8.6, 95% CI (1.21, 1.63)]. Eighteen (60%) of health facility laboratories had in-service trained laboratory professionals on malaria microscopy diagnosis.

Conclusion

Overall quality of malaria microscopy diagnosis was poor and a significant gap in this service was observed that could impact on its diagnostic services.

Test Cost and Test Accuracy in Clinical Laboratories in Kampala, Uganda

OBJECTIVES

To assess the accuracy and costs of laboratory tests in Kampala, Uganda.

METHODS

A random selection of 78 laboratories tested external quality assurance samples at market rates. There were 40 moderate- to high-complexity and 38 low-complexity laboratories. Four percent (3/78) of these laboratories were accredited and 94% (73/78) were private. The 40 moderate- to high-complexity laboratories performed malaria blood smear, urine human chorionic gonadotropin (hCG), human immunodeficiency virus (HIV), syphilis, glucose, and three-panel tests: CBC, liver function tests, and kidney function tests. The 38 low-complexity laboratories performed malaria blood smear, urine hCG, and syphilis testing only. Hematology, HIV, syphilis, and malarial proficiency testing samples were prepared by accredited laboratories in Kampala. All other samples were provided by the Royal College of Pathologists of Australia.

RESULTS

77.1% of all results were accurate (met target values). It varied widely by laboratory (50%-100%), test identity (malaria blood smear, 96%; serum urea nitrogen, 38%), and test type (quantitative: 66% [31%-89%], qualitative: 91% [68%-97%]). Test prices varied by up to 3,600%, and there was no correlation between test cost and accuracy (r2 = 0.02).

CONCLUSIONS

There were large differences in accuracy and price across laboratories in Kampala. Price was not associated with quality.

Management of superficial and deep-seated Staphylococcus aureus skin and soft tissue infections in sub-Saharan Africa: a post hoc analysis of the StaphNet cohort

PURPOSE

The incidence of Staphylococcus aureus skin and soft tissue infection (SSTI) is high in sub-Saharan Africa. This is fueled by a high prevalence of Panton-Valentine leukocidin (PVL), which can be associated with necrotizing disease. The aim was to describe the clinical presentation and the treatment of SSTI in the African setting and to identify challenges in the management.

METHODS

Patients (n = 319) were recruited in DR Congo (n = 56, 17.6%), Gabon (n = 89, 27.9%), Mozambique (n = 79, 24.8%) and Tanzania (n = 95, 29.8%) during the prospective observational StaphNet cohort study (2010-2015). A physician recorded the clinical management in standardized questionnaires and stratified the entity of SSTI into superficial (sSSTI) or deep-seated (dSSTI). Selected virulence factors (PVL, β hemolysin) and multilocus sequence types (MLST) were extracted from whole genome sequencing data.

RESULTS

There were 220/319 (69%) sSSTI and 99/319 (31%) dSSTI. Compared to sSSTI, patients with dSSTI were more often hospitalized (13.2 vs. 23.5%, p = 0.03), HIV-positive (7.6 vs. 15.9%, p = 0.11), and required more often incision and drainage (I&D, 45.5 vs. 76.5%, p = 0.04). The proportion of an adequate antimicrobial therapy increased marginally from day 1 (empirical therapy) to day 3 (definite therapy), for sSSTI (70.7 to 72.4%) and dSSTI (55.4 to 58.9%). PVL was a risk factor for I&D (OR = 1.7, p = 0.02) and associated with MLST clonal complex CC121 (OR = 2.7, p < 0.001).

CONCLUSION

Appropriate antimicrobial agents and surgical services to perform I&D were available for the majority of patients. Results from susceptibility testing should be considered more efficiently in the selection of antimicrobial therapy.

Point-of-care and point-of-'can': leveraging reference-laboratory capacity for integrated diagnosis of fever syndromes in the tropics

BACKGROUND

There is an urgent need for integrated diagnosis of febrile syndromes able to account for multiple pathogens and to inform decisions for clinical care and public health.

AIMS

To reflect on the evolving roles of laboratory-based testing for non-malarial febrile illnesses (NMFIs) in low-resource settings, and to consider how advances in diagnostics, in connectivity and transport, and in implementation of quality systems may substantially enhance the capacity of reference laboratories to bridge the current gap between remote passive surveillance and clinically meaningful integrated fever diagnosis.

SOURCES

Iterative search of PubMed databases, organizational reports, and expert consultation.

CONTENT

Implementation of new technologies-such as very broad molecular panels for surveillance and mass spectrometry-may considerably diminish capability gaps in reference laboratories in low-resource settings. Although the need for clinical bacteriology diagnostics is now recognized, the lack of new simple and rapid phenotypic tests for antimicrobial resistance remains a key deficiency. Several initiatives to strengthen diagnostic preparedness for infectious disease outbreaks have highlighted the need for functional tiered laboratory networks. Recently, dramatic headway in connectivity-such as combining automated readers with the image processing and data transmission capabilities of smartphones-now allows for more complex testing and interfacing with distant laboratory information systems while reducing workload and errors. Together with connectivity to transmit and receive results, new approaches to specimen collection and transport-such as the validation of rectal swabs and the use of aerial drones to transport specimens to distant laboratories-now make remote testing feasible. The above innovations also open up the possibility of implementing quality systems through community-level diagnostic stewardship. Finally, strengthened laboratory networks actively support the feasibility of implementing quality-assured point-of-care testing where it is needed.

IMPLICATIONS

Recent advances offer the present-day possibility of innovations to re-invent the relationship between distant reference laboratories and end-users for integrated diagnosis of NMFIs.

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.

External quality assessment in resource-limited countries

Introduction

Health laboratory services are a critical component of national health systems but face major operational challenges in resource-limited (RL) settings. New funding for health systems strengthening in RL countries has increased the demand for diagnostics and provided opportunities to address these constraints. An approach to sustainably strengthen national laboratory systems in sub-Saharan African countries is the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme. External Quality Assessment (EQA) is a requirement for laboratory accreditation. EQA comprises proficiency testing (PT), rechecking of samples and on-site evaluation.

Materials and methods

A systematic literature search was conducted to identify studies addressing laboratory EQA and quality monitoring in RL countries. Unpublished reports were also sought from national laboratory authorities and personnel.

Results

PT schemes in RL countries are provided by commercial companies, institutions in developed countries and national programmes. Most government-supported PT schemes address single diseases using a vertical approach. Regional approaches to delivering PT have also been implemented across RL countries. Rechecking schemes address mainly tuberculosis (TB), malaria and human immunodeficiency virus (HIV); integrated rechecking programmes have been piloted. Constraints include sample transportation, communication of results, unknown proficiency of referee staff and limited resources for corrective action. Global competency assessment standards for malaria microscopists have been established.

Conclusions

EQA is vital for monitoring laboratory performance and maintaining quality of laboratory services, and is a valuable tool for identifying and assessing technology in use, identifying gaps in laboratory performance and targeting training needs. Accreditation of PT providers and competency of EQA personnel must be ensured.

Improvement of fungal disease identification and management: combined health systems and public health approaches

More than 1·6 million people are estimated to die of fungal diseases each year, and about a billion people have cutaneous fungal infections. Fungal disease diagnosis requires a high level of clinical suspicion and specialised laboratory testing, in addition to culture, histopathology, and imaging expertise. Physicians with varied specialist training might see patients with fungal disease, yet it might remain unrecognised. Antifungal treatment is more complex than treatment for bacterial or most viral infections, and drug interactions are particularly problematic. Health systems linking diagnostic facilities with therapeutic expertise are typically fragmented, with major elements missing in thousands of secondary care and hospital settings globally. In this paper, the last in a Series of eight papers, we describe these limitations and share responses involving a combined health systems and public health framework illustrated through country examples from Mozambique, Kenya, India, and South Africa. We suggest a mainstreaming approach including greater integration of fungal diseases into existing HIV infection, tuberculosis infection, diabetes, chronic respiratory disease, and blindness health programmes; provision of enhanced laboratory capacity to detect fungal diseases with associated surveillance systems; procurement and distribution of low-cost, high-quality antifungal medicines; and concomitant integration of fungal disease into training of the health workforce.

Antimicrobial resistance in West Africa: a systematic review and meta-analysis

Growing data suggest that antimicrobial-resistant bacterial infections are common in low- and middle-income countries. This review summarises the microbiology of key bacterial syndromes encountered in West Africa and estimates the prevalence of antimicrobial resistance (AMR) that could compromise first-line empirical treatment. We systematically searched for studies reporting on the epidemiology of bacterial infection and prevalence of AMR in West Africa within key clinical syndromes. Within each syndrome, the pooled proportion and 95% confidence interval were calculated for each pathogen-antibiotic pair using random-effects models. Among 281 full-text articles reviewed, 120 met the eligibility criteria. The majority of studies originated from Nigeria (70; 58.3%), Ghana (15; 12.5%) and Senegal (15; 12.5%). Overall, 43 studies (35.8%) focused on urinary tract infections (UTI), 38 (31.7%) on bloodstream infections (BSI), 27 (22.5%) on meningitis, 7 (5.8%) on diarrhoea and 5 (4.2%) on pneumonia. Children comprised the majority of subjects. Studies of UTI reported moderate to high rates of AMR to commonly used antibiotics including evidence of the emergence of cephalosporin resistance. We found moderate rates of AMR among common bloodstream pathogens to typical first-line antibiotics including ampicillin, cotrimoxazole, gentamicin and amoxicillin/clavulanate. Among S. pneumoniae strains isolated in patients with meningitis, levels of penicillin resistance were low to moderate with no significant resistance noted to ceftriaxone or cefotaxime. AMR was common in this region, particularly in hospitalized patients with BSI and both outpatient and hospitalized patients with UTI. This raises concern given the limited diagnostic capability and second-line treatment options in the public sector in West Africa.

Urgent needs in fostering neglected tropical diseases (NTDs) laboratory capacity in WHO Western Pacific Region: results from the external quality assessment on NTDs diagnosis in 2012-2015

BACKGROUND

Neglected tropical diseases (NTDs) are a heterogeneous group of mainly chronic, debilitating and often stigmatizing diseases that largely affects low-income and politically marginalized populations, causing a large burden of public health, social and economies in the NTDs endemic countries. NTDs are caused by infections with a range of pathogen, including bacteria, parasites, protozoa and viruses. The accurate diagnosis of NTDs is important for reducing morbidity, preventing mortality and for monitoring of control programs. External Quality Assessment (EQA), a component of laboratory quality assurance, aims to assess the performance of participating laboratories in detecting parasitic infections. The aim of this paper is to report the findings and put forward the recommendations on capacity build from the EQA results of participating NTDs laboratories in selected countries in the WHO Western Pacific Region from 2012 to 2015.

METHODS

Reference or public health laboratories at national level working on NTDs in 6 countries participated in EQAs organized by the National Institute of Parasitic Diseases (NIPD) of Chinese Center for Disease Control and Prevention (CDC) based in Shanghai, China. Two representatives of each participating laboratory were invited to NIPD to detect NTDs' parasitic infections using the same prepared samples for serological tests (IHA and ELISA) and helminth eggs' morphological tests (Direct smear and Kato-Katz). All of the results were scored and analyzed by using SPSS statistics 19.0 software.

RESULTS

The percentage of participants who had EQA score ≥ 60 during 2012-2015 for direct smear test were 80.00% (2012), 71.43% (2013), 100% (2014) and 75.00% (2015), whereas for Kato-Katz test were 80.00% (2012), 57.14% (2013), 100% (2014) and 37.50% (2015), respectively. The detection rate of helminth eggs varied in different species, with Ascaris lumbricoides being the highest at 94.07% in average. All laboratories did very well with ELISA tests as shown by the high scores in all four years except Lab A in the first and last EQA. For the positive or negative judgments of serum samples, the total coincidence rates of ELISA between 2012 and 2015 were 90.00%, 99.29%, 94.29% and 98.75%, respectively. While the total coincidence rates of IHA were respectively 100%, 95.00%, 90.00% and 97.50%. However, detecting low levels of serum antibody remained problematic for IHA when the titres of samples were taken into consideration.

CONCLUSION

This study demonstrate that EQA scheme have been beneficial to the participating laboratories. The EQA programme identifies certain deficiencies which were needed to overcome and improved the laboratories' performance in helminthiasis diagnosis. However, further optimization of accuracy and uniformity in NTDs diagnosis remains a big challenge.

Implementation of quality management for clinical bacteriology in low-resource settings

BACKGROUND

The declining trend of malaria and the recent prioritization of containment of antimicrobial resistance have created a momentum to implement clinical bacteriology in low-resource settings. Successful implementation relies on guidance by a quality management system (QMS). Over the past decade international initiatives were launched towards implementation of QMS in HIV/AIDS, tuberculosis and malaria.

AIMS

To describe the progress towards accreditation of medical laboratories and to identify the challenges and best practices for implementation of QMS in clinical bacteriology in low-resource settings.

SOURCES

Published literature, online reports and websites related to the implementation of laboratory QMS, accreditation of medical laboratories and initiatives for containment of antimicrobial resistance.

CONTENT

Apart from the limitations of infrastructure, equipment, consumables and staff, QMS are challenged with the complexity of clinical bacteriology and the healthcare context in low-resource settings (small-scale laboratories, attitudes and perception of staff, absence of laboratory information systems). Likewise, most international initiatives addressing laboratory health strengthening have focused on public health and outbreak management rather than on hospital based patient care. Best practices to implement quality-assured clinical bacteriology in low-resource settings include alignment with national regulations and public health reference laboratories, participating in external quality assurance programmes, support from the hospital's management, starting with attainable projects, conducting error review and daily bench-side supervision, looking for locally adapted solutions, stimulating ownership and extending existing training programmes to clinical bacteriology.

IMPLICATIONS

The implementation of QMS in clinical bacteriology in hospital settings will ultimately boost a culture of quality to all sectors of healthcare in low-resource settings.

Laboratory systems as an antibacterial resistance containment tool in Africa

INTRODUCTION

As crucial as clinical laboratories are to preventing, identifying and managing resistance problems, laboratory scientists are among the most overlooked stakeholders. This review outlines the contributions that diagnostic laboratory systems should make toward all five of the World Health Organization's 2015 strategic objectives for antimicrobial resistance containment.

LABORATORY SYSTEMS IN RESISTANCE CONTAINMENT

Antimicrobial susceptibility testing and surveillance are central to antibacterial resistance management and control and need to be implemented more commonly and closer to sick patients. However, the scope of tests that promote judicious antimicrobial use extend beyond susceptibility testing. Laboratory tests for pathogens or their associated biomarkers confirm or rule out specific causes of signs and symptoms associated with infection. Laboratory systems also provide critical support to infection control programmes. All of these functions promote rational antimicrobial use and contain the spread of resistance. Routine laboratory data supports the development of vaccines and other technologies that could ease the pressure placed by antimicrobials. Laboratories are also a rich source of information for health professionals, policymakers and the general public about the urgency of the resistance problem and progress in containing it.

CONCLUSION

Laboratory systems are integral to antimicrobial resistance containment and contributions from African laboratories to addressing resistance need to be enhanced.

Quality assurance for HIV point-of-care testing and treatment monitoring assays

In 2015, UNAIDS launched the 90-90-90 targets aimed at increasing the number of people infected with HIV to become aware of their status, access antiretroviral therapies and ultimately be virally suppressed. To achieve these goals, countries may need to scale up point-of-care (POC) testing in addition to strengthening central laboratory services. While decentralising testing increases patient access to diagnostics, it presents many challenges with regard to training and assuring the quality of tests and testing. To ensure synergies, the London School of Hygiene & Tropical Medicine held a series of consultations with countries with an interest in quality assurance and their implementing partners, and agreed on an external quality assessment (EQA) programme to ensure reliable results so that the results lead to the best possible care for HIV patients. As a result of the consultations, EQA International was established, bringing together EQA providers and implementers to develop a strategic plan for countries to establish national POC EQA programmes and to estimate the cost of setting up and maintaining the programme. With the dramatic increase in the number of proficiency testing panels required for thousands of POC testing sites across Africa, it is important to facilitate technology transfer from global EQA providers to a network of regional EQA centres in Africa for regional proficiency testing panel production. EQA International will continue to identify robust and cost-effective EQA technologies for quality POC testing, integrating novel technologies to support sustainable country-owned EQA programmes in Africa.

The WHO AFRO external quality assessment programme (EQAP): Linking laboratory networks through EQA programmes

External Quality Assessment (EQA) surveys performed by the World Health Organization Regional Office for Africa (WHO AFRO) revealed the need for the strengthening of public health microbiology laboratories, particularly for testing of epidemic-prone diseases in the African Region. These surveys revealed common issues such as supply chain management, skilled personnel, logistical support and overall lack of quality standards. For sustainable improvements to health systems as well as global health security, deficiencies identified need to be actively corrected through robust quality assurance programmes and implementation of laboratory quality management systems.

Given all the pathogens of public health importance, an external quality assessment programme with a focus on vaccine-preventable diseases and emerging and re-emerging dangerous pathogens is important, and should not be stand-alone, but integrated within laboratory networks as seen in polio, measles, yellow fever and rubella.

In 2015, WHO AFRO collaborated with the US Centers for Disease Control and Prevention, the London School of Hygiene & Tropical Medicine and partners in a series of consultations with countries and national and regional EQA providers for the development of quality assurance models to support HIV point-of-care testing and monitoring. These consultations revealed similar challenges as seen in the WHO AFRO surveys. WHO AFRO brought forth its experience in implementing quality standards for health programmes, and also opened discussions on how lessons learned through such established programmes can be utilised to supporting and strengthening the introduction of early infant diagnosis of HIV and viral load point-of-care testing.

An optimised external quality assessment programme will impact the ability of countries to meet core capacities, providing improved quality management systems, improving the confidence of diagnostic network services in Africa, and including capacities to detect events of international public health importance.

Assessing the impact of pneumococcal conjugate vaccines on invasive pneumococcal disease using polymerase chain reaction-based surveillance: an experience from South Africa

Background

The use of molecular diagnostic techniques for the evaluation of the impact of pneumococcal conjugate vaccines (PCVs) has not been documented. We aimed to evaluate the impact of PCVs on invasive pneumococcal disease (IPD) using polymerase chain reaction (PCR)-based techniques and compare with results obtained from culture-based methods.

Methods

We implemented two independent surveillance programs for IPD among individuals hospitalized at one large surveillance site in Soweto, South Africa during 2009–2012: (i) PCR-based (targeting the lytA gene) syndromic pneumonia surveillance; and (ii) culture-based laboratory surveillance. Positive samples were serotyped. The molecular serotyping assay included targets for 42 serotypes including all serotypes/serogroups included in the 7-valent (PCV-7) and 13-valent (PCV-13) PCV. The Quellung reaction was used for serotyping of culture-positive cases. We calculated the change in rates of IPD (lytA- or culture-positive) among HIV-uninfected children aged <2 years from the year of PCV-7 introduction (2009) to the post-vaccine years (2011 or 2012).

Results

During the study period there were 607 lytA-positive and 1,197 culture-positive cases that were serotyped. Samples with lytA cycle threshold (Ct)-values ≥35 (30.2 %; 123/407) were significantly less likely to have a serotype/serogroup detected for serotypes included in the molecular serotyping assay than those with Ct-values <35 (78.0 %; 156/200) (p < 0.001). From 2009 to 2012 rates of PCV-7 serotypes/serogroups decreased −63.8 % (95 % CI: −79.3 % to −39.1 %) among lytA-positive cases and −91.7 % (95 % CI: −98.8 % to −73.6 %) among culture-positive cases. Rates of lytA-positive non-vaccine serotypes/serogroups also significantly decreased (−71.7 %; 95 % CI: −81.1 % to −58.5 %) over the same period. Such decline was not observed among the culture-positive non-vaccine serotypes (1.2 %; 95 % CI: −96.7 % to 58.4 %).

Conclusions

Significant downward trends in IPD PCV-7 serotype-associated rates were observed among patients tested by PCR or culture methods; however trends of non-vaccine serotypes/serogroups differed between the two groups. Misclassifications of serotypes/serogroups, affecting the use of non-vaccine serotypes as a control group, may have occurred due to the low performance of the serotyping assay among lytA-positive cases with high Ct-values. Until PCR methods improve further, culture methods should continue to be used to monitor the effects of PCV vaccination programs on IPD incidence.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-015-1198-z) contains supplementary material, which is available to authorized users.

Challenges of Sanitary Compliance Related to Trade in Products of Animal Origin in Southern Africa

Irrespective of the existence of potentially pathogenic organisms carried by animals, foods of animal origin remain the prime nutrition of humans world-wide. As such, food safety continues to be a global concern primarily to safeguard public health and to promote international trade. Application of integrated risk-based quality assurance procedures on-farm and at slaughterhouses plays a crucial role in controlling hazards associated with foods of animal origin. In the present paper we examine safety assurance systems and associated value chains for foods of animal origin based on historical audit results of some Southern African countries with thriving export trade in animal products, mainly to identify areas for improvement. Among the key deficiencies identified were: i) failure to keep pace with scientific advances related to the ever-changing food supply chain; ii) lack of effective national and regional intervention strategies to curtail pathogen transmission and evolution, notably the zoonotic Shiga toxin-producing Escherichia coli; and iii) a lack of effective methods to reduce contamination of foods of wildlife origin. The introduction of foods of wildlife origin for domestic consumption and export markets seriously compounds already existing conflicts in legislation governing food supply and safety. This analysis identifies gaps required to improve the safety of foods of wildlife origin.

Patterns of mixed Plasmodium species infections among children six years and under in selected malaria hyper-endemic communities of Zambia: population-based survey observations

BACKGROUND

Although malaria is preventable and treatable, it still claims 660,000 lives every year globally with children under five years of age having the highest burden. In Zambia, malaria rapid diagnostic tests (RDTs) that only detect Plasmodium falciparum are the main confirmatory means for malaria diagnosis in most health facilities without microscopy services. As a consequence of this P. falciparum species diagnostic approach, non-falciparum malaria is not only under-diagnosed but entirely missed, thereby making the exact disease burden unknown. We thus investigated the prevalence of various Plasmodium spp. and associated burden of infection in selected communities in Zambia.

METHODS

Data from two malaria hyper-endemic provinces (Eastern and Luapula) of the 2012 National Malaria Indicator Survey (MIS), conducted between April and May 2012, were used. The MIS is a nationally representative, two-stage cluster survey conducted to coincide with the end of the malaria transmission season. Social, behavioural and background information were collected from households as part of the survey. Thick blood smears, RDTs and dried blood spots (DBS) were collected from children below six years of age. Slides were stained using Giemsa and examined by microscopy while polymerase chain reaction (PCR) was used to analyse the DBS for malaria Plasmodium spp. Multivariate logistic regression was employed to examine the association between background factors and malaria.

RESULTS

Overall, 873 children younger than six years of age were surveyed. The overall prevalence of Plasmodium spp. by PCR was 54.3% (95% CI 51-57.6%). Of the total Plasmodium isolates, 88% were P. falciparum, 10.6% were mixed infections and 1.4% were non-falciparum mono infections. Among the mixed infections, the majority were a combination of P. falciparum and P. malariae (6.5% of all mixed infections). Children two years and older (2-5 years) had three-fold higher risk of mixed malaria infections (aOR 2.8 CI 1.31-5.69) than children younger than two years of age.

CONCLUSION

The high prevalence of mixed Plasmodium spp. infections in this population stresses review of the current malaria RDT diagnostic approaches. The observed less incidence of mixed infections in children under two years of age compared to their older two-to-five-year-old counterparts is probably due to the protective maternal passive immunity, among other factors, in that age group.

Typhoid fever

Control of typhoid fever relies on clinical information, diagnosis, and an understanding for the epidemiology of the disease. Despite the breadth of work done so far, much is not known about the biology of this human-adapted bacterial pathogen and the complexity of the disease in endemic areas, especially those in Africa. The main barriers to control are vaccines that are not immunogenic in very young children and the development of multidrug resistance, which threatens efficacy of antimicrobial chemotherapy. Clinicians, microbiologists, and epidemiologists worldwide need to be familiar with shifting trends in enteric fever. This knowledge is crucial, both to control the disease and to manage cases. Additionally, salmonella serovars that cause human infection can change over time and location. In areas of Asia, multidrug-resistant Salmonella enterica serovar Typhi (S Typhi) has been the main cause of enteric fever, but now S Typhi is being displaced by infections with drug-resistant S enterica serovar Paratyphi A. New conjugate vaccines are imminent and new treatments have been promised, but the engagement of local medical and public health institutions in endemic areas is needed to allow surveillance and to implement control measures.

Most clinical laboratory testing in Kampala occurs in high-volume, high-quality laboratories or low-volume, low-quality laboratories. A tale of two cities

OBJECTIVES

To describe key characteristics (laboratory quality, test volumes, and complexity) of clinical laboratories in Kampala, Uganda (population ~1.7 million).

METHODS

Cross-sectional survey using a standard questionnaire to document laboratory type and quality, as well as test menus and volumes. Quality was based on the World Health Organization-Africa Region checklist.

RESULTS

Of the 954 laboratories identified (a density of one laboratory per 1,781 persons), 779 (82%) performed only simple kit tests or light microscope examinations. The 95% (907/954) of laboratories for whom volumes were obtained performed an average aggregate of 13,189 tests daily, for a test utilization rate of around 2 tests per individual per year. Laboratories could be segregated into eight groups based on quality, test volume, and complexity. However, 90% of the testing was performed by just two groups: (1) low-volume (≤100 tests daily), low-quality laboratories performing simple tests or (2) high-volume (>100 tests daily), high-quality laboratories. Each of these two groups did 45% of the daily testing volume (90% combined).

CONCLUSIONS

Clinical laboratory density in Kampala (1/1,781 persons) is high, approaching that in the United States (1/1,347 persons). Low-volume/low-quality and high-volume/high-quality laboratories do 90% of the daily aggregate testing. Quality improvement (QI) schemes for Africa must be appropriate to low-volume laboratories as well as to the large laboratories that have been the focus of previous QI efforts.

Proficiency testing for HIV, tuberculosis and malaria diagnosis in clinical laboratories in Nigeria

Background

Proficiency testing (PT) is a means of verifying the reliability of laboratory results, but such programmes are not readily available to laboratories in developing countries. This project provided PT to laboratories in Nigeria.

Objectives

To assess the proficiency of laboratories in the diagnosis of HIV, tuberculosis and malaria.

Methods

This was a prospective study carried out between 2009 and 2011. A structured questionnaire was administered to 106 randomly-selected laboratories. Forty-four indicated their interest in participation and were enrolled. Four rounds of pre-characterised plasma panels for HIV, sputum films for tuberculosis and blood films for malaria were distributed quarterly by courier over the course of one year. The results were returned within two weeks and scores of ≥ 80% were reported as satisfactory. Mentoring was offered after the first and second PT rounds.

Results

Average HIV PT scores increased from 74% to 95% from the first round to the third round, but decreased in the fourth round. For diagnosis of tuberculosis, average scores increased from 42% in the first round to 78% in the second round; but a decrease to 34% was observed in the fourth round. Malaria PT performance was 2% at first, but average scores increased between the second and fourth rounds, culminating in a fourth-round score of 39%. Many participants requested training and mentoring.

Conclusions

There were gross deficiencies in the quality of laboratory services rendered across Nigeria. In-country PT programmes, implemented in conjunction with mentoring, will improve coverage and diagnosis of HIV, tuberculosis and malaria.

A malaria diagnostic tool based on computer vision screening and visualization of Plasmodium falciparum candidate areas in digitized blood smears

Introduction

Microscopy is the gold standard for diagnosis of malaria, however, manual evaluation of blood films is highly dependent on skilled personnel in a time-consuming, error-prone and repetitive process. In this study we propose a method using computer vision detection and visualization of only the diagnostically most relevant sample regions in digitized blood smears.

Methods

Giemsa-stained thin blood films with P. falciparum ring-stage trophozoites (n = 27) and uninfected controls (n = 20) were digitally scanned with an oil immersion objective (0.1 µm/pixel) to capture approximately 50,000 erythrocytes per sample. Parasite candidate regions were identified based on color and object size, followed by extraction of image features (local binary patterns, local contrast and Scale-invariant feature transform descriptors) used as input to a support vector machine classifier. The classifier was trained on digital slides from ten patients and validated on six samples.

Results

The diagnostic accuracy was tested on 31 samples (19 infected and 12 controls). From each digitized area of a blood smear, a panel with the 128 most probable parasite candidate regions was generated. Two expert microscopists were asked to visually inspect the panel on a tablet computer and to judge whether the patient was infected with P. falciparum. The method achieved a diagnostic sensitivity and specificity of 95% and 100% as well as 90% and 100% for the two readers respectively using the diagnostic tool. Parasitemia was separately calculated by the automated system and the correlation coefficient between manual and automated parasitemia counts was 0.97.

Conclusion

We developed a decision support system for detecting malaria parasites using a computer vision algorithm combined with visualization of sample areas with the highest probability of malaria infection. The system provides a novel method for blood smear screening with a significantly reduced need for visual examination and has a potential to increase the throughput in malaria diagnostics.

Implementation of a national external quality assessment program for medical laboratories in Burkina Faso: challenges, lessons learned, and perspectives

OBJECTIVES

The National External Quality Assessment (NEQA) program of Burkina Faso is a proficiency testing program mandatory for all laboratories in the country since 2006. The program runs two cycles per year and covers all areas of laboratories.

METHODS

All panels were validated by the expert committee before dispatch under optimal storage and transport conditions to participating laboratories along with report forms.

RESULTS

Performance in the last 5 years varied by panel, with average annual performance of bacteriology panels for all laboratories rising from 75% in 2006 to 81% in 2010 and with a best average performance of 87% in 2007 and 2008. During the same period, malaria microscopy performance varied from 85% to 94%, with a best average performance of 94% in 2010; chemistry performance increased from 87% to 94%, with a best average annual performance of 97% in 2009. Hematology showed more variation in performance, ranging from 61% to 86%, with a best annual average performance of 90% in 2008. Average annual performance for immunology varied less between 2006 and 2010, recording 97%, 90%, and 95%. Except for malaria microscopy, annual performances for enrolled panels varied substantially from year to year, indicating some difficulty in maintaining consistency in quality.

CONCLUSIONS

The main challenges of the NEQA program observed between 2006 to 2010 were funding, sourcing, and safe transportation of quality panels to all laboratories countrywide.

Diagnosis of Vibrio cholerae O1 infection in Africa

Isolation of Vibrio cholerae O1 is necessary for cholera outbreak confirmation. Rapid diagnostic testing of fecal specimens, based on lipopolysaccharide detection of V. cholerae O1 or O139, may assist in early outbreak detection and surveillance. Cary-Blair transport medium is recommended for specimen transport. Filter paper, although used in epidemics, needs evaluation against rectal swab specimens. Fecal specimens are subcultured onto selective and nonselective media, including 5% blood agar and TCBS agar, for detection of V. cholerae O1 or O139. Suspicious, oxidase-positive isolates are serotyped in monovalent antisera. Antimicrobial-susceptibility testing is performed to detect resistance. Molecular characterization supports phenotypic identification and outbreak investigations. The presence of genes encoding cholera toxin, lipopolysaccharide, and El Tor biotype traits can be confirmed. Standardized pulsed-field gel electrophoresis analysis facilitates strain comparison. Quality management ensures reliability of results through validation and verification of functional laboratory equipment; quality control of testing procedures, laboratory reagents, and consumables; and participation in proficiency-testing schemes.

The good, the bad, and the unknown: quality of clinical laboratories in Kampala, Uganda

Background

Clinical laboratories are crucial in addressing the high rates of communicable and non-communicable diseases seen in sub-Saharan Africa (SSA). However, the most basic information, such as the number and quality of clinical laboratories in SSA, is not available. The objective of this study was to create a practical method for obtaining this information in SSA towns and cities using an initial survey in Kampala, Uganda.

Methods

Kampala city was divided into 5 partially-overlapping regions. Each region was assigned to 2–3 surveyors who identified and surveyed laboratories in their respective regions; in person and on foot. A modified version of the World Health Organization - African Region (WHO/AFRO) Laboratory Strengthening Checklist was used to obtain baseline measures of quality for all clinical laboratories within Kampala city. The surveyors also measured other attributes of each laboratory, such as their affiliation (government, private etc), designation (national hospital, district hospital, standalone etc), staff numbers, and type of staff.

Results

The survey team identified and surveyed 954 laboratories in Kampala city. 96% of laboratories were private. Only 45 (5%) of the laboratories met or surpassed the lowest quality standards defined by the WHO/AFRO-derived laboratory strengthening tool (1-star). These 45 higher-quality laboratories were, on average, larger and had a higher number of laboratory-specific staff (technologists, phlebotomists etc) than the other 909 laboratories. 688 (72%) of the 954 laboratories were not registered with the Ministry of Health (MoH).

Conclusions

This comprehensive evaluation of the number, scope, and quality of clinical laboratories in Kampala is the first published survey of its kind in sub-Saharan Africa. The survey findings demonstrated that laboratories in Kampala that had qualified personnel and those that had higher testing volumes, tended to be of higher-quality.

External quality assessment of Giemsa-stained blood film microscopy for the diagnosis of malaria and sleeping sickness in the Democratic Republic of the Congo

OBJECTIVE

To report the findings of a second external quality assessment of Giemsa-stained blood film microscopy in the Democratic Republic of the Congo, performed one year after the first.

METHODS

A panel of four slides was delivered to diagnostic laboratories in all provinces of the country. The slides contained: (i) Plasmodium falciparum gametocytes; (ii) P. falciparum trophozoites (reference density: 113,530 per µl); (iii) Trypanosoma brucei subspecies; and (iv) no parasites.

FINDINGS

Of 356 laboratories contacted, 277 (77.8%) responded. Overall, 35.0% of the laboratories reported all four slides correctly but 14.1% reported correct results for 1 or 0 slides. Major errors included not diagnosing trypanosomiasis (50.4%), not recognizing P. falciparum gametocytes (17.5%) and diagnosing malaria from the slide with no parasites (19.0%). The frequency of serious errors in assessing parasite density and in reporting false-positive results was lower than in the previous external quality assessment: 17.2% and 52.3%, respectively, (P < 0.001) for parasite density and 19.0% and 33.3%, respectively, (P < 0.001) for false-positive results. Laboratories that participated in the previous quality assessment performed better than first-time participants and laboratories in provinces with a high number of sleeping sickness cases recognized trypanosomes more frequently (57.0% versus 31.2%, P < 0.001). Malaria rapid diagnostic tests were used by 44.3% of laboratories, almost double the proportion observed in the previous quality assessment.

CONCLUSION

The overall quality of blood film microscopy was poor but was improved by participation in external quality assessments. The failure to recognize trypanosomes in a country where sleeping sickness is endemic is a concern.