Antibiotic susceptibility of Enteric pathogens from the Maasai community, Narok and Kajiado Districts, Kenya

The emergence of resistance to antimicrobial agents in bacterial pathogens is a worldwide problem that has been associated with inappropriate use in human and veterinary medicine. Between August 2004 and July 2005 stool samples from 380 patients were cultured for enteric pathogens and characterized by Polymerase Chain Reaction for the presence of virulence properties. Patients were from Narok and Kajiado Districts of Kenya, mainly populated by the Maasai community majority of who practice traditional medicine. 218 patients were from Narok District Hospital and 62 from Entosopia Clinic in Kajiado. A total of 107 E. coli and 35 Shigella isolates were tested. Antibiotic susceptibility testing was done using the E-test strips containing Tetracycline, Gentamicin, Chloramphenicol, Fosfomycin, Amoxicillin/Clavulanic acid, Trimethoprim/Sulphamethoxazole, Ticarcillin/ Clavulanic acid and Ciprofloxacin. The resistance frequencies did not differ significantly between other E. coliand Shiga toxigenic E. coli, respectively; Gentamicin (3% vs. 3%), Chloramphenicol, (24% vs. 23%) and ampicillin (25% vs. 23%), Tetracycline (63% vs. 68%), Fosfomycin (44% vs. 54%) and Trimethoprim/Sulphamethoxazole (84% vs. 84%). Overall antibiotic resistance levels were at much lower levels than those reported from the rest of Kenya, possibly due to the lower levels of exposure and usage of antimicrobials among the Maasai community

Reproducibility of Results and Performance of TB Diagnostics in East Africa Public Health Laboratories Networking Project - in Kenya

No Abstract

Prevalence, virulence genes and Antimicrobial Resistance of Shiga-toxigenic E.coli in diarrhoea patients from Kitale, Kenya

Introduction: Shiga toxin-producing Escherichia coli (STEC) are among the most important causes of food-borne diseases. They cause illnesses ranging from mild diarrhea to more severe conditions that may progress to hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). The burden of STEC in patients with diarrheal illness in Kitale county referral hospital, Trans-Nzoia County had not been established.Objectives: To determine the prevalence of STEC, its associated virulence genes and antimicrobial resistance among patients seeking treatment for diarrhoeal illness at Kitale County Referral Hospital.Methods: Stool samples from patients seeking treatment for diarrheal illness and had consented to participate in the study were collected and cultured for enteric bacteria. Suspect E.coli isolates were further identified using conventional biochemical methods. Conventional multiplex PCR targeting Shiga toxins (stx1, stx2, hlyA and attaching and effacing mechanisms (eaeA) were used to detect STEC virulence markers responsible for the Pathogenicity of STEC infection among other E.coli pathotypes.Results: A total of 295 participants were enrolled; median age 120 months (IQR: 36-312). 39 %( 115) were children aged <5yearsof whom 54% (160) were females. The prevalence of pathogenic E.coli was 19%56/295 and STEC was the most prevalent among E.coli pathotypes at5.4%16/295. The Stx2 gene and the Stx1/Stx2/hlyAcombination were the most prevalent in the STEC strains. The virulence genes (Stx1, Stx2, eaeA* and HlyA*)were observed in 13, 19, 9 and 14 in STEC isolates respectively.The most common gene was Stx2 and combinations of (Stx1+Stx2+hlyA)genes. Antimicrobial resistance to commonly prescribed antibiotics: chloramphenicol, ampicillin 10μg, erythromycin15μg, gentamicin10μg, ciprofloxacin 5μg, tetracycline 30μg, Trimethoprim/Sulfamethoxazole 25 μg, Cefotaxime 30 μg, furazolidine (8μg) and nalidixic acid 30 μg. were observed for all E.coli isolates except one (1.8%; 95% CI=0.1-9.6%). No isolates among STEC showed resistance to Furazolidine drug. However, Trimethoprim / Sulphurmethoxazole) was the drug which exhibited the highest resistance at (94%, 95% CI 70 to 99%).Conclusion and recommendation: Prevalence of STEC was 5.4%, (Stx1/Stx2/hlyA) virulence genes combination was the most common. High resistance to commonly prescribed antibiotics were observed in E.coli isolates and may be an existing problem that needs to be further research investigation.Keywords: Shiga-Toxigenic Escherichia coli (STEC), antimicrobial resistance, Kitale County referral hospitalAfr J Health Sci. 2017; 30(2):105-11

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Authors' reply [5]

Singapore Medical Journal476555-556SIMJ

Application of Barcode Technology to Enhance Electronic Quality-Assured Data Collection and Analysis in Operational Research EAPHLN project study sites in Kenya

Background: Barcode Technology is a replacement for the traditional keyboard data entry. The East Africa Public Health Laboratory Networking (EAPHLN) Project operational research activities anticipated enormous data generation from different geographical sites and health care site teams which necessitated the development of the system. This paper describes the use of barcode technology to enhance electronic quality assured data collection and analysis in operational research studies in Kenya. Methodology: Barcode labels consisting of an encoded 9-digit unique identification figures were generated and centralized at KEMRI for nine study sites. At the sites, the label placement was done in the following sequence: patient card, consent form, questionnaire and clinical forms by the clinicians. Specimens and shipment form from the same patient with two matching identifier labels by the laboratory staff. The specimen barcode label contained additional information including specimen type and collection date. On receipt at the KEMRI laboratories, the specimen barcodes were scanned in the reception module of the electronic data management system (eDMS). An  additional barcode label was generated with a laboratory number that was affixed to the specimen and scanned into the testing equipment that generated outputs. Findings:  Implementation of the barcode technology in the study sites, involved introduction of a new workflow methodology. This impacted positively on patient recruitment and sample collection process. The barcode labels served as identifiers when used during enrollment which provided an accurate patient and specimen tracking system. This was evident as all specimens delivered had complete accompanying documents with 92% of all barcodes being successfully scanned. Poor storage and handling of the barcode labels contributed to the inability to the scanning. Clinical, demographic and laboratory information to be viewed directly without the need to track down the patient’s source documents. The barcode system ensured the following: the confidentiality of patients was maintained;  Automation specimen identification on tests eliminating need for relabeling result output reports; fewer errors. Conclusion: Patients’ data linkages and verification from all study sites and the reference laboratory leading to increased efficiency and effectiveness in maintaining patient records. We recommend refresher trainings and supervisory visits to ensuring proper implementation and utilization of the barcode labels. Keywords: Barcode Scanning; Data Linkages; Patients; Operational Research, Datalogic Powersca

The Role of Monitoring and Evaluation in Assessing Progress of Operational Research in the EAPHLNP Study Sites in Kenya

Introduction: Studies on performance of Operational Research (OR) projects have outlined the various enabling factors leading to  favorable research outcomes. OR plays a key role in filling the gap between what we know from research and what we do with that  knowledge. This has been expressed over time, based on monitoring (progress indicators) and evaluation (performance indicators) results.Objective: To document the performance of OR activities based on Monitoring and Evaluation (M&E) indicators as well as highlighting lessons learned.Methodology:  M&E framework was developed for the OR studies in three thematic areas; Tuberculosis (TB), malaria enterics as well as components of capacity strengthening and administrative. That was done by KEMRI OR Secretariat in consultation with the East Central Southern African – Health Community (ECSA-HC) Secretariat and the principal investigators of each thematic area from East Africa Community partner states (namely Burundi, Rwanda, Tanzania and Uganda). The framework included outcome indicators for each study, target values defined in accordance with approved protocols. Reporting interval was set at quarterly per year. TB studies had 8 reporting indicators, Enterics had 5 reporting indicators, malaria had 11 indicators, while administrative and capacity building had 15 reporting indicators. The framework was then adopted by the region. In Kenya, the initial roll-out of the research in all three thematic areas wasdone in February 2013. The first quarter of M&E was conducted in the study sites, as defined in the editorial of this journal, in June 2013 while the second “quarter” was carried out in June 2014.Findings: Between February 2013 and June 2014, there was little progress in all the three thematic areas. During the first evaluation, the number of enrolled respondents presumed to have TB at the satellite facilities were 185(6.2%) of the expected target number 3,000 persons. Non-satellite sites enrolled 124(8.2%) of the expected 1,520 persons presumed to have TB as well. In the second evaluation, enrollment at the satellite sites was at 13.3% compared to 1.2% in the non-satellite sites. That represented a two-fold percentage increase in the satellite sites compared to nonsatellite sites. Using ZN outcome indicator, there were differences in the number of actual TB cases detected in both sites compared with the target values. Number of TB – cases detected using ZN at satellite sites rose from 7.8% (target of 784 cases) to 11.0% (target of 1725 cases). In the non-satellite sites, there was a decline from 3.1% (target of 508 cases) to 1.1% (target of 1118 cases). In the Enteric Study, there was a marginal decline in the number of patients recruited from 21.6% (target of 1440 patients) as at the first evaluation to 17.2% (target of 1800 patients) in the second evaluation. For malaria study, a total of 333 patients had been enrolled against a targeted of 300 patients into the study representing an over enrollment of 111% from one site. For the administrative indicators, the OR Secretariat had over attained in three target areas namely publication and sharing of OR findings in country and regional bulletins and held OR-Technical working group meetings.Lesson Learnt: Low performance in achieving indicators in both TB and enteric studies was resulted by including; high staff turnover particularly in the non-satellite sites, high workload and breakdown in communication among sites' personnel in regard to participation in research activities. In the satellite sites where study interventions were provided, better performance in achieving indicators was attributed to improved capacity in personnel and other non-financial motivational aspects, such as site exchange visits, refresher courses and frequent attendance of project workshops and meetings. Scientists from KEMRI assisting in patient recruitment, specimen collection and shipment alongside with study site staff resulted to over-attainment of performance indicators. Such was demonstrated in the malaria study. The observed lag time between the various M&E field visits by OR team could have partially contributed to the missed opportunities of identification and correction of any deviations from the project protocols. Changes in leadership especially at the project top management at the Ministry of Health affected the overall performance of OR activitie due to delays in disbursement of funds and delays in obtaining no-objection to incur expenditure on essential activities that were not originally in the approved annual workplans. Conclusion and Recommentdation: Itt was established that several factors, some of which could have been augmented if the M&E exercise was conducted in accordance with the framework, affected the achievement of study indicators. M&E component is a crucial activity especially in tracking research progress and should be conducted consistently within the stipulated timeline. This will subsequently provide opportunities of early identification and correction of any deviations from the protocol. Keywords: Operational Research, Monitoring & Evaluation, indicators, targets, performance, factor

Inter / Intra Examiner Calibration of Clinical Signs and Symptoms in Comparison with Laboratory Results in the Diagnosis of Pulmonary Tuberculosis in Patients from EAPHLN Project Study Sites in Kenya

Introduction: The clinical diagnosis of pulmonary tuberculosis (PTB) is based on occurrence of four cardinal signs and symptoms which include current cough, night sweats, weight loss, or low grade fever. However few studies have determined the validity and reliability of these diagnoses by intra and inter-examiner calibration of clinicians for appropriateness of detection of tuberculosis (TB) in resource constrained settings. Objective: The study's aim was to determine the sensitivity of concordance and reliability (Kappa values) of inter-examiner and intra-examiner findings of clinicians in the EAPHLN project. Methodology: The study was a cross-sectional study in nine sites. It included 155 patients for intraexaminer and 57 patients for inter-examiner calibrations selected from eligible people with symptoms or signs suggestive of TB during the implementation of the East African Public Health Laboratory Network Project (EAPHLNP) in Kenya. TB clinical symptoms and signs were recorded in a structured medical form included the following: productive cough, weight loss, night sweats, low grade fever (classical cardinal signs and symptoms). Using quality assurance sampling for a total population of ten thousand people with symptoms or signs suggestive of TB from the sites with a minimum defective sample acceptable of 0 and a probability of defect accepted of 1% andan alpha of 5%, the sample size of repeatable samples is 262 for total patients for the sites per year. Intra-examiner calibration involved examination of the same patient independently by the same clinician within one day interval. Inter-examiner calibration involved examination of the same patient by two clinicians independently the same day. Calibration of the clinical tools used during examination of patients was done. TB laboratory diagnosis was first done by sputum  smear microscopy Ziehl–Neelsen stain.(ZN), secondly by optimized sputum smear microscopy with a Light Emitting Diode microscope ( LED) or fluorescent microscopy(FM), and thirdly by Gene-expert technique (Gene Xpert or Gx). The results from the clinicians and reference laboratory findings for these patients were entered in a computer, verified and analyzed in SPSS for reliability statistics. These unweighted Cohen Kappa scores were interpreted as follows: poor0.01–0.20, moderate 0.21–0.40, fair 0.41–0.60, good 0.61–0.80, or excellent 0.81–1.0 based on the agreement between the intraexaminer and inter-examiner findings Results: A significant difference was found between concordant diagnosis of a least 4 signs and symptoms of TB compared to fewer by the same examiner on the same patient in all TB test/HIV status categories except the ZN positive /HIV positives and GeneXpert negative /HIV positives and HIV negative categories. The highest sensitivity rate was 81.8 %( 95%CI=52.3-94.9) in the Gx+ve/HIV+ve category. The significance difference in senstivity results of TB/HIV test vs at least presence of the 4 signs and symptoms. However, This did not occur in ZN+ve/HIV+ve, FM+ve/HIV+ve , Gx+ve/HIV+ve Gx+ve/HIV-ve categories. Kappa values for cough and fever were consistently significantly higher than zero kappa. Conclusion: Excellent kappa can be achieved in low resource settings by clinician using all four cardinal signs and symptoms of TB with laboratory results. There is possibility of using the clinical diagnosis using the four signs and symptoms where laboratory diagnosis is not present but specificity is low. Good clinical practice would improve the specificity