Antimicrobial resistance: capacity and practices among clinical laboratories in Kenya, 2013

Introduction: antimicrobial resistance is neglected in developing countries; associated with limited surveillance and unregulated use of antimicrobials. Consequently, delayed patient recoveries, deaths and further antimicrobial resistance occur. Recent gastroenteritis outbreak at a children's home associated with multidrug resistant non-typhoidal Salmonella spp, raised concerns about the magnitude of the problem in Kenya, prompting antimicrobial resistance assessment preceding surveillance system establishment. Methods: eight public medical laboratories were conveniently selected. Questionnaires were administered to key informants to evaluate capacity, practice and utilization of antimicrobial susceptibility tests. Retrospective review of laboratory records determined antimicrobial resistance to isolates. Antimicrobial resistance was defined as resistance of a microorganism to an antimicrobial agent to which it was previously sensitive and multidrug resistance as non-susceptibility to at least one agent in three or more antimicrobial categories. Results: the laboratories comprised; 2(25%) national, 4(50%) sub-national and 2(25%) district. Overall, antimicrobial susceptibility testing capacity was inadequate in all. Seven (88%) had basic capacity for stool cultures, 3(38%) had capacity for blood culture. Resistance to enteric organisms was observed with the following and other commonly prescribed antimicrobials, ampicillin: 40(91%) Salmonella spp isolates; Tetracycline: 16(84%) Shigella flexineri isolates; cotrimoxazole: 20(100%) Shigella spp isolates, 24(91%) Salmonella spp isolates. Comparable patterns of multidrug resistance were evident with Shigella flexineri and Salmonella typhimurium. Ten (100%) clinicians reported not using laboratory results for patient management, for various reasons. Conclusion: antimicrobial susceptibility testing capacity was inadequate and the available approved guidelines for this in Kenya were adhered to by one laboratory. The resistance patterns indicated potential resistance to commonly prescribed antimicrobials

The Rwanda Field Epidemiology and Laboratory Training Program: training skilled disease detectives

Rwanda still suffers from communicable diseases which frequently lead to epidemics. In addition to other health workforce needs, Rwanda also lacks a public health workforce that can operate multi-disease surveillance and response systems at the national and sub-national levels.In 2009 and 2010 the Rwanda Ministry of Health and its partners from the Government of Rwanda (GOR) as well as the United States (US) Centers for Disease Control and Prevention, the African Field Epidemiology Network, and other partners embarked on a series of activities to develop a public health workforce that would be trained to operate disease surveillance and response systems at the national and district levels. The Rwanda Field Epidemiology and Laboratory Training Program (RFELTP) is a 2-year public health leadership development training program that provides applied epidemiology and public health laboratory training while the trainees provide public health service to the Ministry of Health. RFELTP is hosted at the National University of Rwanda School of Public Health for the didactic training. RFELTP is funded by GOR, the US Presidents Emergency Plan for AIDS Relief and the World Bank; it is managed by a multi-sectoral steering committee headed by the Minister of Health. The first RFELTP cohort has 15 residents who were recruited from key health programs in GOR. Over the first year of implementation, these 15 residents have conducted a variety of field investigations and responded to several outbreaks. RFELTP has also trained 145 frontline health workers through its two-week applied short courses. In the future, RFELTP plans to develop a veterinary track to address public health issues at the animal-human interface

Progress towards elimination of measles in Kenya, 2003-2016

Introduction: measles is targeted for elimination in the World Health Organization African Region by the year 2020. In 2011, Kenya was off track in attaining the 2012 pre-elimination goal. We describe the epidemiology of measles in Kenya and assess progress made towards elimination. Methods: we reviewed national case-based measles surveillance and immunization data from January 2003 to December 2016. A case was confirmed if serum was positive for anti-measles IgM antibody, was epidemiologically linked to a laboratory-confirmed case or clinically compatible. Data on case-patient demographics, vaccination status, and clinical outcome and measles containing vaccine (MCV) coverage were analyzed. We calculated measles surveillance indicators and incidence, using population estimates for the respective years. Results: the coverage of first dose MCV (MCV1) increased from 65% to 86% from 2003-2012, then declined to 75% in 2016. Coverage of second dose MCV (MCV2) remained < 50% since introduction in 2013. During 2003-2016, there were 26,188 suspected measles cases were reported, with 9043(35%) confirmed cases, and 165 deaths (case fatality rate, 1.8%). The non-measles febrile rash illness rate was consistently > 2/100,000 population, and "80% of the sub-national level investigated a case in 11 of the 14 years. National incidence ranged from 4 to 62/million in 2003-2006 and decreased to 3/million in 2016. The age specific incidence ranged from 1 to 364/million population and was highest among children aged < 1 year. Conclusion: Kenya has made progress towards measles elimination. However, this progress remains at risk and the recent declines in MCV1 coverage and the low uptake in MCV2 could reverse these gains

Field Epidemiology and Laboratory Training Program, Where Is the L-Track?

Background: Modifications of the Field Epidemiology Training Program (FETP) curricula to include a laboratory track (L-Track), to become Field Epidemiology and Laboratory Training Program (FELTP), began in 2004 in Kenya. The L-Track offered candidates training on laboratory competencies in management, policy, quality systems, and diagnostic methods as well as epidemiology, disease surveillance and outbreak response. Since then several FELTPs have discontinued the L-Track and instead offer all candidates, epidemiologists and laboratorians, a single FETP curriculum. Reasons for these changes are reported here.Methods: A questionnaire was sent to directors of 13 FELTP programs collecting information on the status of the programs, reasons for any changes, basic entry qualifications, source institutions and where residents were post enrollment or after graduation. Data from previous CDC internal assessments on FELTP L-Track was also reviewed.Results: Out of the 13 FELTPs included, directors from 10 FELTPs sent back information on their specific programs. The FELTPs in Kenya, Mozambique, Cameroon and Kazakhstan and Mali have discontinued a separate L-Track while those in Ghana, Georgia, Nigeria, Rwanda, and Tanzania continue to offer the separate L-Track. Reasons for discontinuation included lack of standardized curriculum, unclear strategies of the separate L-Track, and funding constraints. Two countries Kenya and Tanzania reported on the career progression of their graduates. Results show 84% (Kenya) and 51% (Tanzania) of candidates in the FELTP, L-Track were recruited from national/regional medical health laboratories. However post-graduation, 56% (Kenya) and 43% (Tanzania) were working as epidemiologists, program managers, program coordinators, or regulatory/inspection boards. Professional upward mobility was high; 87% (Kenya) and 73% (Tanzania) residents, reported promotions either in the same or in new institutions.Conclusions: The FELTP L-Track residents continue to offer critical contributions to public health workforce development with high upward mobility. While this may be a reflection of professional versatility and demand of the FELTP graduates, the move from core laboratory services underscores the challenges in filling and retaining qualified staff within the laboratory systems. Results suggest different strategies are needed to strengthen laboratory management and leadership programs with a clear focus on laboratory systems and laboratory networks to meet current and future clinical and public health laboratory workforce demands

Strengthening health systems in Africa: a case study of the Kenya field epidemiology training program for local frontline health workers

Abstract The logistical and operational challenges to improve public health practice capacity across Africa are well documented. This report describes Kenya’s Field Epidemiology and Laboratory Training Program’s (KFELTP) experience in implementing frontline public health worker training to transfer knowledge and practical skills that help strengthen their abilities to detect, document, respond to, and report unusual health events. Between May 2014 and May 2015, KFELTP hosted five training courses across the country to address practice gaps among local public health workers. Participants completed a 10-week process: two 1-week didactic courses, a 7-week field project, and a final 1-week course to present and defend the findings of their field project. The first year was a pilot period to determine whether the program could fit into the existing 2-year KFELTP model and whether this frontline-level training would have an impact on local practice. At the end of the first year, KFELTP certified 167 frontline health workers in field epidemiology and data management. This paper concludes that local, national, and international partnerships are critical for improving local public health response capacity and workforce development training in an African setting

Environmental Assessment and Blood Lead Levels of Children in Owino Uhuru and Bangladesh Settlements in Kenya

Background. Lead exposure is linked to intellectual disability and anemia in children. The United States Centers for Disease Control and Prevention (CDC) recommends biomonitoring of blood lead levels (BLLs) in children with BLL ≥5 μg/dL and chelation therapy for those with BLL ≥45 μg/dL. Objectives. This study aimed to determine blood and environmental lead levels and risk factors associated with elevated BLL among children from Owino Uhuru and Bangladesh settlements in Mombasa County, Kenya. Methods. The present study is a population-based, cross-sectional study of children aged 12–59 months randomly selected from households in two neighboring settlements, Owino Uhuru, which has a lead smelter, and Bangladesh settlement (no smelter). Structured questionnaires were administered to parents and 1–3 ml venous blood drawn from each child was tested for lead using a LeadCare ® II portable analyzer. Environmental samples collected from half of the sampled households were tested for lead using graphite furnace atomic absorption spectroscopy. Results: We enrolled 130 children, 65 from each settlement. Fifty-nine (45%) were males and the median age was 39 months (interquartile range (IQR): 30–52 months). BLLs ranged from 1 μg/dL to 31 μg/dL, with 45 (69%) children from Owino Uhuru and 18 (28%) children from Bangladesh settlement with BLLs >5 μg/dL. For Owino Uhuru, the geometric mean BLL in children was 7.4 μg/dL (geometric standard deviation (GSD); 1.9) compared to 3.7 μg/dL (GSD: 1.9) in Bangladesh settlement (p<0.05). The geometric mean lead concentration of soil samples from Owino Uhuru was 146.5 mg/Kg (GSD: 5.2) and 11.5 mg/Kg (GSD: 3.9) (p<0.001) in Bangladesh settlement. Children who resided <200 m from the lead smelter were more likely to have a BLL ≥5 μg/dL than children residing ≥200 m from the lead smelter (adjusted odds ratio (aOR): 33.6 (95% confidence interval (CI): 7.4–153.3). Males were also more likely than females to have a BLL ≥5 μg/dL (39, 62%) compared to a BLL<5 μg/dL [aOR: 2.4 (95% CI: 1.0–5.5)]. Conclusions. Children in Owino Uhuru had significantly higher BLLs compared with children in Bangladesh settlement. Interventions to diminish continued exposure to lead in the settlement should be undertaken. Continued monitoring of levels in children with detectable levels can evaluate whether interventions to reduce exposure are effective. Participant Consent. Obtained Ethics Approval. Scientific approval for the study was obtained from the Ministry of Health, lead poisoning technical working group. Since this investigation was considered a public health response of immediate concern, expedited ethical approval was obtained from the Kenya Medical Research Institute and further approval from the Mombasa County Department of Health Services. The investigation was considered a non-research public health response activity by the CDC. Competing Interests. The authors declare no competing financial interests

Identifying Risk Factors for Recent HIV Infection in Kenya Using a Recent Infection Testing Algorithm: Results from a Nationally Representative Population-Based Survey

<div><p>Introduction</p><p>A recent infection testing algorithm (RITA) that can distinguish recent from long-standing HIV infection can be applied to nationally representative population-based surveys to characterize and identify risk factors for recent infection in a country.</p><p>Materials and Methods</p><p>We applied a RITA using the Limiting Antigen Avidity Enzyme Immunoassay (LAg) on stored HIV-positive samples from the 2007 Kenya AIDS Indicator Survey. The case definition for recent infection included testing recent on LAg and having no evidence of antiretroviral therapy use. Multivariate analysis was conducted to determine factors associated with recent and long-standing infection compared to HIV-uninfected persons. All estimates were weighted to adjust for sampling probability and nonresponse.</p><p>Results</p><p>Of 1,025 HIV-antibody-positive specimens, 64 (6.2%) met the case definition for recent infection and 961 (93.8%) met the case definition for long-standing infection. Compared to HIV-uninfected individuals, factors associated with higher adjusted odds of recent infection were living in Nairobi (adjusted odds ratio [AOR] 11.37; confidence interval [CI] 2.64–48.87) and Nyanza (AOR 4.55; CI 1.39–14.89) provinces compared to Western province; being widowed (AOR 8.04; CI 1.42–45.50) or currently married (AOR 6.42; CI 1.55–26.58) compared to being never married; having had ≥ 2 sexual partners in the last year (AOR 2.86; CI 1.51–5.41); not using a condom at last sex in the past year (AOR 1.61; CI 1.34–1.93); reporting a sexually transmitted infection (STI) diagnosis or symptoms of STI in the past year (AOR 1.97; CI 1.05–8.37); and being aged <30 years with: 1) HSV-2 infection (AOR 8.84; CI 2.62–29.85), 2) male genital ulcer disease (AOR 8.70; CI 2.36–32.08), or 3) lack of male circumcision (AOR 17.83; CI 2.19–144.90). Compared to HIV-uninfected persons, factors associated with higher adjusted odds of long-standing infection included living in Coast (AOR 1.55; CI 1.04–2.32) and Nyanza (AOR 2.33; CI 1.67–3.25) provinces compared to Western province; being separated/divorced (AOR 1.87; CI 1.16–3.01) or widowed (AOR 2.83; CI 1.78–4.45) compared to being never married; having ever used a condom (AOR 1.61; CI 1.34–1.93); and having a STI diagnosis or symptoms of STI in the past year (AOR 1.89; CI 1.20–2.97). Factors associated with lower adjusted odds of long-standing infection included using a condom at last sex in the past year (AOR 0.47; CI 0.36–0.61), having no HSV2-infection at aged <30 years (AOR 0.38; CI 0.20–0.75) or being an uncircumcised male aged <30 years (AOR 0.30; CI 0.15–0.61).</p><p>Conclusion</p><p>We identified factors associated with increased risk of recent and longstanding HIV infection using a RITA applied to blood specimens collected in a nationally representative survey. Though some false-recent cases may have been present in our sample, the correlates of recent infection identified were epidemiologically and biologically plausible. These methods can be used as a model for other countries with similar epidemics to inform targeted combination prevention strategies aimed to drastically decrease new infections in the population.</p></div

A protracted cholera outbreak among residents in an urban setting, Nairobi county, Kenya, 2015

Introduction:&nbsp;in 2015, a cholera outbreak was confirmed in Nairobi county, Kenya, which we investigated to identify risk factors for infection and recommend control measures. Methods:&nbsp;we analyzed national cholera surveillance data to describe epidemiological patterns and carried out a case-control study to find reasons for the Nairobi county outbreak. Suspected cholera cases were Nairobi residents aged &gt;2 years with acute watery diarrhea (&gt;4 stools/≤12 hours) and illness onset 1-14 May 2015. Confirmed cases had&nbsp;Vibrio cholerae&nbsp;isolated from stool. Case-patients were frequency-matched to persons without diarrhea (1:2 by age group, residence), interviewed using standardized questionaires. Logistic regression identified factors associated with case status. Household water was analyzed for fecal coliforms and&nbsp;Escherichia coli. Results:&nbsp;during December 2014-June 2015, 4,218 cholera cases including 282 (6.7%) confirmed cases and 79 deaths (case-fatality rate [CFR] 1.9%) were reported from 14 of 47 Kenyan counties. Nairobi county reported 781 (19.0 %) cases (attack rate, 18/100,000 persons), including 607 (78%) hospitalisations, 20 deaths (CFR 2.6%) and 55 laboratory-confirmed cases (7.0%). Seven (70%) of 10 water samples from communal water points had coliforms; one had&nbsp;Escherichia coli. Factors associated with cholera in Nairobi were drinking untreated water (adjusted odds ratio [aOR] 6.5, 95% confidence interval [CI] 2.3-18.8), lacking health education (aOR 2.4, CI 1.1-7.9) and eating food outside home (aOR 2.4, 95% CI 1.2-5.7). Conclusion:&nbsp;we recommend safe water, health education, avoiding eating foods prepared outside home and improved sanitation in Nairobi county. Adherence to these practices could have prevented this protacted cholera outbreak

Factors associated with malaria microscopy diagnostic performance following a pilot quality-assurance programme in health facilities in malaria low-transmission areas of Kenya, 2014

Abstract Background Malaria accounts for ~21% of outpatient visits annually in Kenya; prompt and accurate malaria diagnosis is critical to ensure proper treatment. In 2013, formal malaria microscopy refresher training for microscopists and a pilot quality-assurance (QA) programme for malaria diagnostics were independently implemented to improve malaria microscopy diagnosis in malaria low-transmission areas of Kenya. A study was conducted to identify factors associated with malaria microscopy performance in the same areas. Methods From March to April 2014, a cross-sectional survey was conducted in 42 public health facilities; 21 were QA-pilot facilities. In each facility, 18 malaria thick blood slides archived during January–February 2014 were selected by simple random sampling. Each malaria slide was re-examined by two expert microscopists masked to health-facility results. Expert results were used as the reference for microscopy performance measures. Logistic regression with specific random effects modelling was performed to identify factors associated with accurate malaria microscopy diagnosis. Results Of 756 malaria slides collected, 204 (27%) were read as positive by health-facility microscopists and 103 (14%) as positive by experts. Overall, 93% of slide results from QA-pilot facilities were concordant with expert reference compared to 77% in non-QA pilot facilities (p < 0.001). Recently trained microscopists in QA-pilot facilities performed better on microscopy performance measures with 97% sensitivity and 100% specificity compared to those in non-QA pilot facilities (69% sensitivity; 93% specificity; p < 0.01). The overall inter-reader agreement between QA-pilot facilities and experts was κ = 0.80 (95% CI 0.74–0.88) compared to κ = 0.35 (95% CI 0.24–0.46) between non-QA pilot facilities and experts (p < 0.001). In adjusted multivariable logistic regression analysis, recent microscopy refresher training (prevalence ratio [PR] = 13.8; 95% CI 4.6–41.4), ≥5 years of work experience (PR = 3.8; 95% CI 1.5–9.9), and pilot QA programme participation (PR = 4.3; 95% CI 1.0–11.0) were significantly associated with accurate malaria diagnosis. Conclusions Microscopists who had recently completed refresher training and worked in a QA-pilot facility performed the best overall. The QA programme and formal microscopy refresher training should be systematically implemented together to improve parasitological diagnosis of malaria by microscopy in Kenya