Background: Globally, 40% of all tuberculosis (TB) cases, 65% paediatric cases and 75% multi-drug resistant TB (MDR-TB) cases are missed due to underreporting and/or under diagnosis. A recent Kenyan TB prevalence survey found that a significant number of TB cases are being missed here. Understanding spatial distribution and patterns of use of TB diagnostic tests as per the guidelines could potentially help improve TB case detection by identifying diagnostic gaps. Methods: We used 2015 Kenya National TB programme data to map TB case notification rates (CNR) in different counties, linked with their capacity to perform diagnostic tests (chest x-rays, smear microscopy, Xpert MTB/RIF®, culture and line probe assay). We then ran hierarchical regression models for adults and children to specifically establish determinants of use of Xpert® (as per Kenyan guidelines) with county and facility as random effects. Results: In 2015, 82,313 TB cases were notified and 7.8% were children. The median CNR/100,000 amongst 0-14yr olds was 37.2 (IQR 20.6, 41.0) and 267.4 (IQR 202.6, 338.1) for ≥15yr olds respectively. 4.8% of child TB cases and 12.2% of adult TB cases had an Xpert® test done, with gaps in guideline adherence. There were 2,072 microscopy sites (mean microscopy density 4.46/100,000); 129 Xpert® sites (mean 0.31/100,000); two TB culture laboratories and 304 chest X-ray facilities (mean 0.74/100,000) with variability in spatial distribution across the 47 counties. Retreatment cases (i.e. failures, relapses/recurrences, defaulters) had the highest odds of getting an Xpert® test compared to new/transfer-in patients (AOR 7.81, 95% CI 7.33-8.33). Children had reduced odds of getting an Xpert® (AOR 0.41, CI 0.36-0.47). HIV-positive individuals had nearly twice the odds of getting an Xpert® test (AOR 1.82, CI 1.73-1.92). Private sector and higher-level hospitals had a tendency towards lower odds of use of Xpert®. Conclusions: We noted under-use and gaps in guideline adherence for Xpert® especially in children. The under-use despite considerable investment undermines cost-effectiveness of Xpert®. Further research is needed to develop strategies enhancing use of diagnostics, including innovations to improve access (e.g. specimen referral) and overcoming local barriers to adoption of guidelines and technologies.
Kenya is administratively divided into 47 counties, that are now largely responsible for health care since devolution in 2013 [29]. Health services are provided by public, private, non-profit non-governmental organisations (NGO) and faith based organisations (FBO). The healthcare system is structured in a hierarchical manner, starting with primary healthcare in the community and complicated cases referred upwards to secondary and tertiary levels of healthcare [29]. According to the Kenyan Master Facility List, there are approximately 10,000 health facilities in the country and just about half are TB treatment sites [30–32]. For this analysis, we aggregated TB health facilities into two: lower level (dispensaries, health centres, and maternity/nursing homes) for primary care; and higher level (county hospitals and national referral facilities) that provide secondary and tertiary referral services. We included patients of all ages who were notified to the Kenya National TB programme and started TB treatment in 2015. We wished to explore the possible influence on use of Xpert MTB/RIF® of variables in three hierarchical levels: county, health facility and individual. Individual level co-variates included: age; gender; HIV status; nutritional status; and type of TB patient i.e. new/transfer-in or retreatment cases (relapse/defaults/treatment failures). An age cut-off of 15yrs for children is used locally and internationally for TB programming [14], therefore “child” here refers to 0-14yr olds. For nutrition status, weight-for-age Z (WAZ) scores were computed for those aged 0-23yr and body mass index (BMI) truncated at -5 to +5SD for those ≥10yr, and patients classified as underweight according to the scores. Those 10-23yr who met criteria of underweight by either criterion were also classified as underweight. Health facility level co-variates included: sector of care (public, private, or FBOs), level of care provided (higher vs lower level) and whether they were an Xpert® site or not. County level co-variates included: poverty; maternal education levels; travel time to nearest health facilities; and availability of Xpert® facilities per 100,000. All co-variates were determined for each of the 47 counties for 2015. These factors were decided upon a priori following review of literature on drivers of use of TB and health care services in general and data availability [21, 22]. The primary outcome of interest was evidence of Xpert® being done in patients who had been started on TB treatment. According to the 2015 Kenyan guidelines, all presumptive paediatric, HIV-infected smear negative, drug resistant (DR) cases, or retreatment cases i.e. relapse (recurrence)/defaults/treatment failures should have had at least one Xpert® assay as part of their diagnostic work up (Additional file 1) [15, 16]. We considered the best data sources for the three levels of variables of interest. For the individual level, de-identified data from the Kenya National TB Programme patients’ treatment register for 2015 were used (patients who were notified and/or started treatment in 2015). TB case definitions were as per Guidance for National TB programmes (Additional file 1) [33]. Health facility level data were from the Kenya Master Health Facility list [30] and Kenya Services Availability and Readiness Assessment Mapping Report (SARAM) 2014 [34]. Health facilities in the national TB register were geocoded using KEMRI-Wellcome Trust’s Kenya Health Facilities Database, which was last updated in 2016 using online digital place-name gazetteers and Global Positioning System (GPS) sources. County level data were from each county governments’ integrated development plans for 2015 [35]. The projected 2015 Kenya gridded population distribution surface at 100m spatial resolution was obtained from the WorldPop project [36, 37]. Stata version 15MP (StataCorp.2017, College Station, TX, USA) and ArcGIS 10.5 (ESRI, Redlands, CA, USA) were used for statistical analysis, and mapping and spatial analysis respectively. We described the proportion of adults and children reported to the TB programme, their socio-demographic characteristics, use of TB diagnostic tests and outcomes. We used the 2015 Kenya National TB programme data to construct maps for each TB case notification rate (CNR) in different counties and linked this with their capacity to perform diagnostic tests (chest x-rays, smear microscopy, Xpert®, culture and line probe assay) from the SARAM report [34]. For adherence to guidelines, we only had data for those who had tests done, and used these patients to describe patterns of use of TB diagnostic tests. Co-variates of theoretical and/or statistical significance were used to build hierarchical logistic regression models to establish determinants of use of Xpert® in adults and children. Possible collinearity was assessed using the variance inflation factor (VIF). Variables with VIF less than 10 were considered for analysis. The models converged at five integration points for complete case analysis, with county and health facility as random effects [38]. Models were built for the 0-14yrs and ≥15yrs separately and a model for the total population, with likelihood ratio tests, exploration for interactions in pre-specified covariates (HIV and nutrition status) and quantile-quantile plots of residuals used to determine best fit as seen in Additional file 2 [38, 39].