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

Abstract

BackgroundAdequate 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.MethodsA 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.ResultsAmong 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.ConclusionsWe 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.

A Situation Analysis of the Capacity of Laboratories in Zambia to Conduct Surveillance of Antimicrobial Resistance: Strengths, Weaknesses, Opportunities, and Challenges

“…Our findings are evidenced by the low overall score regarding the indicators used in assessing the capacity of laboratories to test for AMR and perform all bacteriological processes. These findings align with those reported in other studies [6,61,62]. A recent study conducted in Zambia in secondary and tertiary hospitals found an overall capacity of 52%, with the highest-scoring hospital having scored 63% and the lowest having scored 38% [63].…”

“…Our findings resonate with another study conducted in Ethiopia where, despite the availability of laboratories, there was a lack of basic equipment and consumables to conduct AMR testing [6]. Another study in Kenya reported similar findings where nearly one-third of the healthcare facilities examined did not offer bacterial culture testing, and only [61]. This was due to poor access to LIS, low participation in external quality assessment programs for cultures, severe infrastructural gaps and lack of equipment [61].…”

“…Another study in Kenya reported similar findings where nearly one-third of the healthcare facilities examined did not offer bacterial culture testing, and only [61]. This was due to poor access to LIS, low participation in external quality assessment programs for cultures, severe infrastructural gaps and lack of equipment [61]. In Rwanda, critical gaps in equipment and supplies were found in district hospitals, similar to those found in our study [67].…”

Prevalence of Antimicrobial Resistance and Association with Patient Outcomes in a Rural Kenyan Hospital

“…Of those sampled, the majority of facilities ( n = 135, 61%) did not perform bacterial culture testing, and even fewer performed antimicrobial susceptible testing ( n = 37, 17%). 12 …”

The Fragmented Picture of Antimicrobial Resistance in Kenya: A Situational Analysis of Antimicrobial Consumption and the Imperative for Antimicrobial Stewardship

“…The inadequacy of laboratory infrastructure, especially in rural areas where basic requirements are rarely met, poses a significant barrier to reliable pathogen detection and AST [ 8 ]. Moreover, there exists a persistent healthcare delivery imbalance across counties, with over twice the laboratory technology accessibility in urban areas compared to their rural counterparts in Kenya [ 19 ].…”