Diagnostic Underuse and Antimicrobial Resistance Patterns Among Hospitalized Children in a National Referral Hospital in Kenya: A Five-Year Retrospective Study

Background: Antimicrobial resistance (AMR) is a growing global health threat, with children in low- and middle-income countries bearing a disproportionate burden. Data on resistance patterns and diagnostic practices in pediatric populations remain limited. This study evaluated diagnostic utilization and AMR among children hospitalized with bacterial infections at a national referral hospital in Kenya. Methods: We conducted a retrospective cohort study of pediatric inpatients (0–12 years) admitted with bacterial infections between 2017 and 2021. Patient records were identified using ICD-10 codes and reviewed for diagnostic testing and antimicrobial susceptibility. Descriptive statistics were conducted to show infection counts, diagnostic testing, and resistance outcomes. Results: Among 1608 patients, 1009/1608 (63%) were infants under one year. Culture was conducted in 640/1608 (40%) and antimicrobial sensitivity testing in 111/640 (17%) patients. Gastroenteritis (46%) was the most common infection and blood the most frequently collected specimen (31%). Of 1039 cultured specimens, 896/1039 (86%) showed no growth. The most commonly isolated organisms were Klebsiella pneumoniae 19/128 (15%), Staphylococcus epidermidis (13%, 17/128), and Enterococcus faecium (13%, 16/128). Notably, K. pneumoniae showed 100% resistance to third-generation cephalosporins, suggestive of ESBL production. Among the tested samples, 92/128 (72%) had MDROs, and 26/92 (28%) were extensively drug-resistant (XDR). Among the patients tested, 84/111 (76%) had MDROs, of which 25/84 (30%) were XDR. Children under 5 years had higher odds (OR = 5.84, 95% CI: 1.17-38.21) of having MDRO infections, as well as those with multiple admissions (OR = 3.77, 95% CI: 1.06–20.34). Further, increasing age was inversely associated with MDRO presence. The odds of MDRO infection decreased by 24% for every year increase in age (aOR = 0.76; 95% CI: 0.60–0.93; p = 0.006). Conclusions: The findings highlight the limited diagnostic use and a high burden of MDROs and XDR infections in hospitalized children. Strengthening diagnostic capacity and pediatric antimicrobial stewardship is urgently needed in such settings.