Spatial clustering and genetic diversity of Mycobacterium tuberculosis and associated diagnostic delays in Nairobi County, Kenya

The molecular and spatial epidemiology of Mycobacterium tuberculosis (Mtb) in relation to diagnostic delays remains underexplored in Kenya. This study was conducted to map the spatial clustering and characterize circulating lineages/sub-lineages of Mtb, and their transmission patterns associated with diagnostic delays in Nairobi County. DNA was extracted from 101 Mtb isolates collected from newly diagnosed pulmonary tuberculosis (PTB) patients in Nairobi County and genotyped using the mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU VNTR) method. Spatial analysis was conducted using ArcMap version 10.8.2, and statistical associations were assessed using logistic regression. The majority of isolates were Mtb (92/101, 91.1%; 95% CI: 85.5–96.7). Lineage 4 (Euro-American) was the predominant lineage (64/101, 63.4%; 95% CI: 54.0–72.8), followed by Lineage 2 (East Asian; 16.8%), Lineage 3 (South Asian; 10.9%), and Lineage 5 (West African; 8.9%). The most common sublineages were LAM (33/101, 32.7%), Beijing (17/101, 16.8%), S (15/101, 14.9%), Delhi/CAS (11/101, 10.9%), and UgandaI/II (10/101, 9.9%). The molecular clustering rate was 12.7%. After adjustment, Mtb lineage was not associated with diagnostic delay (Ancestral vs Modern: aOR = 1.05, 95% CI 0.38–2.91, p = 1.000). This study identified considerable Mtb strain diversity in Nairobi County. Although molecular clustering was low (12.7%), suggesting that most cases were not part of recent transmission chains, a small number of strains, including Beijing and Uganda I/II, appeared in compact molecular clusters. These clusters may represent localized transmission but cannot be definitively interpreted as such without epidemiologic linkage.