Abstract
The study provides the first comprehensive molecular and epidemiological investigation of tuberculosis (TB) in Fiji and the wider Pacific region, integrating clinical data, treatment outcomes, and whole-genome sequencing (WGS). Out of the 612 laboratory-confirmed TB cases recorded over a three-year period, 100 isolates were collected, of which 66 met quality criteria for genomic analysis.
Epidemiological assessment revealed that most cases originated from the Central Division, reflecting the centralised diagnostic role of Tamavua Twomey Hospital. Young adults constituted the majority of cases, with a median age of 35 years, and treatment outcomes fell short of World Health Organization (WHO) End TB Strategy target of 90% treatment success. Only 66.7% of patients were cured, while loss to follow-up (19.7%) and mortality (10.6%) were unacceptably high, underscoring persistent programmatic gaps and inequities across divisions.
WGS established, for the first time in Fiji, the predominance of M. tuberculosis Lineage 4, with additional contributions from Lineages 1, 2, and 3, confirming both endemic circulation and repeated introductions. Drug resistance was uncommon but included mutations associated with isoniazid, streptomycin, and ethionamide resistance. One rifampicin-resistant case was successfully treated with second-line therapy, highlighting both the fragility and adaptability of Fiji’s TB control services. Importantly, WGS unexpectedly identified zoonotic Mycobacterium bovis in four human cases, a finding not detected by routine diagnostics, indicating that these patients were receiving suboptimal treatment regimens, as M. bovis is intrinsically resistant to pyrazinamide and the patients were on a drug-sensitive regimen of Isoniazid, Rifampicin, Pyrazinamide, and Ethambutol (HRZE).
Phylogenetic analysis demonstrated household and social transmission clusters, particularly involving resistant strains, alongside genetically distinct isolates consistent with imported cases. This dual pattern indicates that Fiji’s TB epidemic is shaped by both local transmission and regional mobility. Disruptions caused by the COVID-19 pandemic further reduced isolate recovery, reflecting the vulnerability of TB control systems in small island nations.
Together, these findings provide novel insights into the burden, diversity, and transmission of TB in Fiji. These findings established a genomic baseline for national surveillance, highlights diagnostic and programmatic gaps, and underscored the importance of integrating WGS into TB control. Beyond Fiji, this work has regional significance: it demonstrated the feasibility and value of genomics in small island developing states, supports a One Health approach to zoonotic TB, and provides a model for Pacific-wide genomic surveillance.