Slow-growing <i>Salmonella enterica</i> Typhi mis-identified as <i>Salmonella</i> Gallinarum in Ibadan, Nigeria

Abstract

ABSTRACT Salmonella enterica s erovar Typhi is endemic in Nigeria where S. G allinarum is rarely reported. Probable S . Gallinarum was blood-cultured from three Ibadan patients within 10-days leading to suspicion of an outbreak. All three isolates were re-identified using VITEK-2, whole genome sequenced on Illumina and Oxford Nanopore platforms and confirmed as S . Typhi genotype 3.1.1. Two isolates from the same household had no single nucleotide polymorphisms, suggesting a point-source, but the third was an independent infection event. The isolates formed small colonies, were negative for motility by hanging drop method, and in Sulphide-Indole-Motility medium at 24h, but positive after 48h incubation. Hybrid genome assemblies revealed chromosomal fragment arrangements with imbalances on either side of ori and ter , which has been shown to slow S . Typhi growth. Suspected S . Gallinarum isolates in typhoid endemic areas should be evaluated biochemically and for motility after extended incubation, and verified by serological or molecular methods. Main contributions of the research This study demonstrates that slow-growing Salmonella Typhi can be mis-identified as S . Gallinarum in resource-limited endemic countries. Extended motility testing and confirmatory testing can avoid S. Gallinarum miss-calls. The genetic basis for slow-growth may be chromosomal rearrangements at rrn operons, which are known to occur in S. Typhi