Slow-growing Salmonella enterica serovariety Typhi mis-identified as serovariety Gallinarum in Ibadan, Nigeria

TL;DR

Slow-growing Salmonella Typhi was misidentified as Gallinarum in Nigeria, highlighting the need for careful testing to avoid outbreak misdiagnosis.

Contribution

Demonstrates how genomic and biochemical analyses can correct misidentification of Salmonella strains in clinical settings.

Findings

Three isolates initially identified as S. Gallinarum were confirmed as S. Typhi using VITEK2 and whole genome sequencing.

Slow growth and delayed motility led to misidentification, with chromosomal rearrangements contributing to the anomaly.

A household cluster of S. Typhi infections was identified, with one case being an independent infection.

Abstract

Salmonella enterica subsp. enterica serovar Typhi is endemic in Nigeria where serovar Gallinarum is rarely reported. Following routine blood culture and identification, three patients with probable S. Gallinarum infections were reported in Ibadan within 10-days, precipitating an outbreak investigation. All three isolates were re-identified using VITEK2, motility-tested using Sulphide-Indole-Motility (SIM) medium and whole genome sequenced (WGS) on Illumina and Oxford Nanopore platforms. Short reads were used to determine sequence type, serotype and phylogenetic relationships to previously characterized S. Typhi from Nigeria. Chromosomal configurations were deduced from hybrid assemblies using socru v2.2.4. The three isolates, initially identified as S. Gallinarum, re-identified as gamma glutamyl transferase-positive S. Typhi genotype 3.1.1 by VITEK-2 and WGS. Two individuals in the same household yielded isolates with no single nucleotide polymorphisms, suggesting a point-source and the third case was an independent infection event. Motility was negative by hanging drop method and in SIM medium at 24h, but positive after 48h incubation. The three isolates formed smaller colonies than typical Salmonella strains. Hybrid genome assemblies revealed chromosomal fragments arrangements with imbalances on either side of ori and ter, recently been shown to slow S. Typhi growth. We have shown that slow-growing S. Typhi can be mistaken for S. Gallinarum and that a cluster of blood culture-derived S. Typhi, with imbalanced chromosome rearrangements, was thereby mistaken for a zoonotic S. Gallinarum outbreak. 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.

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