Early use of genomics to guide acquisition investigation of Salmonella Typhi

Abstract

Background
As most Salmonella Typhi (S. Typhi) cases notified to public health units in Australia are acquired overseas, a case without recent travel raises concerns of local transmission. We describe a case of S. Typhi in a hospital inpatient without recent travel, where early use of genomic sequencing suggested remote acquisition from Chile in the 1980s, with chronic asymptomatic carriage. This facilitated the stand-down of a complex acquisition investigation.

Case
A notification of S. Typhi on stool culture was received for a female aged over 90 years living in Melbourne, Australia in October 2023. She had been hospitalised for three weeks (unrelated illness) and transferred into a residential aged care facility (RACF) six days prior to the result being known. She was asymptomatic and the sample was collected due to a recent ward gastroenteritis outbreak.

Investigation
Epidemiological investigation identified the case had emigrated to Australia in 1981 from Chile. Recent typhoid-like illness, overseas travel or contact with travellers from endemic areas were excluded. Subsequent genomic sequencing identified the isolate was multilocus sequence type 2 and did not cluster with any strains isolated in Victorian or international databases, most closely clustering with historical South American strains, with potential in-host changes over time.

Management
The case was presumed infectious throughout their hospital stay, with chronic carriage. There were 18 contacts, of whom 14 provided screening samples and were negative. Antibiotic case clearance was not recommended by the treating clinician due to patient comorbidity, treatment toxicity risks and unlikely treatment success without gallbladder removal. Enhanced infection control measures were instituted in the RACF (e.g. private bathroom, contact precautions for personal care, no food preparation). No additional cases were reported after two incubation periods (60 days).

Conclusion
Early genomic sequencing enhanced the efficiency of the public health investigation by rapidly confirming overseas acquisition and chronic carriage, obviating the need for extensive local upstream investigation.