A healthy three-year-old boy became unwell during a holiday to Karachi, Pakistan in June-July 2018. Before his return to Canada, he developed fever, abdominal pain, diarrhea, and vomiting for two days. He attended a local physician, who prescribed cefixime and advised the family to follow up at the Emergency Department (ED) in Canada. There were no known infective contacts and he stayed with maternal grandparents in Karachi throughout the visit. The family only visited relatives and attended a family wedding in the same area. They consumed locally prepared food and drank bottled water. The family did not seek pre-travel advice and did not receive typhoid vaccine, malaria prophylaxis, or other travel related medication.
The child was seen at the ED at Toronto's Hospital for Sick Children soon after returning to Canada and was diagnosed with presumed enteric fever, empirically started on ceftriaxone and admitted to a nearby pediatric unit for further management. Stool and blood cultures obtained during the initial ED visit subsequently grew Salmonella enterica serovar Typhi (S. Typhi).
Antimicrobial susceptibility testing of the isolate identified resistance to chloramphenicol, ampicillin, trimethoprim-sulfamethoxazole (TMP-SMX), ciprofloxacin and ceftriaxone but susceptible to meropenem and azithromycin (Table 1). After consultation with the Pediatric Infectious Disease service, the patient was switched to intravenous meropenem at a dose of 20 mg/kg/dose on day two of admission. Blood cultures remained positive twenty-four hours after starting meropenem, but the cultures taken three days later were negative. Despite being treated with appropriate antibiotics, the child continued to have daily high grade fevers thirteen days into meropenem treatment albeit less frequent. Abdominal ultrasound scans only demonstrated mild hepatosplenomegaly which resolved and daily full-systems examinations were unremarkable. He completed fourteen days of meropenem following which he was afebrile and clinically well. Three stool cultures obtained after completion of meropenem therapy were negative.
This patient's S. Typhi isolate (S. Typhi strain PHL5950) underwent whole genome sequencing which was assessed using the ResFinder, SPIFindertools, SeqSero-1.2 Server, and PlasmidFinder. Initially, the raw Illumina reads were trimmed generating 3,625,048 high quality reads corresponding to 866,576,883 detected bases and assembled using de novo assembler in CLC Genomics Workbench version 8.0.1 (CLC bio, Germantown, MD, USA) providing 85 contigs (accession no. RHPM00000000). The closest reference using functional comparison on the RAST server was found to be Salmonella enterica subspecies enterica serovar Typhi Ty2 reference genome NCBI:txid209261 (score, 534). BLAST result of the longest contigs (488765 bp) showed 100% identity to S. enterica subsp. enterica serovar Typhi (accession no. LT882486.1), a recently identified extensively drug-resistant S. Typhi strain from an outbreak in Pakistan, which encodes a chromosomally located resistance region and harbours a plasmid encoding additional resistance elements, including the blaCTX-M-15 extended-spectrum beta-lactamase, and carrying the qnrS fluoroquinolone resistance gene (Fig. 1). The ResFinder tool identified multiple resistance genes conferring resistance to various antibiotics (Supplementary Table 1). In addition, mutation at S83 of the gyrA gene was also identified. Based on the PlasmidFinder tool, we identified two plasmids: IncY plasmid, which matched 100% to the plasmid that was isolated in the Pakistan outbreak-strain (accession no. LT906492), and IncQ1 plasmid.