We report a draft genome sequence of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi isolated from a returned traveler from Pakistan who developed sepsis. Whole-genome sequencing revealed relatedness to a previously reported outbreak in Pakistan and identified the blaCTX-M-15 and qnrS resistance genes.
ABSTRACT
We report a draft genome sequence of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi isolated from a returned traveler from Pakistan who developed sepsis. Whole-genome sequencing revealed relatedness to a previously reported outbreak in Pakistan and identified the blaCTX-M-15 and qnrS resistance genes.
ANNOUNCEMENT
The emergence of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi (S. Typhi) is a significant public concern due to the potential for severe disease with few antimicrobial treatment options (1). Whole-genome sequencing (WGS) is a valuable tool for tracking and characterizing transmission of S. Typhi and other pathogens (1, 2). Here, we performed WGS on an XDR S. Typhi isolate from a traveler who had visited Pakistan (Table 1) and developed sepsis upon return to California.
TABLE 1.
Salmonella enterica serovar Typhi antimicrobial susceptibility testing results
| Antibiotic | MIC (mg/liter) | Susceptibility |
|---|---|---|
| Amikacin | ≤16 | Susceptible |
| Ampicillin | >16 | Resistant |
| Ampicillin-sulbactam | >16/18 | Resistant |
| Azithromycin | 4 | Susceptible |
| Cefazolin | >4 | Resistant |
| Cefepime | >16 | Resistant |
| Cefotaxime | >32 | Resistant |
| Ceftazidime | >16 | Resistant |
| Ceftriaxone | >32 | Resistant |
| Cefoxime | >16 | Resistant |
| Ertapenem | ≤0.5 | Susceptible |
| Gentamicin | ≤2 | Susceptible |
| Imipenem | ≤1 | Susceptible |
| Levofloxacin | 4 | Intermediate |
| Meropenem | ≤1 | Susceptible |
| Piperacillin-tazobactam | 32 | Intermediate |
| Tobramycin | ≤4 | Susceptible |
| Trimethoprim-sulfamethoxazole | >2/38 | Resistant |
Blood cultures were performed using Bactec (BD) culture bottles and the Bactec FX instrument. Susceptibility testing was performed using the MicroScan WalkAway 96 plus instrument (Beckman Coulter). DNA extraction was carried out using the Zymo Quick-DNA fungal/bacterial kit according to the manufacturer’s instructions, followed by library preparation using the NEBNext Ultra II DNA kit. Illumina sequencing was carried out on a MiSeq instrument to yield 6,805,326 150-bp reads (2). Assembly with Unicycler v0.4.8 (3) yielded 64 contigs with an N50 value of 204,170 bp and a draft genome size of 4,757,010 bp. The GC content (52.04%) was comparable to that of other S. Typhi strains from Pakistan (1).
The short reads were adapter trimmed, quality controlled with fastp v0.20.0, and analyzed using the core single-nucleotide polymorphism (SNP) detection pipeline SPID v0.4.0 (https://github.com/czbiohub/Spid.jl) with a previously reported Pakistan chromosomal reference sequence for alignment (1, 4). The consensus sequence alignment was used as input to RAxML v8.2.12 to build a phylogenetic tree (5). Alignment against the plasmid reference sequence was performed with Bowtie 2 v2.4.1 (6). Mobile genetic elements were annotated with Prokka v1.14.0 (7). Draft assembly annotation was added with the NCBI Prokaryotic Genome Annotation Pipeline (8). All software was used with default settings.
WGS revealed the isolate to be clonal with previously identified XDR S. Typhi isolates from Pakistan (Fig. 1). However, no plasmids were assembled, and alignment of the short-read data to the Pakistan reference IncY plasmid containing the qnrS and blaCTX-M-15 genes revealed that only partial genomic content of the plasmid could be detected. As previously reported (1), the plasmid shares several regions of homology with a chromosomally integrated antimicrobial resistance cassette, which could mediate partial integration of the plasmid into the chromosome by transposition or homologous recombination, potentially explaining this finding. Annotation of the sequences homologous to the IncY plasmid revealed both resistance genes and known mobile genetic elements, including IS1380 family transposase ISEcp1, IS110 family transposase IS5075, and the Tn3 transposon.
FIG 1.
Phylogenetic tree showing the relatedness of the California XDR S. Typhi isolate to a subset of isolates from patients in Pakistan (1). The tree was built using RAxML with the SPID alignment as input. The label color corresponds to sample collection location. Nodes are colored by genotype according to an SNP-based typing scheme. The scale bar indicates the mean number of substitutions per site.
The draft genome sequence from this patient and the case report extends our understanding of XDR S. Typhi clinical presentation, pathogen evolution, and global transmission.
Analyses in this study were carried out under University of California Institutional Review Board (IRB) protocol number 17-24056.
Data availability.
All the data are available under BioProject number PRJNA588448. The short reads are available under SRA accession number SRX7117257. The genome assembly is available under GenBank accession number GCA_009724275.1.
ACKNOWLEDGMENTS
This work was supported by the National Heart, Lung, and Blood Institute (grant number K23HL138461-01A1 to C.L.) and the Chan Zuckerberg Biohub, San Francisco, CA.
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Associated Data
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Data Availability Statement
All the data are available under BioProject number PRJNA588448. The short reads are available under SRA accession number SRX7117257. The genome assembly is available under GenBank accession number GCA_009724275.1.