Genomic Signature of Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates Related to a Massive Outbreak in Zambia between 2010 and 2012

Abstract

Retrospectively, we investigated the epidemiology of a massive Salmonella enterica serovar Typhi outbreak in Zambia during 2010 to 2012. Ninety-four isolates were susceptibility tested by MIC determinations. Whole-genome sequence typing (WGST) of 33 isolates and bioinformatic analysis identified the multilocus sequence type (MLST), haplotype, plasmid replicon, antimicrobial resistance genes, and genetic relatedness by single nucleotide polymorphism (SNP) analysis and genomic deletions. The outbreak affected 2,040 patients, with a fatality rate of 0.5%. Most (83.0%) isolates were multidrug resistant (MDR). The isolates belonged to MLST ST1 and a new variant of the haplotype, H58B. Most isolates contained a chromosomally translocated region containing seven antimicrobial resistance genes, catA1, blaTEM-1, dfrA7, sul1, sul2, strA, and strB, and fragments of the incompatibility group Q1 (IncQ1) plasmid replicon, the class 1 integron, and the mer operon. The genomic analysis revealed 415 SNP differences overall and 35 deletions among 33 of the isolates subjected to whole-genome sequencing. In comparison with other genomes of H58, the Zambian isolates separated from genomes from Central Africa and India by 34 and 52 SNPs, respectively. The phylogenetic analysis indicates that 32 of the 33 isolates sequenced belonged to a tight clonal group distinct from other H58 genomes included in the study. The small numbers of SNPs identified within this group are consistent with the short-term transmission that can be expected over a period of 2 years. The phylogenetic analysis and deletions suggest that a single MDR clone was responsible for the outbreak, during which occasional other S. Typhi lineages, including sensitive ones, continued to cocirculate. The common view is that the emerging global S. Typhi haplotype, H58B, containing the MDR IncHI1 plasmid is responsible for the majority of typhoid infections in Asia and sub-Saharan Africa; we found that a new variant of the haplotype harboring a chromosomally translocated region containing the MDR islands of IncHI1 plasmid has emerged in Zambia. This could change the perception of the term “classical MDR typhoid” currently being solely associated with the IncHI1 plasmid. It might be more common than presently thought that S. Typhi haplotype H58B harbors the IncHI1 plasmid or a chromosomally translocated MDR region or both. INTRODUCTION Typhoid fever is an ancient but still important cause of human illness, mostly in developing countries with poor sanitation and a lack of potable water (1). It is estimated that typhoid fever is responsible for up to 26.9 million annual cases, of which 223,000 have a fatal outcome, predominately among children (2). Typhoid fever has been reported to have the highest incidence in Asia, whereas the incidence rate has decreased in Latin America due to improved sanitation and economic development (3–5). In sub-Saharan Africa, nontyphoidal Salmonella strains have been reported to predominate in contrast to those causing typhoid fever (3, 6). Despite this, large outbreaks of typhoid fever are still frequently reported from the sub-Saharan African region (7–10). Beginning in early November 2010, there were large typhoid fever outbreaks in Zambia, Zimbabwe, and the Democratic Republic of Congo. These outbreaks have to a large extent been overlooked in a region plagued by many needs and with few resources (11). For future surveillance and control of S. Typhi infections in the region, it is important to know whether the outbreak in 2010 to 2012 was a result of a single novel introduction or reflected a situation of endemicity with multiple clones and lineages. Thus, the main purpose of the present study was to determine the genetic relatedness of contemporary clinical S. Typhi isolates using whole-genome sequence typing. In addition, another purpose was to determine if this outbreak was the result of the presence of the expanding globally dominant H58 haplotype containing the incompatibility group HI1 (IncHI1) plasmid type associated with multidrug resistance (MDR) by investigation of the occurrence and genetic mechanisms of antimicrobial resistance and plasmid replicons.