Abstract
Waterborne epidemics of tularaemia caused by Francisella tularensis are increasingly reported in Turkey. We have used whole genome sequencing to investigate if F. tularensis isolated from patients could be traced back to drinking water sources. Tonsil swabs from 33 patients diagnosed with oropharyngeal tularaemia in three outbreaks and 140 water specimens were analysed. F. tularensis subsp. holarctica was confirmed by microagglutination and PCR in 12 patients and five water specimens. Genomic analysis of three pairs of patient and water isolates from outbreaks in Sivas, Çorum, and Kocaeli showed the isolates to belong to two new clusters of the F. tularensis B.12 genetic clade. The clusters were defined by 19 and 15 single nucleotide polymorphisms (SNPs) in a multiple alignment based on 507 F. tularensis genomes. One synonymous SNP was chosen as a new canonical SNP (canSNP) for each cluster for future use in diagnostic assays. No SNP was identified between the genomes from the patient–water pair of isolates from Kocaeli, one SNP between the pair of isolates from Sivas, whereas the pair from Çorum differed at seven SNPs. These results illustrate the power of whole genome sequencing for tracing F. tularensis patient isolates back to their environmental source.
Highlights
Tularaemia is a bacterial zoonosis caused by Francisella tularensis, a small Gram-negative coccobacillus
We investigated possible genetic links between F. tularensis subsp. holarctica strains isolated from patients and drinking water in the same areas and at the same time
In the 140 drinking water samples, growth of F. tularensis subsp. holarctica colonies was identified in five samples
Summary
Tularaemia is a bacterial zoonosis caused by Francisella tularensis, a small Gram-negative coccobacillus. The dose required for human infection depends on the transmission route; less than 10 bacteria may be sufficient for infection via inhalation or the subcutaneous route, while infection via the oral route requires greater than 106 bacteria [1,2]. Several clinical forms of tularaemia (including ulceroglandular/glandular, oculoglandular, oropharyngeal and respiratory) may develop, depending on the infection route. Ulceroglandular tularaemia is most frequently reported in the literature, the clinical form most frequently seen in Turkey is oropharyngeal tularaemia [3,4]. Epidemiological surveys have revealed a seasonal pattern of the disease in Turkey, where it is endemic in large areas. Most reported cases occur during the winter (December to March), frequently resulting from ingestion of infected food or contaminated water [3,5]
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