Author:
Grillova Linda,Cokelaer Thomas,Mariet Jean-François,da Fonseca Juliana Pipoli,Picardeau Mathieu
Abstract
AbstractThe life-threatening pathogenLeptospira interrogansis the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are circulating worldwide due to the fastidious nature of the bacteria and its difficulty to be culture isolated. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material.Here, to elucidate the genomic diversity ofLeptospiracirculating strains, hybridization capture followed by Illumina sequencing of the core genome was performed directly from 20 biological samples that were PCR positive for pathogenicLeptospira. A set of samples subjected to capture with RNA probes covering theL. interroganscore genome resulted in 72 to 13,000-fold increase in pathogen reads when compared to standard sequencing without capture. A SNP analysis of the genomes sequenced from the biological samples using 273Leptospirareference genome was then performed in order to determine the genotype of the infecting strain. For samples with sufficent coverage (19/20 samples with coverage >8X), we could unambigously identifyL. interroganssv Icterohaemorrhagiae (14 samples),L. kirschnerisv Grippotyphosa (4 samples) andL. interroganssv Pyrogenes (1 sample) as the infecting strain.In conclusion, we obtained for most of our biological samples high quality genomic data at suitable coverage for confident core genome genotyping of the agent of leptospirosis. The ability to generate culture-free genomic data opens new opportunities to better understand the epidemiology and evolution of this fastidious pathogen.
Publisher
Cold Spring Harbor Laboratory
Cited by
2 articles.
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