In silico species identification and serotyping for Cronobacter isolates by use of whole-genome sequencing data.
Cronobacter spp. are foodborne pathogens that can cause severe infections in neonates through contaminated powdered infant formula. Accurate and rapid pathogen identification and serotyping are crucial to limit the detrimental effects of bacterial infections, and to prevent outbreaks and sporadic infections. Conventional serotyping is tedious, laborious, and time-consuming; however, with whole-genome sequencing (WGS) becoming faster and cheaper, WGS has vast potential in routine typing and surveillance. Hence, in this study, we developed a publicly available tool, CroTrait (CronobacterTraits), for in silico species identification and O serotyping of Cronobacter isolates based on WGS data. CroTrait showed excellent performance in species identification and O serotyping when 810 genomes with known species identities and 276 genomes with known O serotype were tested. Moreover, CroTrait allows rapid prediction of new potential O serotypes. We identified 11 novel potential O serotypes of Cronobacter using CroTrait. Therefore, CroTrait is a convenient and promising tool for species identification and O serotyping of Cronobacter isolates.
['Wang|Lu|L|', 'Zhu|Wenxuan|W|', 'Lu|Gege|G|', 'Wu|Pan|P|', 'Wei|Yi|Y|', 'Su|Yingying|Y|', 'Jia|Tianyuan|T|', 'Li|Linxing|L|', 'Guo|Xi|X|', 'Huang|Min|M|', 'Yang|Qian|Q|', 'Huang|Di|D|', 'Liu|Bin|B|']
D003198:Computer Simulation D059126:Cronobacter D044083:Cronobacter sakazakii D006801:Humans D007223:Infant D007231:Infant, Newborn D065288:Serogroup D012703:Serotyping D000073336:Whole Genome Sequencing
Species identification Serotyping Cronobacter CroTrait