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Wang L, Zhu W, Lu G, Wu P, Wei Y, Su Y, Jia T, Li L, Guo X, Huang M, Yang Q, Huang D, Liu B. In silico species identification and serotyping for Cronobacter isolates by use of whole-genome sequencing data. Int J Food Microbiol 2021; 358:109405. [PMID: 34563883 DOI: 10.1016/j.ijfoodmicro.2021.109405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
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.
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Affiliation(s)
- Lu Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Wenxuan Zhu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Gege Lu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Pan Wu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Yi Wei
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Yingying Su
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Tianyuan Jia
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Linxing Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Min Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Qian Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China
| | - Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China.
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, People's Republic of China; The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China; Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Tianjin, People's Republic of China.
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Uelze L, Grützke J, Borowiak M, Hammerl JA, Juraschek K, Deneke C, Tausch SH, Malorny B. Typing methods based on whole genome sequencing data. ONE HEALTH OUTLOOK 2020; 2:3. [PMID: 33829127 PMCID: PMC7993478 DOI: 10.1186/s42522-020-0010-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/08/2020] [Indexed: 05/12/2023]
Abstract
Whole genome sequencing (WGS) of foodborne pathogens has become an effective method for investigating the information contained in the genome sequence of bacterial pathogens. In addition, its highly discriminative power enables the comparison of genetic relatedness between bacteria even on a sub-species level. For this reason, WGS is being implemented worldwide and across sectors (human, veterinary, food, and environment) for the investigation of disease outbreaks, source attribution, and improved risk characterization models. In order to extract relevant information from the large quantity and complex data produced by WGS, a host of bioinformatics tools has been developed, allowing users to analyze and interpret sequencing data, starting from simple gene-searches to complex phylogenetic studies. Depending on the research question, the complexity of the dataset and their bioinformatics skill set, users can choose between a great variety of tools for the analysis of WGS data. In this review, we describe the relevant approaches for phylogenomic studies for outbreak studies and give an overview of selected tools for the characterization of foodborne pathogens based on WGS data. Despite the efforts of the last years, harmonization and standardization of typing tools are still urgently needed to allow for an easy comparison of data between laboratories, moving towards a one health worldwide surveillance system for foodborne pathogens.
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Affiliation(s)
- Laura Uelze
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Josephine Grützke
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Katharina Juraschek
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Simon H. Tausch
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Straße 8-10, 10589 Berlin, Germany
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