title: New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.
abstract: A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections.
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Xie
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Shengjie
authors.initials: S
authors.lastname: Yi
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Chaojie
authors.initials: C
authors.lastname: Yang
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Jichao
authors.initials: J
authors.lastname: Sun
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Liu
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Zhihao
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Ligui
authors.initials: L
authors.lastname: Wang
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Rongzhang
authors.initials: R
authors.lastname: Hao
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
authors.forename: Leili
authors.initials: L
authors.lastname: Jia
authors.affiliation: The Second Convalescent District of Lintong Sanatorium, Lanzhou Military Area, Xi'an, China.
authors.forename: Kaiqin
authors.initials: K
authors.lastname: Li
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China hongbinsong@263.net qiushf0613@hotmail.com.
authors.forename: Shaofu
authors.initials: S
authors.lastname: Qiu
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China hongbinsong@263.net qiushf0613@hotmail.com.
authors.forename: Hongbin
authors.initials: H
authors.lastname: Song
mesh_terms: D002681:China; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D003365:Costs and Cost Analysis; D004269:DNA, Bacterial / Q000235:genetics*; D006801:Humans; D058889:Molecular Typing / Q000191:economics / Q000379:methods*; D012480:Salmonella Infections / Q000382:microbiology; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial