Typing of Clostridium difficile isolates endemic in Japan by sequencing of slpA and its application to direct typing.
A typing system for Clostridium difficile using sequencing of the surface-layer protein A encoding gene (slpA) was evaluated and used to analyse clinical isolates in Japan. A total of 160 stool specimens from symptomatic patients in Japan was examined and 87 C. difficile isolates were recovered. slpA sequence typing was found to have reliable typability and discriminatory power in comparison with PCR ribotyping, and the typing results were highly reproducible and comparable. slpA sequence typing was used to type C. difficile in DNA extracted directly from stool specimens. Among the 90 stool specimens in which direct typing results were obtained, 77 specimens were positive for C. difficile culture, and typing results from isolated strains agreed with those from direct typing in all 77 specimens. The slpA sequence type smz was dominant at all four hospitals examined, and this endemic type was detected by culture and/or direct typing in 61 (62 %) of 99 stool specimens positive for toxic culture and/or direct slpA sequence typing. Comparison of epidemic strains reported throughout the world revealed one isolate identified as slpA sequence type gc8, which was found to correspond to PCR ribotype 027 (BI/NAP1/027), whereas no isolates were found with the slpA gene identical to that of PCR ribotype 078 strain. slpA sequence typing is valuable for comparison of C. difficile strains epidemic in diverse areas because the typing results are reproducible and can easily be shared. In addition, slpA sequence typing could be applied to direct typing without culture.
Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
Haru
H
Kato
Toyokawa City Hospital, Aichi, Japan.
Hideaki
H
Kato
Gifu Red Cross Hospital, Gifu, Japan.
Yoichiro
Y
Ito
Azumino Red Cross Hospital, Nagano, Japan.
Takayuki
T
Akahane
Toyokawa City Hospital, Aichi, Japan.
Sayuri
S
Izumida
Kumiai Kosei Hospital, Gifu, Japan.
Toshiyuki
T
Yokoyama
Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
Chiharu
C
Kaji
Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
Yoshichika
Y
Arakawa
D001426:Bacterial Proteins / Q000235:genetics*; D015373:Bacterial Typing Techniques; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D003015:Clostridium Infections / Q000453:epidemiology / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019353:Endemic Diseases; D005243:Feces / Q000382:microbiology; D005838:Genotype; D006801:Humans; D007564:Japan / Q000453:epidemiology; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D021521:Ribotyping; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D004269:DNA, Bacterial; C070683:surface layer protein A, Bacteria