Multilocus sequence typing of Clostridium difficile.
A robust high-throughput multilocus sequence typing (MLST) scheme for Clostridium difficile was developed and validated using a diverse collection of 50 reference isolates representing 45 different PCR ribotypes and 102 isolates from recent clinical samples. A total of 49 PCR ribotypes were represented overall. All isolates were typed by MLST and yielded 40 sequence types (STs). A web-accessible database was set up (http://pubmlst.org/cdifficile/) to facilitate the dissemination and comparison of C. difficile MLST genotyping data among laboratories. MLST and PCR ribotyping were similar in discriminatory abilities, having indices of discrimination of 0.90 and 0.92, respectively. Some STs corresponded to a single PCR ribotype (32/40), other STs corresponded to multiple PCR ribotypes (8/40), and, conversely, the PCR ribotype was not always predictive of the ST. The total number of variable nucleotide sites in the concatenated MLST sequences was 103/3,501 (2.9%). Concatenated MLST sequences were used to construct a neighbor-joining tree which identified four phylogenetic groups of STs and one outlier (ST-11; PCR ribotype 078). These groups apparently correlate with clades identified previously by comparative genomics. The MLST scheme was sufficiently robust to allow direct genotyping of C. difficile in total stool DNA extracts without isolate culture. The direct (nonculture) MLST approach may prove useful as a rapid genotyping method, potentially benefiting individual patients and informing hospital infection control.
Griffiths
David
D
Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
Fawley
Warren
W
Kachrimanidou
Melina
M
Bowden
Rory
R
Crook
Derrick W
DW
Fung
Rowena
R
Golubchik
Tanya
T
Harding
Rosalind M
RM
Jeffery
Katie J M
KJ
Jolley
Keith A
KA
Kirton
Richard
R
Peto
Tim E
TE
Rees
Gareth
G
Stoesser
Nicole
N
Vaughan
Alison
A
Walker
A Sarah
AS
Young
Bernadette C
BC
Wilcox
Mark
M
Dingle
Kate E
KE
D015373:Bacterial Typing Techniques / Q000379:methods*; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D003015:Clostridium Infections / Q000382:microbiology; D016172:DNA Fingerprinting / Q000379:methods*; D005838:Genotype; D006801:Humans; D007223:Infant; D011110:Polymorphism, Genetic; D021521:Ribotyping; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*