title: Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile.
abstract: Despite the development of novel typing methods based on whole genome sequencing, most laboratories still rely on classical molecular methods for outbreak investigation or surveillance. Reference methods for Clostridium difficile include ribotyping and pulsed-field gel electrophoresis, which are band-comparing methods often difficult to establish and which require reference strain collections. Here, we present the double locus sequence typing (DLST) scheme as a tool to analyse C. difficile isolates. Using a collection of clinical C. difficile isolates recovered during a 1-year period, we evaluated the performance of DLST and compared the results to multilocus sequence typing (MLST), a sequence-based method that has been used to study the structure of bacterial populations and highlight major clones. DLST had a higher discriminatory power compared to MLST (Simpson's index of diversity of 0.979 versus 0.965) and successfully identified all isolates of the study (100 % typeability). Previous studies showed that the discriminatory power of ribotyping was comparable to that of MLST; thus, DLST might be more discriminatory than ribotyping. DLST is easy to establish and provides several advantages, including absence of DNA extraction [polymerase chain reaction (PCR) is performed on colonies], no specific instrumentation, low cost and unambiguous definition of types. Moreover, the implementation of a DLST typing scheme on an Internet database, such as that previously done for Staphylococcus aureus and Pseudomonas aeruginosa ( http://www.dlst.org ), will allow users to easily obtain the DLST type by submitting directly sequencing files and will avoid problems associated with multiple databases.
authors.affiliation: Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland. milos.stojanov@chuv.ch.|Institute of Microbiology, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland. milos.stojanov@chuv.ch.
authors.forename: M
authors.initials: M
authors.lastname: Stojanov
authors.affiliation: Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland.
authors.forename: B
authors.initials: B
authors.lastname: Magalhaes
authors.affiliation: Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland.
authors.forename: V
authors.initials: V
authors.lastname: Terletsky
authors.affiliation: Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland.
authors.forename: P
authors.initials: P
authors.lastname: Basset
authors.affiliation: Institute of Microbiology, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland.
authors.forename: G
authors.initials: G
authors.lastname: Prod'hom
authors.affiliation: Institute of Microbiology, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland.
authors.forename: G
authors.initials: G
authors.lastname: Greub
authors.affiliation: Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland.
authors.forename: L
authors.initials: L
authors.lastname: Senn
authors.affiliation: Service of Hospital Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland.|Institute of Microbiology, Lausanne University Hospital, Rue du Bugnon 46, 1011, Lausanne, Switzerland.
authors.forename: D S
authors.initials: DS
authors.lastname: Blanc
mesh_terms: D001483:Base Sequence; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D003015:Clostridium Infections / Q000175:diagnosis* / Q000453:epidemiology / Q000382:microbiology; D003428:Cross Infection / Q000382:microbiology; D004269:DNA, Bacterial / Q000235:genetics; D006801:Humans; D017720:Molecular Epidemiology; D058885:Multilocus Sequence Typing / Q000379:methods*; D017422:Sequence Analysis, DNA; D013557:Switzerland / Q000453:epidemiology
chemical_list: D004269:DNA, Bacterial