Development and evaluation of double locus sequence typing for molecular epidemiological investigations of Clostridium difficile

• Published in: European journal of clinical microbiology & infectious diseases Vol. 35; no. 2; pp. 175 - 181
• Main Authors: Stojanov, M., Magalhaes, B., Terletsky, V., Basset, P., Prod’hom, G., Greub, G., Senn, L., Blanc, D. S.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-02-2016; Springer Nature B.V
• Subjects: Base Sequence; Biomedical and Life Sciences; Biomedicine; Clostridium difficile; Clostridium difficile - classification; Clostridium difficile - genetics; Clostridium difficile - isolation & purification; Clostridium Infections - diagnosis; Clostridium Infections - epidemiology; Clostridium Infections - microbiology; Cross Infection - microbiology; DNA, Bacterial - genetics; Epidemics; Epidemiology; Genomes; Humans; Instrumentation; Internal Medicine; Laboratories; Medical Microbiology; Methods; Molecular Epidemiology; Multilocus Sequence Typing - methods; Nosocomial infections; Original Article; Polymerase chain reaction; Pseudomonas aeruginosa; Sequence Analysis, DNA; Staphylococcus aureus; Switzerland - epidemiology; United States > US; Switzerland; Polymerase Chain Reaction Ribotype; Epidemiological Link; Multilocus Sequence Typing; Clostridium Difficile; MLST Type
• ISSN: 0934-9723; 1435-4373
• DOI: 10.1007/s10096-015-2525-4

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.