MOST: a modified MLST typing tool based on short read sequencing.
Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches.
Infectious Disease Informatics Unit, Public Health England , London , United Kingdom.
Rediat
R
Tewolde
Gastrointestinal Bacteria Reference Unit, Public Health England , London , United Kingdom.
Timothy
T
Dallman
Infectious Disease Informatics Unit, Public Health England , London , United Kingdom.
Ulf
U
Schaefer
Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England , London , United Kingdom.
Carmen L
CL
Sheppard
Gastrointestinal Bacteria Reference Unit, Public Health England , London , United Kingdom.
Philip
P
Ashton
Antimicrobial Resistance and Healthcare Associated Infection Unit, Public Health England, NIS , London , United Kingdom.
Bruno
B
Pichon
Antimicrobial Resistance and Healthcare Associated Infection Unit, Public Health England, NIS , London , United Kingdom.
Matthew
M
Ellington
Gastrointestinal Bacteria Reference Unit, Public Health England , London , United Kingdom.
Craig
C
Swift
Infectious Disease Informatics Unit, Public Health England , London , United Kingdom.
Jonathan
J
Green
Infectious Disease Informatics Unit, Public Health England , London , United Kingdom.
Anthony
A
Underwood
Assembly-based approach; Mapping-based approach; Multilocus sequence typing; Whole genome sequencing