MOST: A modified MLST typing tool based on short read sequencing

Abstract

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 325 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 325 samples, 92.9% (n=302), 97.2% (n=316) and 99.7% (n=324) 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, 90.9% (n=50) 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 42 (n=37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. 43 In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When 44 comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the 45 mapping based approach described here derives quality metrics, which are difficult to determine 46 quantitatively using conventional and WGS-assembly based approaches.

Toxigenic Corynebacterium ulcerans associated with upper respiratory infections in cats and dogs

“…2016, Tewolde et al . 2016). Alleles, allelic profiles and sequence types (STs) were determined by comparison with the MLST database (https://pubmlst.org/cdiphtheriae/ accessioned August 8, 2019).…”

Nosocomial Outbreak of Drug-Resistant Streptococcus pneumoniae Serotype 9V in an Adult Respiratory Medicine Ward

“…Whole-genome sequencing (WGS) of the three cluster isolates was undertaken using Illumina HiSeq 2500 (Illumina, USA), and raw reads (reads submitted under PHE Pathogens BioProject PRJEB14267 at the European Nucleotide Archive; see Table S1 in the supplemental material) were assembled using SPAdes ( 18 ). MOST ( 19 ) was used to call multilocus sequence type (MLST) and SRST2 ( 20 ) was used for antibiotic resistance genes. Single nucleotide polymorphisms (SNPs) were called using BWA ( 21 ) and GATK ( 22 ) with acapsular S. pneumoniae R6 ( NC_003098 ) used as a reference.…”

Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

“…In-silico serotyping was performed using three different tools: MOST 1.0 [66] and SeqSero 1.0 [67] on raw data, and SISTR 1.0.2 [68] on assembled data. Results were compared, and only samples being in-silico serotyped as S. Napoli by at least two out of three tools were subjected to downstream analyses.…”