Journal article
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 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
Actions
Access Document
- Files:
-
-
(Preview, Version of record, pdf, 187.2KB, Terms of use)
-
- Publisher copy:
- 10.7717/peerj.2308
Authors
- Publisher:
- PeerJ
- Journal:
- PeerJ More from this journal
- Volume:
- 4
- Article number:
- e2308
- Publication date:
- 2016-08-17
- Acceptance date:
- 2016-07-10
- DOI:
- EISSN:
-
2167-8359
- Language:
-
English
- Keywords:
- Pubs id:
-
pubs:830809
- UUID:
-
uuid:b259158c-d9db-4f19-87db-e42b6a0add76
- Local pid:
-
pubs:830809
- Source identifiers:
-
830809
- Deposit date:
-
2019-01-23
Terms of use
- Copyright holder:
- Tewolde et al
- Copyright date:
- 2016
- Notes:
- © 2016 Tewolde et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed.
- Licence:
- CC Attribution (CC BY)
If you are the owner of this record, you can report an update to it here: Report update to this record