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emmtyper: A tool for in silico EMM typing of Streptococcus pyogenes |
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30 October 2019 |
paper.bib |
Bacterial pathogen subtyping is a corner-stone of public health microbiology and epidemiology. By classifying bacterial strains at levels below species and sub-species, bacterial subtyping allows public health officials and epidemiologists to identify and track outbreaks, identify particularly virulent strains, and make decisions about vaccination programmes. As public health microbiology transitions to a workflow primarily based on genomic data, there is an increasing need for Bioinformatic tools to perform in silico bacterial subtyping. Such tools are essential to enable the carryover of vast troves of historical data and allow for a smooth transition to genomics-based public health.
emmtyper is an in silico bacterial subtyping tool written in Python for emm-typing and emm-cluster typing of Streptococcus pyogenes, also known as Group A Streptococcus (GAS). S. pyogenes is the causative agent of strep throat, necrotizing fasciitis, and Scarlet fever. emm-typing targets variation at the emm gene that produces the surface antigen known as M protein. The M protein was initially used as a target for GAS subtyping because it is essential for evading the human immune system, and thus essential to the bacteria's virulence. emm-cluster typing groups emm-types into functionally equivalent clusters, facilitating vaccine development.
Essential to the working of emmtyper is a FASTA database of sequences annotated with the M-type. The database consists of a set of sequences typically of 180bp in length that covers a portion of the emm gene, and is curated by the CDC Streptococcus laboratory (CDC). The database is updated on a regular basis, adding newly characterized sequences. To ensure the local database used by emmtyper is up to date, we provide facilities for the user to check if their database is out-of-date, and if so, to download and update the local database. We check the database integrity by checking for and removing any duplicate sequences using the tool seqkit [CITATION]. emmtyper keeps a JSON formatted log of database updates, providing the user with a history of changes over time and is what permits the tool to check if the local database is out-of-date.
To give users flexibility about how they wish to use emmtyper, we provide two distinct modes of operation: blast and in silico PCR. The blast mode is the default mode of operation, and it blasts the contigs of the assembly supplied by the user against the database of emm-type annotated sequences. The in silico mode uses the in silico PCR tool isPcr [CITATION] to identify one or more PCR fragments in the contigs of the assembly suppplied by the user, and then subsequently, the fragments are blasted against the database of emm-type annotated sequences. At the moment, two sets of PCR primers are shipped with emmtyper, the canonical PCR primers recommended by the CDC M-typing protocol [CITATION], and a set of redesigned primers published more recently by Frost et al. [CITATION]. The CDC canonical primers are used by default, but the user is able to select the Frost et al. in silico PCR primers by setting the --pcr-primer option to frost. The user is also able to supply their own primers by setting the --primer-db to the path to the appropriately formatted file.
emmtyper is now routinely used for emm-typing and emm-cluster typing of Streptococcus pyogenes at the Microbiological Diagnostic Unit Public Health Lab, has been used in a number of papers, and has been added to bacterial pathogen Bioinformatic pipelines (e.g., Bactopia). Importantly, the tool has been fully validated and is ready for use in the field. emmtyper is available on PyPI, and on Bioconda, to make it easy for the user to install the tool.
Transition to genomics in public health.
Bacterial subtyping in public health.
EMM typing in GAS.
GAS epidemiology.
Prior use of emmtyper (Lacey).
Statement of need: what it provides: support for transition to genomics. Validated tool.