PointFinder databases contain incorrect insertions and deletions

Issue description

The species-specific PointFinder databases available for download with the Microbial Genomics Module tool Download Resistance Database contain resistance conferring point mutations, insertions and deletions. For databases that contain insertions and deletions, all insertions and some deletions are incorrectly represented in the database reference sequences.

Impact

The PointFinder databases are used with the Microbial Genomics Module tool Find Resistance with PointFinder that maps sequencing reads against the reference database to detect presence of known resistance conferring mutations. As insertions and some deletions are incorrectly represented in the PointFinder databases, the tool will be unable to detect these variants if present in the sequencing data. Consequently, known antibiotic resistance conferring insertions and deletions may go undetected. In addition, reported insertions and deletions may be wrong.

Affected databases

The following species-specific PointFinder databases are impacted:

• PointFinder database for E.faecium (2019-08)
• PointFinder database for E.coli (2019-08)
• PointFinder database for Klebsiella (2019-08)
• PointFinder database for M.tuberculosis (2019-08)
• PointFinder database for N.gonorrhoeae (2019-08)
• PointFinder database for S.aureaus (2019-08)

Databases for the remaining species do not contain insertions and deletions and are therefore not affected by this issue.