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Incorrect ARO numbers on some ResFinder entries in QMI-AR databases

Issue description

Due to a processing error, some of the 373 entries in the QIAGEN Microbial Insight – Antimicrobial Resistance (QMI-AR) database originating from ResFinder have been assigned incorrect ARO (Antibiotic Resistance Ontology) numbers.

Two versions of the affected database are available: the QMI-AR Nucleotide Database, which contains nucleotide sequences and the QMI-AR Peptide Marker Database, which contains peptide markers.

Expected impact and recommendations

QMI-AR Nucleotide Database

Impact: Using the “Find Resistance with Nucleotide DB” tool with the nucleotide version of QMI-AR may yield misleading results as some of the genes originating from the ResFinder Database are associated with incorrect ARO numbers.

Recommendations: Affected gene entries originate from the ResFinder database. Entries originating from ResFinder are clearly marked in the QMI-AR database with the prefix “RESF_” in the “Find Resistance table”. We do not have a list of which of the 373 entries are affected by the problem described here and thus recommend that entries from the ResFinder database reported when using the QMI-AR (2019-05) database are ignored.

QMI-AR Peptide Database

Impact: Results using “Find Resistance with ShortBRED” with QMI-AR (2019-05) are likely less affected by this problem because homologous genes are clustered during the preparation of this database. Due to this clustering step, we expect the CARD ARO assignment to take precedence over any potentially incorrect ResFinder ARO assignments. However, any misannotated gene may give rise to a nonspecific annotation on the resulting markers as the ARO assignments will be lifted to an LCA of all constituent sequences of a given cluster.

Recommendation: While we do not expect the resistance(s) identified with the “Find Resistance with ShortBRED” tool to be misleading, we cannot say definitively that they will be meaningful when entries from ResFinder are included. We unfortunately have no specific recommendations in this case except to interpret results bearing this in mind.

Affected versions

– QMI-AR Nucleotide Database (2019-05)
– QMI-AR Peptide Marker Database (2019-05)

These were made available for download using the Download Resistance Database tool of CLC Microbial Genomics 4.5 on June 27, 2019. This problem was corrected in updates to these databases (2019-09) released on September 16, 2019.