AcinetobacterPlasmidTyping comprises a database of Acinetobacter baumannii plasmid replication initiation protein-encoding rep sequences corresponding to an updated plasmid rep typing scheme for Acinetobacter baumannii. Rep types are categorised firstly by family (Rep1, Rep3 or RepPriCT; designated R1, R3 and RP respectively in the typing scheme) and secondly type based on homology with a threshold of 95% nucleotide identity. For example, the Rep3 family comprises 69 distinct plasmid rep types (i.e. groups) designated R3-T1 through to R3-T69. Note that multiple rep sequence variants (i.e. allelic variants) can therefore be assigned to the same type/group.
| Rep Family | Number of types | Designation |
|---|---|---|
| Rep1 (R1) | 6 | R1-T1 to R1-T6 |
| Rep3 (R3) | 69 | R3-T1 to R3-T69 |
| RepPriCT (RP) | 5 | RP-T1 to RP-T5 |
Accessions and isolate metadata for the complete plasmid sequences used to develop the rep typing scheme are available in FigShare via the following DOIs:
- Rep1 family: 10.6084/m9.figshare.20372613
- Rep3 family: 10.6084/m9.figshare.20372598
- RepPriCT family: 10.6084/m9.figshare.20372595
Using the AcinetobacterPlasmidTyping database as a reference, users are able to screen their genome assemblies or reads for plasmid rep types with BLAST and SRST2 (https://github.com/katholt/srst2) respectively.
- To screen genome assemblies, users will need to have BLAST installed before executing the following command:
[pathway to directory containing blast installation]/bin/blastn -query acinetobacterplasmidtyper.fasta -subject [pathway to directory containing genome assemblies] -outfmt 6 -out results.txt -perc_identity 95
- To screen reads (use
--input_pefor paired end and--input_sefor single end; refer to SRST2 documentation for more information), users will need to have SRST2 installed before executing the following command:
srst2 --input_pe reads_1.fastq.gz reads_2.fastq.gz --gene_db acinetobacterplasmidtyper.fasta --output results --log