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 by type based on homology with a threshold of 95% nucleotide identity. For example, the Rep3 family comprises 78 distinct plasmid rep types (i.e. groups) designated R3-T1 through to R3-T79. Note that multiple rep sequence variants (i.e. allelic variants) can be assigned to the same type/group.
| Rep Family | Number of types | Designation |
|---|---|---|
| Rep1 (R1) | 7 | R1-T1 to R1-T8 |
| Rep3 (R3) | 78 | R3-T1 to R3-T79 |
| RepPriCT_1 (RP) | 6 | RP-T1 to RP-T6 |
VERSION 2.0 (September 2023)
- R1-T3 has been retired due to sequencing/assembly error
- R3-T49 has been retired (the sequence originally named R3-T49 has been re-named R3-T26*)
Accessions and isolate metadata for the complete plasmid sequences used to develop the rep typing scheme are available in FigShare via the following DOIs:
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Rep1 family: 10.6084/m9.figshare.20372613 (December 2022)
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Rep3 family: 10.6084/m9.figshare.20372598 (December 2022)
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RepPriCT_1 family: 10.6084/m9.figshare.20372595 (December 2022)
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Summary of strains carrying plasmids, their metadata, and AMR genes carried by their plasmids: https://doi.org/10.6084/m9.figshare.24076776 (September 2023)
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Summary of complete plasmids, their Rep types, metadata and antibiotic resistance gene: https://doi.org/10.6084/m9.figshare.24076779 (September 2023)
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
- Lam MMC, Koong J, Holt KE, Hall RM, Hamidian M. Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins. Microbiol Spectr. 2023 Feb 14;11(1):e0247822. doi: 10.1128/spectrum.02478-22. PMID: 36472426; PMCID: PMC9927589. https://pubmed.ncbi.nlm.nih.gov/36472426/
- Lam MMC, Hamidian M. Examining the role of Acinetobacter baumannii plasmid types in disseminating antimicrobial resistance. npj Antimicrob Resist 2, 1 (2024). https://doi.org/10.1038/s44259-023-00019-y