Invited Speaker Australian Society for Microbiology Annual Scientific Meeting 2022

Analysis of the putative replication initiation proteins encoded by plasmids found in Acinetobacter baumannii (82456)

Margaret MC Lam 1 , Jonathan Koong 2 , Kathryn E Holt 1 3 , Ruth M Hall 4 , Mehrad Hamidian 2
  1. Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
  2. Australian Institute for Microbiology and Infection (AIMI), University of Technology Sydney, Ultimo, New South Wales, Australia
  3. London School of Hygiene & Tropical Medicine, London, UK
  4. School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia

Acinetobacter baumannii is a Gram-negative opportunistic pathogen associated with various nosocomial infections. It is known for its ability to rapidly acquire resistance to antibiotics, mainly via mobile genetic elements including plasmids, which can readily transmit between cells. Historically, plasmid Rep typing has been used to type and track plasmids in many bacterial genera. Here, bioinformatics approaches were used to develop an updated typing scheme for A. baumannii plasmids by analysing 620 complete A. baumannii plasmids available in GenBank as of February 2021.

478 complete plasmids encoded an identifiable replication initiation protein (Rep) and 142 did not. Interrogation of the Rep sequences showed that they belonged to three main protein families, namely Rep_3 (pfam01051), Rep (or RepPri; pfam01446) and Rep_1 (pfam03090); accounting for 359, 107 and 12 rep sequences, respectively. Hence, the new typing system incorporates information about Rep families.

The CD-HIT program (http://cd-hit.org) was used to compare all rep sequences at various thresholds before deciding on a workable threshold of 95% DNA identity, which yielded 98 groups. The Rep_3 group included 69 types, which were named r3-T1 to r3-T69 (encoding R3-T1 to R3-T69) indicating significant diversity within this group. However, over 30 types comprised only a single representative. The most prevalent groups were R3-T1 (n=95) and R3-T2 (n=30) (known as Aci1 and Aci2, respectively). The RepPri group (n=107) included 5 rep types (rP-T1 to rP-T5) with the majority (n=96) belonging to rP-T1 (known as Aci6). Members of this group are large conjugative plasmids that often carry aphA6 amikacin resistance and/or oxa23 carbapenem resistance genes. The Rep_1 group included only 12 plasmids and 5 types (r1-T1 to r1-T5). These are small cryptic plasmids.

Inclusion of additional rep sequences from a greater number of plasmids provides a significant update that will boost efforts to type and track Acinetobacter plasmids. Development of this new scheme is a significant step towards facilitating studies and surveillance of A. baumannii plasmids.