Comprehensive identification of sequence types belonging to Acinetobacter baumannii clonal complexes

Acinetobacter baumannii is a major nosocomial pathogen, with multiply antibiotic-resistant (MAR) isolates primarily belonging to two globally disseminated clonal complexes, Global Clone 1 (GC1) and Global Clone 2 (GC2). A. baumannii has two MLST schemes: the Pasteur and the Oxford scheme. However, the Pasteur scheme identifies clones more simply. Under the Pasteur MLST scheme, these clones centre on sequence types 1 (ST1) and 2 (ST2), respectively, but both encompass related single-locus variants (SLVs) and double-locus variants (DLVs) and even some triple-locus variants (TLVs). Despite their clinical importance, no systematic and up-to-date catalogue of sequence types (STs) belonging to GC1 or GC2 was available.

A workflow was developed using a custom Python workflow to identify SLVs and DLVs of founder STs. This identified 63 STs associated with ST1 and 163 associated with ST2. The impact of accounting for these additional ST was evaluated by analysing 41,951 publicly available A. baumannii genome assemblies from GenBank. Inclusion of SLVs and DLVs increased the number of GC1 genomes significantly from 1,083 ST1 to 1,428 genomes total, but GC2 only from 26,962 to 28,002 genomes. Relatively few SLVs or DLVs found in PubMLST were represented among genome assemblies (22 out of 64 for ST1 and 65 out of 164 for ST2), suggesting incomplete genome coverage or erroneous MLST profiles. Other successful clones, including ST25, ST79, ST85 and ST499, each showed diversification. This framework provides a method for consistent clone definition across clinically important A. baumannii clonal complexes and can be applied more broadly to other important MAR bacteria such as Klebsiella pneumoniae .