Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

Abstract

Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1-L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1-L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.

Keywords: Acinetobacter baumannii; GC1; ST1; antibiotic resistance; global clone; whole genome sequence.

Fig. 1.

Linearized map of pEx003 and its comparison to pRCH52-1. Central thick grey arrows show the plasmid backbones with horizontal arrows indicating the extent and orientation of genes/ORFs. Vertical black bars show pdif sites and vertical purple bars at the beginning of each plasmid indicate the location of iterons. This figure was drawn to scale in Inkscape v.0.92 using sequences in GenBank accession numbers CP049315 (pEx003) and KT346360.1 (pRCH52-1).

Fig. 2.

Phylogenetic tree of all publicly available GC1 strains. Filled nodes indicate complete genomes with Ax270 and Ex003 coloured red. The right-hand panel (from left to right) contains metadata, isolation date, isolation source, ST_IP, ST_OX, K, OC, the presence/absence of IS (insertion sequence) upstream of the chromosomal ampC gene, whether the comM gene is interrupted and the number of antibiotic resistance genes present with antibiotic families indicated above. Main clades, C1 and C2, and lineages L1–5 are shown using uppercase letters and numbers. All BAPS groups (lineages and sublineages) are shown with their branches coloured. Minor variants of each K/OC type are indicated using a small letter on the box.

Fig. 3.

Genetic structure of transposons occupying the comM gene of complete L3 strains compared to D36. (a) The structure of Tn6022::ISAba42 found in comM in strain VB2486 (GenBank accession number CP050403.1); (b) AbaR4 found in comM of strain D36 (GenBank accession number CP012952.1); and (c) the structure of AbaR4∆ found in comM of strain 5457 (GenBank accession number CP045541.1). Horizontal arrows indicate the extent and direction of genes with transposition genes coloured dark blue, the oxa23 carbapenem resistance gene red, and ORFs encoding unknown functions white. ISAba1 copies are shown using filled green boxes with white arrows (inside the boxes) indicating the orientation of their transposition genes . The extent of AbaR4 and Tn2006 are also shown using thin horizontal boxes.

Fig. 4.

Gene clusters at the capsular polysaccharide K locus in GC1 genomes. Colours of genes represent categories of functions of the encoded products and the colour scheme is shown on the top right. Figure is drawn to scale.

Fig. 5.

Gene clusters at the OCL for LOS (Lipooligosaccharide) outer core biosynthesis in GC1 genomes. Colours of genes represent categories of functions of the encoded products and the colour scheme is shown below. Figure is drawn to scale.