Regional distribution of carbapenemase-producing Acinetobacter baumannii isolates in southern Spain (Andalusia)

Abstract

Objectives: This is the first study conducted in southern Spain to determine i) the population structure (PS) of carbapenem-resistant (CR) Acinetobacter baumannii isolates by multilocus sequencing typing (MLST) and core genome MLST (cgMLST) and ii) the association between the sequence type ST and the bla_OXA-51 variant, capsule polysaccharide locus (KL) and lipooligosaccharide outer core locus (OCL) types.

Methods: Of 336 isolates submitted to the Andalusian reference laboratory (PIRASOA; December 2017-2020), 73 were subjected to WGS (MiSeq). The following analyses were performed: bacterial identification (ribosomal MLST), carbapenemase gene detection (Resfinder 4.0), PS delineation (MLST by MLSTfinder 2.0 and cgMLST by Ridom SeqSphere⁺), and KL types and OCL types (Kaptive tool).

Results: The carbapenemases detected were bla_OXA-23 (n = 41), bla_OXA-58 (n = 26), bla_OXA-24 (n = 5), bla_OXA-72 (n = 1) and bla_NDM-1 (n = 2). The PS revealed one major ST2 clone (n = 54) and seven minor ST clones by MLST, and 41 lineages by cgMLST_. Thirty-five lineages were detected only in a single hospital whereas five lineages were observed in several hospitals and provinces. bla_OXA-66 was the most frequent bla_OXA-51 variant and was mainly associated with the ST2 clone. Eleven KL types and 3 OCL types were assigned, with KL2 (n = 27), KL7 (n = 16) and OCL1 being the most frequent.

Conclusions: The PS of CR A. baumannii in Andalusia is characterized by a dominant ST2/bla_OXA-23 clone and several lineages, showing local spread of lineages in most hospitals, and intercenter or interregional spread of a few lineages. Single-locus bla_OXA-51-like typing and KL typing may be useful as complementary preliminary typing tool.

Keywords: Acinetobacter baumannii; Interregional spread; KL type; Southern of Spain.

Fig. 1

Dendrogram generated from the scheme that combines 1083 accessory genes and 2390 cgMLST genes (Ridom SeqSphere +). A box with dotted lines indicates isolates with the same cgMLST detected in different hospitals in different provinces

Fig. 2

Minimum spanning tree for bla_OXA-23 isolates (panel A) and bla_OXA-58 (panel B) isolates based on cgMLST using the `pairwise ignore missing values´ during distance calculations. The numbers on the connecting lines illustrate the numbers of target genes with different alleles. Different colors of isolates indicate the assigned cgMLST