Comparative genomic analysis of Acinetobacter bereziniae strains revealed an overall proximity between two geographically-separated carbapenem-resistant strains containing plasmids bearing blaNDM-1

BROVEDAN, MARCOS; REPIZO, GUILLERMO D.; ESPARIZ, MARTIN; MARCHIARO, P.; VIALE, ALEJANDRO M.; LIMANSKY, ADRIANA

Simposio; 11th International Symposium on the Biology of Acinetobacter.; 2017

Acinetobacter bereziniae is primarily isolated fromclinical specimens and health-care associated environments. Clinical A. bereziniae isolates were generallysusceptible to most antimicrobials, but recently different carbapenem-resistantisolates bearing metallo-beta-lactamases have been described. We previouslyreported the complete sequence of a blaNDM-1-harboringplasmid (pNDM229) isolated from A.bereziniae HPC229, a clinical strain obtained in Argentina (1).Whole-genome sequencing of HPC229 (2) now allowed us to conduct a comparativeanalysis with other Acinetobactergenomes deposited in databases and assigned to A. bereziniae. First we determined the average nucleotide identity(ANI) of each genome against the representative species, A. bereziniae CIP70.12, using JSpecies with BLAST algorithm (3).The results allowed us to more confidently assign to A. bereziniae the 6 strains whose genomes were available, and alsoto assign two Acinetobacter sp strains(Ag2 and WC-743) to this species. Second, to determine the phylogeneticrelationships between A. bereziniaestrains we first perform Multilocus sequence analysis (MLSA) of the sequencedata, and then a maximum likelihood (ML) tree was constructed from theconcatenated sequences of 597 core genes using the corresponding genes from A. gerneri DSM14967 and A. guillouiae CIP63.46 type strains asoutgroups (see ref. 4 forprocedures). ThisML tree indicated a close phylogenic relationship between HPC229 and CHI-40-1, thelatter strain also carrying a plasmid harbouring blaNDM-1 (1). Third, the predicted proteome of HPC229was compared against the proteomes of the other A. bereziniae strains by using OrthoMCL for ortholog groups (OGs) assignment(4). This analysis indicated 3,341 different OGs, which represented 71.1 % ofthe total OGs in HPC229. Among them, 21 (0.62%) were unique to this strain,while 2,084 (62.4 %) were shared by all A.bereziniae strains. When core plus accessory genomes were compared, HPC229shared the highest number of coding sequences (CDSs) (2,229) with CHI-40-1. Inagreement with the ML tree, a hierarchical clustering analysis based on genefunction repertoires also showed a close relationship between HPC229 andCHI-40-1. In turn, Mauve analysis also indicated  elevated genome synteny between them. A more exhaustiveinspection, however, showed some variations between these two strains whichwere mostly restricted to chromosomal regions harbouring different phages andgenomic islands as well as some plasmids present only in HPC229. The overall resultsled us to postulate that the closely-related carbapenem-resistant A. bereziniae CHI-40-1 and HPC229strains form part of a recently emerging ecotype, thus reflecting the ongoingadaptation of this species to the clinical setting.