Comparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes

Area of Science:

• Microbiology
• Genomics
• Epidemiology

Background:

• Acinetobacter calcoaceticus-baumannii (Acb) complex bacteria cause significant human infections.
• Two multi-locus sequence typing (MLST) schemes, Oxford and Pasteur, are used to study Acb population structure.
• These schemes have overlapping genes but different nomenclatures, complicating genotype communication.

Purpose of the Study:

• To compare the characteristics and reliability of the Oxford and Pasteur MLST schemes for Acb complex.
• To recommend the most appropriate MLST scheme for population biology and epidemiological studies of Acb.

Main Methods:

• Comparative analysis of genome sequences from 730 Acb complex strains.
• Evaluation of phylogenetic congruence, sequence type correspondence, and genotyping reliability.
• Statistical testing of MLST-based phylogenies against core-genome and whole-genome SNP reference phylogenies.

Main Results:

• The Oxford scheme's gdhB locus has a paralogous copy in 553/730 genomes, creating artefactual profiles and sequence types.
• The Pasteur scheme is less affected by homologous recombination and better classifies clonal groups.
• Statistical tests indicated the Oxford scheme's tree was more similar to reference trees, but overall issues favor Pasteur.

Conclusions:

• The Oxford scheme suffers from gdhB paralogy, recombination, and primer issues, impacting reliability.
• The Pasteur scheme, despite being less discriminant for closely related isolates, is more robust for population and epidemiological studies.
• The Pasteur scheme is proposed as the preferred choice for Acb complex genotyping during the transition to core genome MLST.