Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis

• Published in: Journal of applied genetics Vol. 62; no. 3; pp. 511 - 521
• Main Authors: Kotlowski, Roman, Nowak-Zaleska, Alicja, Wegrzyn, Grzegorz
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-09-2021; Springer; Springer Nature B.V
• Subjects: Acinetobacter baumannii; Acinetobacter baumannii - drug effects; Acinetobacter baumannii - genetics; Acinetobacter Infections - microbiology; Alignment; Analysis; Animal Genetics and Genomics; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Biomedical and Life Sciences; Chloramphenicol; Chloromycetin; Clinical isolates; CRISPR; Deoxyribonucleic acid; Differentiation; Disease susceptibility; DNA; DNA biosynthesis; DNA polymerase; DNA-directed DNA polymerase; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Multiple, Bacterial - genetics; E coli; Epidemiology; Gene polymorphism; Gene sequencing; Genetic polymorphisms; Genomes; Genomics; Genotypes; Gentamicin; GTP cyclohydrolase; Homology; Hospitals; Human Genetics; Humans; Imipenem; Life Sciences; Microbial Genetics and Genomics; Microbial Genetics • Original Paper; Nucleotides; Plant Genetics and Genomics; Polymorphism; Sulfamethoxazole; Trimethoprim; Whole Genome Sequencing; Poland; Assembled matrix data; DNA polymerase III gene DNA polymerase III subunit gamma/tau; Antibiotics; Hospital infections; Genetic polymorphisms; Acinetobacter baumannii
• ISSN: 1234-1983; 2190-3883
• DOI: 10.1007/s13353-021-00640-5

An optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51
Acinetobacter baumannii
multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation in the gene encoding the EmrA-homologue of
E. coli
, and antibiotic resistance patterns, in combination with three newly identified polymorphic regions in the genomes of
A. baumannii
clinical isolates. Differential analysis of two similarity matrices between different genotypes and resistance patterns allowed to distinguish three significant correlations (
p
 < 0.05) between 172 bp DNA insertion combined with resistance to chloramphenicol and gentamycin. Interestingly, 45 and 55 bp DNA insertions within the CRISPR region were identified, and combined during analyses with resistance/susceptibility to trimethoprim/sulfamethoxazole. Moreover, 184 or 1374 bp DNA length polymorphisms in the genomic region located upstream of the GTP cyclohydrolase I gene, associated mainly with imipenem susceptibility, was identified. In addition, considerable nucleotide polymorphism of the gene encoding the gamma/tau subunit of DNA polymerase III, an enzyme crucial for bacterial DNA replication, was discovered. The differentiation analysis performed using the above described approach allowed us to monitor the distribution of
A. baumannii
isolates in different wards of the hospital in the time frame of several years, indicating that the optimized method may be useful in hospital epidemiological studies, particularly in identification of the source of primary infections.