Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains

• Published in: PloS one 2019-06, Vol.14 (6), p.e0218204-e0218204
• Main Authors: Yakkala, Harshita, Samantarrai, Devyani, Gribskov, Michael, Siddavattam, Dayananda
• Format: Article
• Language: English
• Subjects: Acinetobacter baumannii; Acinetobacter baumannii - genetics; Acinetobacter baumannii - isolation & purification; Adaptability; Agricultural equipment; Agricultural land; Antibiotics; Antimicrobial agents; Bacteria; Biofilms; Biology; Biology and Life Sciences; Biosynthesis; Carbon compounds; Catabolism; Chemotherapy; Comparative Genomic Hybridization - methods; Deoxyribonucleic acid; DNA; DNA sequencing; Drug resistance; Ecological niches; Environmental conditions; Environmental quality; Gene pool; Gene sequencing; Genes; Genes, Bacterial - genetics; Genetic aspects; Genome - genetics; Genomes; Genomics; Genomics - methods; Genotype; Hospitals; Infections; Iron; Life sciences; Medicine and Health Sciences; Microbiology; Multidrug resistance; Niches; Niches (Ecology); Nosocomial infection; Nucleotide sequence; Ostomy; Pathogens; Phenotype; Phenotypes; Physical Sciences; Physiological aspects; Siderophores; Soil Microbiology; Soil water; Soils; Virulence - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0218204

The nosocomial pathogen Acinetobacter baumannii acquired clinical significance due to the rapid development of its multi-drug resistant (MDR) phenotype. A. baumannii strains have the ability to colonize several ecological niches including soil, water, and animals, including humans. They also survive under extremely harsh environmental conditions thriving on rare and recalcitrant carbon compounds. However, the molecular basis behind such extreme adaptability of A. baumannii is unknown. We have therefore determined the complete genome sequence of A. baumannii DS002, which was isolated from agricultural soils, and compared it with 78 complete genome sequences of A. baumannii strains having complete information on the source of their isolation. Interestingly, the genome of A. baumannii DS002 showed high similarity to the genome of A. baumannii SDF isolated from the body louse. The environmental and clinical strains, which do not share a monophyletic origin, showed the existence of a strain-specific unique gene pool that supports niche-specific survival. The strains isolated from infected samples contained a genetic repertoire with a unique gene pool coding for iron acquisition machinery, particularly those required for the biosynthesis of acinetobactin. Interestingly, these strains also contained genes required for biofilm formation. However, such gene sets were either partially or completely missing in the environmental isolates, which instead harbored genes required for alternate carbon catabolism and a TonB-dependent transport system involved in the acquisition of iron via siderophores or xenosiderophores.