Whole-genome evaluation and prophages characterization associated with genome of carbapenem-resistant Acinetobacter...

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an emerging threat to healthcare settings in many countries, principally in South Asia. The current study was aimed to identify, evaluate whole-genome and characterize the prophages in genome of CRAB strain, recovered from patients of Lahore General Hospital, Lahore. More than 200 samples were collected and identified by morphological and biochemical tests. These strains were also subjected to a comprehensive antimicrobial susceptibility evaluation using Kirby-Bauer method and further confirmed as CRAB strains by exploring bla_OXA-51. In addition, the whole-genome evaluation of a Acinetobacter baumannii UOL-KIMZ-24-2 was carried out using various Bioinformatics tools. A total of 150 strains of A. baumannii were recovered and identified in the current study. Among them, 49% strains were found resistant to carbapenem. The bla_OXA-51 was found prevalent in the genome of A. baumannii recovered from medical ICU (38%). In addition, the UOL-KIMZ-24-2 genome analysis based on multilocus sequence typing (MLST) highlighted that UOL-KIMZ-24-2 belonged to ST2 (Pasteur scheme) sequence type. A total of 29 antimicrobial resistance (AMR) genes were present, importantly, bla_OXA-66, bla_OXA-23 and bla_OXA-25. The mobile genetic elements (MGEs) were identified as transposases and belonged to four classes e.g. IS15d1, ISAba24, ISEc29, and ISEc35. A total of 14 virulence factors encoded by 58 different genes were detected in UOL-KIMZ-24-2. In addition, the phage sequences were identified in genome of UOL-KIMZ-24-2, divided into 3 regions. In conclusion, UOL-KIMZ-24-2 contained a mixture of AMR genes, MGEs. prophages sequences and virulence genes.