Genome sequence analysis of an indigo-pigmented Acinetobacter baumannii strain depicts evidence of increase genome plasticity

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Acinetobacter baumannii are multi-drug resistant bacteria which are hard to treat and cause high mortality rates. They undergo genetic exchange frequently and are responsible for a variety of diseases such as pneumonia, meningitis, and skin infections. This article describes scientists’ investigation of a 2013 hospital outbreak of indigo-pigmented Acinetobacter baumannii bacteria in Argentina and their further analysis to identify important genetic characteristics. After reporting the outbreak in the hospital, scientists decided to further study this bacteria through a controlled experiment from which they hoped to gain further knowledge about its genetics, pathogenicity, physiology, and molecular basis of antibiotic resistance.

In this experiment, scientists compared the genetic makeup of other Acinetobacter baumannii bacteria strains to indigo-pigmented strain in order to expose genetic variation and genome plasticity among the species. They also wanted to find reasons behind the indigo-pigmented strain’s antibiotic resistance. As a first step, an indigo-pigmented Acinetobacter baumannii strain, which was genetically similar to the ones in Argentina, was isolated from the body of a 65-year-old male patient. All of this bacteria’s DNA and protein coding sequences were obtained and cloned. Then, scientists obtained genetic information from 2,895 Acinetobacter genomes to use for comparison. From this set of genomes, 2,545 genomes that contained a sequence of 49 ribosomal protein-coding genes were used for further phylogenetical analysis. All the similar sets of genomes were grouped together to form 95 groups and 1 genome was selected from each group to ensure the genetic diversity of the genus. 656 orthologous genes were identified among these genomes and were coded into amino acids sequences and finally into protein sequences. Using all this information, a phylogenetic tree of Acinetobacter bacteria inclusive of the indigo-pigmented strain was constructed.

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From the tree, Scientists were able to analyze evolutionary relationships between the cloned DNA of indigo-pigmented strain and the DNA of other similar strains of the same species. In addition, through specifically studying the indigo-pigmented strain’s DNA, they were able to discover many factors that influence its genome plasticity and genetic variation.

Gene prediction (identifying regions of DNA that encode specific genes) was also performed on this indigo-pigmented bacteria. Genomes of phylogenetically closely related strains were used as reference genomes for the testing. The scientists then conducted antibiotic susceptibility tests which tested for resistance as well as several elements that were related to the bacteria’s genetic exchange and variation. From the results of both tests, scientists were able to figure out the antibiotics that the indigo-pigmented strain of bacteria were resistant to. They were also able to identify the locations of these resistance genes in the genome. Finally, they were able to figure out the conditions in which these bacteria functioned best and were most immune.

From the phylogenetic tree, scientists figured out that the indigo-pigmented Acinetobacter baumannii strain is very similar to A. calcoaceticus and different strains of bacteria from its own species. Through the antibiotic susceptibility tests, Scientists identified 13 different antibiotic-resistant intrinsic genes present in the core of the indigo-pigmented strain of the Acinetobacter baumannii which consists of trimethoprim, florfenicol, β-lactams, aminoglycosides, sulfonamide as well as the adeIJK genes, capsule locus (KL), and outer core locus (OCL). In addition, they discovered many mobile elements in its genome associated with Horizontal Gene Transfer(intake and release of genetic material) such as insertion sequences, transposons, genomic islands, plasmids, integrons, and prophage sequences that help this bacteria acquire some of these antibiotic-resistant genes.

There were also several virulence factors discovered by scientists which contributes to the indigo-pigmented Acinetobacter baumannii bacteria’s long-term survival and immunological success. Iron uptake systems that exist help the bacteria survive in iron-limiting conditions through the production of different enzymes. The Capsular polysaccharide is a key element which allows the bacteria to resist bactericidal activity and a T6SS system helps mediate the killing of bacterial competitors around it. The image below explains some the results of this whole experiment:

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In conclusion, the results of this scientific experiment identified the different genetic characteristics in indigo-pigmented Acinetobacter baumannii bacteria which lead to its antibiotic resistance. These results were obtained through genomic comparison using different strains of this speciesScientists were able to identify specific antibiotic resistance genes, virulence traits, and different mobile genetic elements responsible for its increased genome plasticity, genetic variation and multi-drug resistance. These results prove the fact that this bacteria can evolve and adapt rapidly through genetic exchange/variation and further explains the reason for its outbreak in the hospital environment.

 

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