Abstract
Background
Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance.
Objectives
The aim of this study was to characterize the mobile genetic elements present in the chromosome of six Mexican P. aeruginosa strains isolated from adults with pneumonia and children with bacteremia.
Methods
The genomic DNA of six P. aeruginosa strains were isolated and sequenced using PacBio RS-II platform. They were annotated using Prokaryotic Genome Annotation Pipeline and manually curated and analyzed for the presence of mobile genetic elements, antibiotic resistances genes, efflux pumps and virulence factors using several bioinformatics programs and databases.
Results
The global analysis of the strains chromosomes showed a novel chromosomal rearrangement in two strains, possibly mediated by subsequent recombination and inversion events. They have a high content of mobile genetic elements: 21 genomic islands, four new islets, four different integrative conjugative elements, 28 different prophages, one CRISPR-Cas arrangements, and one class 1 integron. The acquisition of antimicrobials resistance genes into these elements are in concordance with their phenotype of multi-drug resistance.
Conclusion
The accessory genome increased the ability of the strains to adapt or survive to the hospital environment, promote genomic plasticity and chromosomal rearrangements, which may affect the expression or functionality of the gene and might influence the clinical outcome, having an impact on the treatment.
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Acknowledgements
We are grateful to Dr. Jorge Castañon and Dra. Guadalupe Miranda for providing the collection of Pseudomonas aeruginosa strains used in this study. We thank José Mendez Sanchez and Francisca Trujillo Jimenez for their technical support, Dra. Luisa Beatriz Sandner for her helpful discussions; Guillin Wang from the Yale Center for Genome Analysis, Yale University, for the skillful PacBio sequencing. This paper is part of the doctoral research carried out by L.F.E-C., a doctoral student from the Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM) and has received CONACyT fellowship 619928.
Funding
This research was funded by DGAPA-PAPIIT grant number IN213816 from Universidad Nacional Autónoma de México. The funder has no role in the study design, data collection, and analysis, decision to publish, or preparation of the manuscript.
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Methodology, GD, and LFE-C; formal analysis, GD, LFE-C and RM-E; data curation, LFE-C; writing original draft preparation, LFE-C, and RM-E; supervision, GD, AC and RM-E; Conceptualization, resources, project administration and funding acquisition, RM-E. All authors have read and agreed to the published version of the manuscript.
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13258_2021_1155_MOESM1_ESM.tif
Fig. S1 CRISPR arrays and CRISPR-Cas. (A) Sequences in yellow show the direct repeat sequences and sequences in multicolor show the spacer sequences of the CRISPR-array identified in Pa58 strain; (B) Sequences in yellow show the direct repeat sequences and sequences in multicolor show the spacer sequences of the first CRISPR-array identified in Pa84 strain; (C) Sequences in yellow show the direct repeat sequences and sequences in multicolor show the spacer sequences of the second CRISPR-array identified in Pa84 strain; (D) Structure of the CRISPR-Cas operon located in the RGP12, adjacent to the PA1243 locus of the Pa84 strain (TIF 2284 KB)
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Espinosa-Camacho, L.F., Delgado, G., Cravioto, A. et al. Diversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains. Genes Genom 44, 53–77 (2022). https://doi.org/10.1007/s13258-021-01155-3
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DOI: https://doi.org/10.1007/s13258-021-01155-3