Comparative genome analysis reveals putative and novel antimicrobial resistance genes common to the nosocomial infection pathogens

Sahayarayan JJ 1 , Thiyagarajan R 2 , Prathiviraj R 3 , Tn K 4 , Rajan KS 5 , Manivannan P 6 Show all authors , Balasubramanian S 7 , Mohd Zainudin MH 8 , Alodaini HA 9 , Moubayed NM 10 , Hatamleh AA 11 , Ravindran B 12 , Mani RR 13

Affiliations 

  • 1 Department of Bioinformatics, Alagappa University, Karaikudi, 630003, Tamil Nadu, India. Electronic address: josephj@alagappauniversity.ac.in
  • 2 Department of Bioinformatics, Alagappa University, Karaikudi, 630003, Tamil Nadu, India. Electronic address: thiyagaramesh@gmail.com
  • 3 Department of Microbiology, Pondicherry University, Pondicherry, 605014, Tamil Nadu, India. Electronic address: raj.prathivi@gmail.com
  • 4 Department of Microbiology, Pondicherry University, Pondicherry, 605014, Tamil Nadu, India. Electronic address: kumaresann48@gmail.com
  • 5 Department of Bioinformatics, Alagappa University, Karaikudi, 630003, Tamil Nadu, India. Electronic address: soundarrajan.k1996@gmail.com
  • 6 Department of Microbiology, The American College, Madurai, 625002, Tamil Nadu, India. Electronic address: manivannan3065@gmail.com
  • 7 Department of Bioinformatics, Alagappa University, Karaikudi, 630003, Tamil Nadu, India. Electronic address: balakrr1998@gmail.com
  • 8 Laboratory of Sustainable Animal Production and Biodiversity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia. Electronic address: mohdhuzairi@upm.edu.my
  • 9 Department of Botany and Microbiology, college of science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia. Electronic address: halodaini@ksu.edu.sa
  • 10 Department of Botany and Microbiology, college of science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia. Electronic address: nmoubayed@ksu.edu.da
  • 11 Department of Botany and Microbiology, college of science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia. Electronic address: ahatamleh@ksu.edu.sa
  • 12 Department of Civil & Energy System Engineering, Kyonggi University, Suwon, Gyeonggi-Do, 16227, South Korea; Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India. Electronic address: kalamravi@gmail.com
  • 13 Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, 56000, Kuala Lumpur, Malaysia. Electronic address: Ravishankar@ucsiuniversity.edu.my
Microb Pathog, 2024 Dec;197:107028.
PMID: 39426637 DOI: 10.1016/j.micpath.2024.107028

Abstract

The 21st century has witnessed several clinical outcomes regarding AMR. One health concept has been foreseen as a standard global public health initiative in ensuring human, animal and environmental health. The present study explores critical Gram-negative ESKAPE pathogens encompassing Acinetobacter baumannii (ACB), Klebsiella pneumoniae (KPX) and Pseudomonas aeruginosa (PAE). A comparative genomic analysis approach was utilized for identifying novel and putative genes coercing global health consequences stressing the significance of the above iatrogenic and nosocomial pathogens. O findings reveal that Pseudomonas aeruginosaPAO1 (PAE) possesses the largest genome, measuring 62,64,404 base pairs, containing 14,342 protein-coding genes and an elevated count of ORFs, surpassing other organisms. Notably, P. aeruginosa PAO1 exhibits a comprehensive metabolic landscape with 355 pathways and 1659 metabolic reactions, encompassing 200 biosynthesis and 132 degradation pathways. Transferases are the predominant enzyme category across all three genomes, followed by oxidoreductases and hydrolases. The pivotal role of beta-lactamase in conferring resistance against antibiotics is also evident in all three microbes. This investigation underscores the PAE genome harbours genes and enzymes associated with heightened virulence in antibiotic resistance. The holistic review combined with comparative genomics underlines the significance of delving into the genomes of these antimicrobial-resistant organisms. In silico methodologies are increasingly stressed in aiding the successful accomplishment of the United Nations Sustainable Development Goal -3: Good Health and Well-being. The prominent findings establish Carbapenem resistance and evolutionary lineages of the MCR-1 gene conferring AMR landscapes for future research.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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