Are Virulence and Antibiotic Resistance Genes Linked? A Comprehensive Analysis of Bacterial Chromosomes and Plasmids
Helena Darmancier,
Célia P. F. Domingues,
João S. Rebelo,
Ana Amaro,
Francisco Dionísio,
Joël Pothier,
Octávio Serra,
Teresa Nogueira
Affiliations
Helena Darmancier
Bacteriology and Mycology Laboratory, INIAV—National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
Célia P. F. Domingues
Bacteriology and Mycology Laboratory, INIAV—National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
João S. Rebelo
cE3c—Center for Ecology, Evolution and Environmental Change & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
Ana Amaro
Bacteriology and Mycology Laboratory, INIAV—National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
Francisco Dionísio
cE3c—Center for Ecology, Evolution and Environmental Change & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
Joël Pothier
Atelier de Bioinformatique, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle, CP 50, 45 Rue Buffon, F-75005 Paris, France
Octávio Serra
INIAV—National Institute for Agrarian and Veterinary Research, Portuguese Plant Germoplasm Bank, 4700-859 Braga, Portugal
Teresa Nogueira
Bacteriology and Mycology Laboratory, INIAV—National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
Although pathogenic bacteria are the targets of antibiotics, these drugs also affect hundreds of commensal or mutualistic species. Moreover, the use of antibiotics is not only restricted to the treatment of infections but is also largely applied in agriculture and in prophylaxis. During this work, we tested the hypothesis that there is a correlation between the number and the genomic location of antibiotic resistance (AR) genes and virulence factor (VF) genes. We performed a comprehensive study of 16,632 reference bacterial genomes in which we identified and counted all orthologues of AR and VF genes in each of the locations: chromosomes, plasmids, or in both locations of the same genome. We found that, on a global scale, no correlation emerges. However, some categories of AR and VF genes co-occur preferentially, and in the mobilome, which supports the hypothesis that some bacterial pathogens are under selective pressure to be resistant to specific antibiotics, a fact that can jeopardize antimicrobial therapy for some human-threatening diseases.
