Investigation of mobile genetic elements and their association with antibiotic resistance genes in clinical pathogens worldwide.
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Johansson Markus H K, Petersen Thomas N, Nag Sidsel, Lagermann Timmie M R, Birkedahl Laura E K, Tafaj Silva, Bradbury Susan, Collignon Peter, Daley Denise, Dougnon Victorien, Fabiyi Kafayath, Coulibaly Boubacar, Dembélé Réné, Magloire Natama, Ouindgueta Isidore J, Hossain Zenat Z, Begoum Anowara, Donchev Deyan, Diggle Mathew, Turnbull LeeAnn, Lévesque Simon, Berlinger Livia, Søgaard Kirstine K, Guevara Paula D, Duarte Carolina, Maikanti Panagiota, Amlerova Jana, Drevinek Pavel, Tkadlec Jan, Dilas Milica, Kaasch Achim, Westh Henrik T, Bachtarzi Mohamed A, Amhis Wahiba, Salazar Carolina E S, Villacis José E, Lúzon Mária A D, Palau Dàmaris B, Duployez Claire, Paluche Maxime, Asante-Sefa Solomon, Møller Mie, Ip Margaret, Mareković Ivana, Pál-Sonnevend Agnes, Cocuzza Clementiza E, Dambrauskiene Asta, Macanze Alexandre, Cossa Anelsio, Mandomando Inácio, Nwajiobi-Princewill Philip, Okeke Iruka N, Kehinde Aderemi O, Adebiyi Ini, Akintayo Ifeoluwa, Popoola Oluwafemi, Onipede Anthony, Blomfeldt Anita, Nyquist Nora E, Bocker Kiri, Ussher James, Ali Amjad, Ullah Nimat, Khan Habibullah, Gustafson Natalie W, Jarrar Ikhlas, Al-Hamad Arif, Luvira Viravarn, Paveenkittiporn Wantana, Baran Irmak, Mwansa James C L, Sikakwa Linda, Yamba Kaunda, Aarestrup Frank M
Аннотация
METHODS: We analysed 3,095 whole-genome sequenced clinical bacterial isolates from over 100 species to study the relationship between resistance genes and MGEs. The mobiliome of Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, and Klebsiella pneumoniae were further examined for geographic differences, as these species were prevalent in all countries. Genes potentially mobilized by MGEs were identified by finding DNA segments containing MGEs and ARGs preserved in multiple species. Network analysis was used to investigate potential MGE interactions, host range, and transmission pathways.
RESULTS: The prevalence and diversity of MGEs and resistance genes varied among species, with E. coli and S. aureus carrying more diverse elements. MGE composition differed between bacterial lineages, indicating strong vertical inheritance. 102 MGEs associated with resistance were found in multiple species, and four of these elements seemed to be highly transmissible as they were found in different phyla. We identified 21 genomic regions containing resistance genes potentially mobilized by MGEs, highlighting their importance in transmitting genes to clinically significant bacteria.
CONCLUSION: Resistance genes are spread through various MGEs, including plasmids and transposons. Our findings suggest that multiple factors influence MGE prevalence and their transposability, thereby shaping the MGE population and transmission pathways. Some MGEs have a wider host range, which could make them more important for mobilizing genes. We also identified 103 resistance genes potentially mobilised by MGEs, which could increase their transmissibility to unrelated bacteria.