Comprehensive Genomic Landscape of Antibiotic Resistance in

Overview

Journal mSystems

Publisher American Society for Microbiology

Specialty Microbiology

Date 2024 May 10

PMID 38727238

Authors

Do-Hoon Lee

Kihyun Lee

Yong-Seok Kim

Chang-Jun Cha

Affiliations

Soon will be listed here.

Abstract

Importance: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between and revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.

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References

Kim D, Cha C . Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med. 2021; 53(3):301-309. PMC: 8080597. DOI: 10.1038/s12276-021-00569-z. View

Zhu W, Clark N, Patel J . pSK41-like plasmid is necessary for Inc18-like vanA plasmid transfer from Enterococcus faecalis to Staphylococcus aureus in vitro. Antimicrob Agents Chemother. 2012; 57(1):212-9. PMC: 3535934. DOI: 10.1128/AAC.01587-12. View

Djordjevic S, Jarocki V, Seemann T, Cummins M, Watt A, Drigo B . Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet. 2023; 25(2):142-157. DOI: 10.1038/s41576-023-00649-y. View

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

Brown M, Horswill A . Staphylococcus epidermidis-Skin friend or foe?. PLoS Pathog. 2020; 16(11):e1009026. PMC: 7660545. DOI: 10.1371/journal.ppat.1009026. View

Mansson E, Johannesen T, Nilsdotter-Augustinsson A, Soderquist B, Stegger M . Comparative genomics of from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence. Microb Genom. 2021; 7(2). PMC: 8208700. DOI: 10.1099/mgen.0.000504. View

Diekema D, Pfaller M, Schmitz F, Smayevsky J, Bell J, Jones R . Survey of infections due to Staphylococcus species: frequency of occurrence and antimicrobial susceptibility of isolates collected in the United States, Canada, Latin America, Europe, and the Western Pacific region for the SENTRY Antimicrobial.... Clin Infect Dis. 2001; 32 Suppl 2:S114-32. DOI: 10.1086/320184. View

Marraffini L, Sontheimer E . CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science. 2008; 322(5909):1843-5. PMC: 2695655. DOI: 10.1126/science.1165771. View

Meric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B . Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nat Commun. 2018; 9(1):5034. PMC: 6261936. DOI: 10.1038/s41467-018-07368-7. View

10.

Lowy F . Staphylococcus aureus infections. N Engl J Med. 1998; 339(8):520-32. DOI: 10.1056/NEJM199808203390806. View

11.

Letunic I, Bork P . Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021; 49(W1):W293-W296. PMC: 8265157. DOI: 10.1093/nar/gkab301. View

12.

Severn M, Horswill A . Staphylococcus epidermidis and its dual lifestyle in skin health and infection. Nat Rev Microbiol. 2022; 21(2):97-111. PMC: 9903335. DOI: 10.1038/s41579-022-00780-3. View

13.

Rogers K, Fey P, Rupp M . Coagulase-negative staphylococcal infections. Infect Dis Clin North Am. 2009; 23(1):73-98. DOI: 10.1016/j.idc.2008.10.001. View

14.

Sabate Bresco M, Harris L, Thompson K, Stanic B, Morgenstern M, OMahony L . Pathogenic Mechanisms and Host Interactions in Device-Related Infection. Front Microbiol. 2017; 8:1401. PMC: 5539136. DOI: 10.3389/fmicb.2017.01401. View

15.

Miragaia M, Couto I, de Lencastre H . Genetic diversity among methicillin-resistant Staphylococcus epidermidis (MRSE). Microb Drug Resist. 2005; 11(2):83-93. DOI: 10.1089/mdr.2005.11.83. View

16.

Price M, Dehal P, Arkin A . FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010; 5(3):e9490. PMC: 2835736. DOI: 10.1371/journal.pone.0009490. View

17.

Rossi C, Souza-Silva T, Araujo-Alves A, Giambiagi-deMarval M . CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci. Front Microbiol. 2017; 8:1545. PMC: 5559504. DOI: 10.3389/fmicb.2017.01545. View

18.

Meric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L . Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol. 2015; 7(5):1313-28. PMC: 4453061. DOI: 10.1093/gbe/evv066. View

19.

Wick R, Judd L, Cerdeira L, Hawkey J, Meric G, Vezina B . Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol. 2021; 22(1):266. PMC: 8442456. DOI: 10.1186/s13059-021-02483-z. View

20.

Krediet T, Mascini E, van Rooij E, Vlooswijk J, Paauw A, Gerards L . Molecular epidemiology of coagulase-negative staphylococci causing sepsis in a neonatal intensive care unit over an 11-year period. J Clin Microbiol. 2004; 42(3):992-5. PMC: 356815. DOI: 10.1128/JCM.42.3.992-995.2004. View