Acknowledgement
This study was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean government (NRF-2019R1I1A1A01059574 and NRF-2022R1F1A1074068). This paper was supported by research funds for newly appointed professors of Jeonbuk National University in 2020.
References
- 1. Aminov RI. 2009. The role of antibiotics and antibiotic resistance in nature. Environ. Microbiol. 11: 2970-2988.
- Davies J, Davies D. 2010. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74: 417-433.
- D'Costa VM, McGrann KM, Hughes DW, Wright GD. 2006. Sampling the antibiotic resistome. Science 311: 374-377.
- Surette MD, Wright GD. 2017. Lessons from the environmental antibiotic resistome. Annu. Rev. Microbiol. 71: 309-329.
- Perry JA, Westman EL, Wright GD. 2014. The antibiotic resistome: what's new? Curr. Opin. Microbiol. 21: 45-50.
- Kim DW, Cha CJ. 2021. Antibiotic resistome from the one-health perspective: understanding and controlling antimicrobial resistance transmission. Exp. Mol. Med. 53: 301-309.
- Larsson D, Flach CF. 2022. Antibiotic resistance in the environment. Nat. Rev. Microbiol. 20: 257-269.
- Pessoa RBG, de Oliveira WF, Marques DSC, dos Santos Correia MT, de Carvalho EVMM, Coelho LCBB. 2019. The genus Aeromonas: a general approach. Microb. Pathog. 130: 81-94.
- Beaz-Hidalgo R, Figueras M. 2013. Aeromonas spp. whole genomes and virulence factors implicated in fish disease. J. Fish Dis. 36: 371-388.
- Janda JM, Abbott SL. 2010. The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin. Microbiol. Rev. 23: 35-73.
- Baron S, Granier SA, Larvor E, Le Bouquin S, Kempf I, Chauvin C. 2017. Aeromonas diversity and antimicrobial susceptibility in freshwater-an attempt to set generic epidemiological cut-off values. Front. Microbiol. 8: 231406.
- Citterio B, Francesca B. 2015. Aeromonas hydrophila virulence. Virulence 6: 417-418.
- Reines HD, Cook FV. 1981. Pneumonia and bacteremia due to Aeromonas hydrophila. Chest 80: 264-267.
- Brouqui P, Raoult D. 2001. Endocarditis due to rare and fastidious bacteria. Clin. Microbiol. Rev. 14: 177-207.
- Chen PL, Lamy B, Ko WC. 2016. Aeromonas dhakensis, an increasingly recognized human pathogen. Front. Microbiol. 7: 198504.
- Pessoa R, Marques D, Lima R, Oliveira M, Lima G, de Carvalho EM, et al. 2020. Molecular characterization and evaluation of virulence traits of Aeromonas spp. isolated from the tambaqui fish (Colossoma macropomum). Microb. Pathog. 147: 104273.
- Bello-Lopez JM, Cabrero-Martinez OA, Ibanez-Cervantes G, Hernandez-Cortez C, Pelcastre-Rodriguez LI, Gonzalez-Avila LU, et al. 2019. Horizontal gene transfer and its association with antibiotic resistance in the genus Aeromonas spp. Microorganisms 7: 363.
- Piotrowska M, Popowska M. 2014. The prevalence of antibiotic resistance genes among Aeromonas species in aquatic environments. Ann. Microbiol. 64: 921-934.
- Lee K, Kim DW, Lee DH, Kim YS, Bu JH, Cha JH, et al. 2020. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome 8: 2.
- Marti E, Variatza E, Balcazar JL. 2014. The role of aquatic ecosystems as reservoirs of antibiotic resistance. Trends Microbiol. 22: 36-41.
- Baquero F, Martinez J-L, Canton R. 2008. Antibiotics and antibiotic resistance in water environments. Curr. Opin. Biotechnol. 19: 260-265.
- Lesher GY, Froelich EJ, Gruett MD, Bailey JH, Brundage RP. 1962. 1, 8-Naphthyridine derivatives. A new class of chemotherapeutic agents. J. Med. Chem. 5: 1063-1065.
- Pham TD, Ziora ZM, Blaskovich MA. 2019. Quinolone antibiotics. Medchemcomm 10: 1719-1739.
- Hooper DC, Jacoby GA. 2015. Mechanisms of drug resistance: quinolone resistance. Ann. N. Y. Acad. Sci. 1354: 12-31.
- Aldred KJ, Kerns RJ, Osheroff N. 2014. Mechanism of quinolone action and resistance. Biochemistry 53: 1565-1574.
- Bush NG, Diez-Santos I, Abbott LR, Maxwell A. 2020. Quinolones: mechanism, lethality and their contributions to antibiotic resistance. Molecules 25: 5662.
- Rodriguez-Martinez JM, Machuca J, Cano ME, Calvo J, Martinez-Martinez L, Pascual A. 2016. Plasmid-mediated quinolone resistance: two decades on. Drug Resist. Updat. 29: 13-29.
- Ruiz J. 2019. Transferable mechanisms of quinolone resistance from 1998 onward. Clin. Microbiol. Rev. 32: e00007-19.
- Martinez-Martinez L, Pascual A, Jacoby GA. 1998. Quinolone resistance from a transferable plasmid. Lancet 351: 797-799.
- Fabrega A, Madurga S, Giralt E, Vila J. 2009. Mechanism of action of and resistance to quinolones. Microb. Biotechnol. 2: 40-61.
- Jacoby GA, Hooper DC. 2013. Phylogenetic analysis of chromosomally determined qnr and related proteins. Antimicrob. Agents Chemother. 57: 1930-1934.
- Hegde SS, Vetting MW, Roderick SL, Mitchenall LA, Maxwell A, Takiff HE, et al. 2005. A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA. Science 308: 1480-1483.
- Shimizu K, Kikuchi K, Sasaki T, Takahashi N, Ohtsuka M, Ono Y, et al. 2008. Smqnr, a new chromosome-carried quinolone resistance gene in Stenotrophomonas maltophilia. Antimicrob. Agents Chemother. 52: 3823-3825.
- Velasco C, Rodriguez-Martinez J, Briales A, Diaz de Alba P, Calvo J, Pascual A. 2010. Smaqnr, a new chromosome-encoded quinolone resistance determinant in Serratia marcescens. J. Antimicrob. Chemother. 65: 239-242.
- Rodriguez-Martinez J, Velasco C, Briales A, Garcia I, Conejo M, Pascual A. 2008. Qnr-like pentapeptide repeat proteins in Grampositive bacteria. J. Antimicrob. Chemother. 61: 1240-1243.
- Xiong X, Bromley EH, Oelschlaeger P, Woolfson DN, Spencer J. 2011. Structural insights into quinolone antibiotic resistance mediated by pentapeptide repeat proteins: conserved surface loops direct the activity of a Qnr protein from a Gram-negative bacterium. Nucleic Acids Res. 39: 3917-3927.
- Poirel L, Rodriguez-Martinez J-M, Mammeri H, Liard A, Nordmann P. 2005. Origin of plasmid-mediated quinolone resistance determinant QnrA. Antimicrob. Agents Chemother. 49: 3523-3525.
- Cattoir V, Poirel L, Aubert C, Soussy CJ, Nordmann P. 2008. Unexpected occurrence of plasmid-mediated quinolone resistance determinants in environmental Aeromonas spp. Emerg. Infect. Dis. 14: 231.
- Xia R, Guo X, Zhang Y, Xu H. 2010. qnrVC-like gene located in a novel complex class 1 integron harboring the IS CR1 element in an Aeromonas punctata strain from an aquatic environment in Shandong Province, China. Antimicrob Agents Chemother. 54: 3471-3474.
- Sanchez MB, Hernandez A, Rodriguez-Martinez JM, Martinez-Martinez L, Martinez JL. 2008. Predictive analysis of transmissible quinolone resistance indicates Stenotrophomonas maltophilia as a potential source of a novel family of Qnr determinants. BMC Microbiol. 8: 148.
- Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703.
- Yoon SH, Ha SM, Kwon S, Lim J, KIM Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613-1617
- Wiegand I, Hilpert K, Hancock RE. 2008. Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat. Protoc. 3: 163-175.
- Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.
- Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068-2069.
- Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9: 5114.
- Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ. 2019. PIRATE: a fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience 8: giz119.
- Nakamura T, Yamada KD, Tomii K, Katoh K. 2018. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 34: 2490-2492.
- Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
- Letunic I, Bork P. 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49: W293-W296.
- Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, et al. 2023. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res. 51: D690-D699.
- Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28: 3150-3152.
- Mirdita M, Schutze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. 2022. ColabFold: making protein folding accessible to all. Nat. Methods 19: 679-682.
- Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, et al. 2023. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32: e4792.
- Vetting MW, Hegde SS, Fajardo JE, Fiser A, Roderick SL, Takiff HE, et al. 2006. Pentapeptide repeat proteins. Biochemistry 45: 1-10.
- Park KS, Lee JH, Jeong DU, Lee JJ, Wu X, Jeong BC, et al. 2011. Determination of pentapeptide repeat units in Qnr proteins by the structure-based alignment approach. Antimicrob. Agents Chemother. 55: 4475-4478.
- Nilsson SV, Magnusson G. 1982. Sealing of gaps in duplex DNA by T4 DNA ligase. Nucleic Acids Res. 10: 1425-1437.
- Barco R, Garrity G, Scott J, Amend J, Nealson K, Emerson D. 2020. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 11: e02475-19.
- Strahilevitz J, Jacoby GA, Hooper DC, Robicsek A. 2009. Plasmid-mediated quinolone resistance: a multifaceted threat. Clin. Microbiol. Rev. 22: 664-689.
- Vetting MW, Hegde SS, Wang M, Jacoby GA, Hooper DC, Blanchard JS. 2011. Structure of QnrB1, a plasmid-mediated fluoroquinolone resistance factor. J. Biol. Chem. 286: 25265-25273.
- Hegde SS, Vetting MW, Mitchenall LA, Maxwell A, Blanchard JS. 2011. Structural and biochemical analysis of the pentapeptide repeat protein EfsQnr, a potent DNA gyrase inhibitor. Antimicrob. Agents Chemother. 55: 110-117.
- Takeshita S, Sato M, Toba M, Masahashi W, Hashimoto-Gotoh T. 1987. High-copy-number and low-copy-number plasmid vectors for lacZα-complementation and chloramphenicol-or kanamycin-resistance selection. Gene 61: 63-74.
- Poirel L, Liard A, Rodriguez-Martinez JM, Nordmann P. 2005. Vibrionaceae as a possible source of Qnr-like quinolone resistance determinants. J. Antimicrob. Chemother. 56: 1118-1121.
- Feng L, Mundy JE, Stevenson CE, Mitchenall LA, Lawson DM, Mi K, et al. 2021. The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic. Proc. Natl. Acad. Sci. USA 118: e2016705118.