Whole genome global insight of antibiotic resistance gene repertoire and virulome of high - risk multidrug-resistant Uropathogenic Escherichia coli

Microbial Pathogenesis - Tập 161 - Trang 105256 - 2021
Susweta Das Mitra1, Pir Irshad1, M. Anusree1, Injeti Rekha1, S. Shailaja1, Janshi Suresh1, G. Aishwarya1, Smeeta Shrestha1, Bibek Ranjan Shome2
1Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
2ICAR- National Institute of Veterinary Epidemiology & Disease Informatics, Bangalore, India

Tài liệu tham khảo

Dadi, 2020, Distribution of virulence genes and phylogenetics of uropathogenic Escherichia coli among urinary tract infection patients in Addis Ababa, Ethiopia, BMC Infect. Dis., 20, 108, 10.1186/s12879-020-4844-z Foxman, 2010, The epidemiology of urinary tract infection, Nat. Rev. Urol., 7, 653, 10.1038/nrurol.2010.190 Flores-Mireles, 2015, Urinary tract infections: epidemiology, mechanisms of infection and treatment options, Nat. Rev. Microbiol., 13, 269, 10.1038/nrmicro3432 Tabasi, 2016, Genotypic characterization of virulence factors in Escherichia coli isolated from patients with acute cystitis, pyelonephritis and asymptomatic bacteriuria, J. Clin. Diagn. Res., 10.7860/JCDR/2016/21379.9009 Mathers, 2015, The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant enterobacteriaceae, Clin. Microbiol. Rev., 28, 565, 10.1128/CMR.00116-14 Ramakrishnan, 2021, Whole Genomic analysis of a clinical isolate of Uropathogenic Escherichia coli strain of Sequence Type - 101 carrying the drug resistance NDM-7 in IncX3 plasmid, Bioinformation, 17 Hammoudi Halat, 2020, The current burden of carbapenemases: review of significant properties and dissemination among gram-negative bacteria, Antibiotics, 9, 186, 10.3390/antibiotics9040186 Egorov, 2018, Rubtsova, bacterial enzymes and antibiotic resistance, Acta Naturae, 10, 33, 10.32607/20758251-2018-10-4-33-48 Mitra, 2020, Molecular detection of the New Delhi metallo-β-lactamase clinical variant with double mutation- V88L and M154L in Escherichia coli isolates from South India, Gene Rep., 21, 100880, 10.1016/j.genrep.2020.100880 Critchley, 2019, The burden of antimicrobial resistance among urinary tract isolates of Escherichia coli in the United States in 2017, PLoS One, 14, 10.1371/journal.pone.0220265 Hooper, 2015, Mechanisms of drug resistance: quinolone resistance: mechanisms of quinolone resistance, Ann. N. Y. Acad. Sci., 1354, 12, 10.1111/nyas.12830 Volcão, 2018, High frequency of aac(6 ′ )-Ib -cr gene associated with double mutations in gyrA and parC in Escherichia coli isolates from patients with urinary tract infections, J. Glob. Antimicrob. Resist., 13, 180, 10.1016/j.jgar.2017.12.013 Carattoli, 2009, Resistance plasmid families in enterobacteriaceae, Antimicrob. Agents Chemother., 53, 2227, 10.1128/AAC.01707-08 Mukherjee, 2019, Characterization and bio-typing of multidrug resistance plasmids from uropathogenic Escherichia coli isolated from clinical setting, Front. Microbiol., 10, 2913, 10.3389/fmicb.2019.02913 Rozwandowicz, 2018, Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae, J. Antimicrob. Chemother., 73, 1121, 10.1093/jac/dkx488 Mahérault, 2019, Advantage of the F2:A1:B- IncF pandemic plasmid over IncC plasmids in in vitro acquisition and evolution of bla CTX-M gene-bearing plasmids in Escherichia coli, Antimicrob. Agents Chemother., 63, 10.1128/AAC.01130-19 Emdy, 2003, Virulence factors of uropathogenic Escherichia coli, Int. J. Antimicrob. Agents, 22, 29, 10.1016/S0924-8579(03)00236-X Kammili, 2020, Plasmid-mediated antibiotic resistance among uropathogens in primigravid women—Hyderabad, India, PLoS One, 15, 10.1371/journal.pone.0232710 Paniagua-Contreras, 2018, Multiple antibiotic resistances and virulence markers of uropathogenic Escherichia coli from Mexico, Pathog. Glob. Health, 112, 415, 10.1080/20477724.2018.1547542 Su, 2019, Genome-based prediction of bacterial antibiotic resistance, J. Clin. Microbiol., 57, 10.1128/JCM.01405-18 Hendriksen, 2019, Using genomics to track global antimicrobial resistance, Front. Public Health, 7, 242, 10.3389/fpubh.2019.00242 Afgan, 2018, 8 Rutherford, 2000, Artemis: sequence visualization and annotation, Bioinformatics, 16, 944, 10.1093/bioinformatics/16.10.944 Zankari, 2012, Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother., 67, 2640, 10.1093/jac/dks261 Carattoli, 2014, In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing, Antimicrob. Agents Chemother., 58, 3895, 10.1128/AAC.02412-14 Sabino, 2019, Characterization of antibiotic resistance genes in the species of the rumen microbiota, Nat. Commun., 10, 5252, 10.1038/s41467-019-13118-0 Joensen, 2014, Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli, J. Clin. Microbiol., 52, 1501, 10.1128/JCM.03617-13 Larsen, 2012, Multilocus sequence typing of total-genome-sequenced bacteria, J. Clin. Microbiol., 50, 1355, 10.1128/JCM.06094-11 Darling, 2004, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res., 14, 1394, 10.1101/gr.2289704 Elshamy, 2020, A review on bacterial resistance to carbapenems: epidemiology, detection and treatment options, Future Sci. OA., 6, FSO438, 10.2144/fsoa-2019-0098 Novais, 2012, Characterization of globally spread Escherichia coli ST131 isolates (1991 to 2010), Antimicrob. Agents Chemother., 56, 3973, 10.1128/AAC.00475-12 Kondratyeva, 2020, Meta-analysis of pandemic Escherichia coli ST131 plasmidome proves restricted plasmid-clade associations, Sci. Rep., 10, 36, 10.1038/s41598-019-56763-7 Nawaz, 2019, Identification of novel plasmid replicons harboring β-lactamase resistant genes in ampicillin-resistant uropathogenic Escherichia coli, SOJ Microbiol. Infect. Dis., 7, 1, 10.15226/sojmid/7/1/00199 Li, 2020, The new perspective of old antibiotic: in vitro antibacterial activity of TMP-SMZ against Klebsiella pneumoniae, J. Microbiol. Immunol. Infect., 53, 757, 10.1016/j.jmii.2018.12.013 Yasir, 2020, Genomic and antimicrobial resistance genes diversity in multidrug-resistant CTX-M-positive isolates of Escherichia coli at a health care facility in Jeddah, J. Infect. Public Health, 13, 94, 10.1016/j.jiph.2019.06.011 Kot, 2019, Antibiotic resistance among uropathogenic Escherichia coli, Pol. J. Microbiol., 68, 403, 10.33073/pjm-2019-048 Foley Steven L., Kaldhone Pravin R., Ricke Steven C., Han Jing, Incompatibility group I1 (IncI1) plasmids: their genetics, biology, and public health relevance, Microbiol. Mol. Biol. Rev. 85 (n.d.) e00031-20. https://doi.org/10.1128/MMBR.00031-20. Sidjabat, 2014, Expansive spread of IncI1 plasmids carrying blaCMY-2 amongst Escherichia coli, Int. J. Antimicrob. Agents, 44, 203, 10.1016/j.ijantimicag.2014.04.016 Rotondo, 2017, Inhibitors of metallo-β-lactamases, Curr. Opin. Microbiol., 39, 96, 10.1016/j.mib.2017.10.026 Tooke, 2019, β-Lactamases and β-lactamase inhibitors in the 21st century, J. Mol. Biol., 431, 3472, 10.1016/j.jmb.2019.04.002 Mahony, 2020, Multidrug-resistant organisms in urinary tract infections in children, Pediatr. Nephrol., 35, 1563, 10.1007/s00467-019-04316-5 Qian, 2020, Discovery of seven novel mutations of gyrB, parC and parE in Salmonella Typhi and Paratyphi strains from Jiangsu Province of China, Sci. Rep., 10, 7359, 10.1038/s41598-020-64346-0 Esmaeel, 2020, Detection of chromosomal and plasmid-mediated quinolone resistance among Escherichia coli isolated from urinary tract infection cases; Zagazig University Hospitals, Egypt, Infect. Drug Res., 13, 413, 10.2147/IDR.S240013 Russo, 2001, Identification of a new iron-regulated virulence gene, ireA , in an extraintestinal pathogenic isolate of Escherichia coli, Infect. Immun., 69, 6209, 10.1128/IAI.69.10.6209-6216.2001 Khasheii, 2016, Frequency evaluation of genes encoding siderophores and the effects of different concentrations of Fe ions on growth rate of uropathogenic Escherichia coli, Iran. J. Microbiol., 8, 359 Hossain, 2020, Genotype–phenotype correlation of β-lactamase-producing uropathogenic Escherichia coli (UPEC) strains from Bangladesh, Sci. Rep., 10, 14549, 10.1038/s41598-020-71213-5 Vrancianu, 2020, Targeting plasmids to limit acquisition and transmission of antimicrobial resistance, Front. Microbiol., 11, 761, 10.3389/fmicb.2020.00761