Clinical Perspective of Antimicrobial Resistance in Bacteria

References

• Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18(3):268–281. doi:10.1111/j.1469-0691.2011.03570.x
   PubMed Web of Science ®Google Scholar
• O’neill J. Tackling drug-resistant infections globally; 2016.
   Google Scholar
• Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev. 2018;31(4):UNSPe00088–17. doi:10.1128/cmr.00088-17
   Web of Science ®Google Scholar
• Heuer H, Schmitt H, Smalla K. Antibiotic resistance gene spread due to manure application on agricultural fields. Curr Opin Microbiol. 2011;14(3):236–243. doi:10.1016/j.mib.2011.04.009
   PubMed Web of Science ®Google Scholar
• von Wintersdorff CJH, Penders J, van Niekerk JM, et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front Microbiol. 2016;7:173. doi:10.3389/fmicb.2016.00173.
   PubMed Web of Science ®Google Scholar
• Carattoli A. Plasmids and the spread of resistance. Int J Med Microbiol. 2013;303(6–7):298–304. doi:10.1016/j.ijmm.2013.02.001
   PubMed Web of Science ®Google Scholar
• Modi SR, Collins JJ, Relman DA. Antibiotics and the gut microbiota. J Clin Invest. 2014;124(10):4212–4218. doi:10.1172/jci72333
   PubMed Web of Science ®Google Scholar
• Liu YY, Wang Y, Walsh TR, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis. 2016;16(2):161–168. doi:10.1016/s1473-3099(15)00424-7
   PubMed Web of Science ®Google Scholar
• Zhu YG, Johnson TA, Su JQ, et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc Natl Acad Sci USA. 2013;110(9):3435–3440. doi:10.1073/pnas.1222743110
   PubMed Web of Science ®Google Scholar
• Karkman A, Do TT, Walsh F, Virta MPJ. Antibiotic-resistance genes in waste water. Trends Microbiol. 2018;26(3):220–228. doi:10.1016/j.tim.2017.09.005
   PubMed Web of Science ®Google Scholar
• Jia B, Raphenya AR, Alcock B, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017;45(D1):D566–D573. doi:10.1093/nar/gkw1004
   PubMed Web of Science ®Google Scholar
• World Health Organization. WHO publishes list of bacteria for which now antibiotics are urgently needed. Available from: https://www.who.int/news/item/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed. Accessed January 20, 2022.
   Google Scholar
• Lakhundi S, Zhang K. Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology. Clin Microbiol Rev. 2018;31(4). doi:10.1128/CMR.00020-18
   PubMed Web of Science ®Google Scholar
• Liu J, Chen D, Peters BM, et al. Staphylococcal chromosomal cassettes mec (SCCmec): a mobile genetic element in methicillin-resistant Staphylococcus aureus. Microb Pathog. 2016;101:56–67. doi:10.1016/j.micpath.2016.10.028
   PubMed Web of Science ®Google Scholar
• Paterson GK, Harrison EM, Holmes MA. The emergence of mecC methicillin-resistant Staphylococcus aureus. Trends Microbiol. 2014;22(1):42–47. doi:10.1016/j.tim.2013.11.003
   PubMed Web of Science ®Google Scholar
• Becker K, van Alen S, Idelevich EA, et al. Plasmid-encoded transferable mecb-mediated methicillin resistance in Staphylococcus aureus. Emerg Infect Dis. 2018;24(2):242–248. doi:10.3201/eid2402.171074
   PubMed Web of Science ®Google Scholar
• Frieden TR, Munsiff SS, Low DE, et al. Emergence of vancomycin-resistant enterococci in New York City. Lancet. 1993;342(8863):76–79. doi:10.1016/0140-6736(93)91285-t
   PubMed Web of Science ®Google Scholar
• Lee T, Pang S, Abraham S, Coombs GW. Antimicrobial-resistant CC17 Enterococcus faecium: the past, the present and the future. J Glob Antimicrob Resist. 2019;16:36–47. doi:10.1016/j.jgar.2018.08.016
   PubMed Web of Science ®Google Scholar
• Ahmed MO, Baptiste KE. Vancomycin-resistant enterococci: a review of antimicrobial resistance mechanisms and perspectives of human and animal health. Microb Drug Resist. 2018;24(5):590–606. doi:10.1089/mdr.2017.0147
   PubMed Web of Science ®Google Scholar
• El Moujaber G, Osman M, Rafei R, Dabboussi F, Hamze M. Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region. J Med Microbiol. 2017;66(7):847–858. doi:10.1099/jmm.0.000503
   PubMed Web of Science ®Google Scholar
• Straume D, Stamsas GA, Havarstein LS. Natural transformation and genome evolution in Streptococcus pneumoniae. Infect Genet Evol. 2015;33:371–380. doi:10.1016/j.meegid.2014.10.020
   Web of Science ®Google Scholar
• Dever LA, Dermody TS. Mechanisms of bacterial resistance to antibiotics. Arch Intern Med. 1991;151(5):886–895. doi:10.1001/archinte.1991.00400050040010
   PubMedGoogle Scholar
• Chong Y, Shimoda S, Shimono N. Current epidemiology, genetic evolution and clinical impact of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Infect Genet Evol. 2018;61:185–188. doi:10.1016/j.meegid.2018.04.005
   PubMed Web of Science ®Google Scholar
• Munita JM, Arias CA. Mechanisms of antibiotic resistance. Microbiol Spectr. 2016;4(2). doi:10.1128/microbiolspec.VMBF-0016-2015
   PubMed Web of Science ®Google Scholar
• Peirano G, Pitout JDD. Extended-spectrum beta-lactamase-producing Enterobacteriaceae: update on molecular epidemiology and treatment options. Drugs. 2019;79(14):1529–1541. doi:10.1007/s40265-019-01180-3
   PubMed Web of Science ®Google Scholar
• Smet A, Martel A, Persoons D, et al. Broad-spectrum beta-lactamases among Enterobacteriaceae of animal origin: molecular aspects, mobility and impact on public health. FEMS Microbiol Rev. 2010;34(3):295–316. doi:10.1111/j.1574-6976.2009.00198.x
   Web of Science ®Google Scholar
• Bevan ER, Jones AM, Hawkey PM. Global epidemiology of CTX-M beta-lactamases: temporal and geographical shifts in genotype. J Antimicrob Chemother. 2017;72(8):2145–2155. doi:10.1093/jac/dkx146
   PubMed Web of Science ®Google Scholar
• Ghosh H, Doijad S, Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Chakraborty T. blaCTX-M-27-encoding Escherichia coli sequence type 131 lineage C1-M27 clone in clinical isolates, Germany. Emerg Infect Dis. 2017;23(10):1754–1756. doi:10.3201/eid2310.170938
   Web of Science ®Google Scholar
• Jacoby GA. AmpC beta-lactamases. Clin Microbiol Rev. 2009;22(1):161–82, Table of Contents. doi:10.1128/CMR.00036-08
   PubMed Web of Science ®Google Scholar
• Xia J, Gao J, Tang W. Nosocomial infection and its molecular mechanisms of antibiotic resistance. Biosci Trends. 2016;10(1):14–21. doi:10.5582/bst.2016.01020
   PubMed Web of Science ®Google Scholar
• van Duin D, Doi Y. The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence. 2017;8(4):460–469. doi:10.1080/21505594.2016.1222343
   PubMed Web of Science ®Google Scholar
• Samuelsen O, Overballe-Petersen S, Bjornholt JV, et al. Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014. PLoS One. 2017;12(11):e0187832. doi:10.1371/journal.pone.0187832
   Web of Science ®Google Scholar
• Jesús Rodríguez-Baño B-G-G, Machuca I, Pascuala A. Treatment of infections caused by extended-spectrum-betalactamase-, ampc-, and carbapenemase-producing Enterobacteriaceae. Clin Microbiol Rev. 2017. doi:10.1128/CMR.00079-17
   Web of Science ®Google Scholar
• Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol. 2007;5(12):939–951. doi:10.1038/nrmicro1789
   PubMed Web of Science ®Google Scholar
• Lee CR, Lee JH, Park M, et al. Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options. Front Cell Infect Microbiol. 2017;7:55. doi:10.3389/fcimb.2017.00055
   PubMed Web of Science ®Google Scholar
• Antunes LC, Visca P, Towner KJ. Acinetobacter baumannii: evolution of a global pathogen. Pathog Dis. 2014;71(3):292–301. doi:10.1111/2049-632X.12125
   PubMed Web of Science ®Google Scholar
• Subedi D, Vijay AK, Willcox M. Overview of mechanisms of antibiotic resistance in Pseudomonas aeruginosa: an ocular perspective. Clin Exp Optom. 2018;101(2):162–171. doi:10.1111/cxo.12621
   PubMed Web of Science ®Google Scholar
• Wright GD. Bacterial resistance to antibiotics: enzymatic degradation and modification. Adv Drug Deliv Rev. 2005;57(10):1451–1470. doi:10.1016/j.addr.2005.04.002
   PubMed Web of Science ®Google Scholar
• Olaitan AO, Morand S, Rolain JM. Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria. Front Microbiol. 2014;5:643. doi:10.3389/fmicb.2014.00643
   PubMed Web of Science ®Google Scholar
• Chevalier S, Bouffartigues E, Bodilis J, et al. Structure, function and regulation of Pseudomonas aeruginosa porins. FEMS Microbiol Rev. 2017;41(5):698–722. doi:10.1093/femsre/fux020
   PubMed Web of Science ®Google Scholar
• Correia S, Poeta P, Hébraud M, Capelo JL, Igrejas G. Mechanisms of quinolone action and resistance: where do we stand? J Med Microbiol. 2017;66(5):551–559. doi:10.1099/jmm.0.000475
   PubMed Web of Science ®Google Scholar
• Li XZ, Plesiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in gram-negative bacteria. Clin Microbiol Rev. 2015;28(2):337–418. doi:10.1128/CMR.00117-14
   PubMed Web of Science ®Google Scholar
• The center for disease dynamics Economics & Policy. ResistanceMap: Antibiotic Resistance. Available from: https://resistancemap.cddep.org/AntibioticResistance.php. Accessed January 20, 2022.
   Google Scholar
• CARA. Antibiogram. Available from: http://www.can-r.com/study.php?study=antb2017&year=2017. Accessed January 20, 2022.
   Google Scholar
• ECED. Surveillance Atlas of Infectious Diseases. Available from: https://atlas.ecdc.europa.eu/public/index.aspx?Dataset=27&HealthTopic=4. Accessed January 20, 2022.
   Google Scholar
• Coombs GW, Daley DA, Lee YT, Pang S. Australian Group on Antimicrobial Resistance (AGAR) Australian Enterococcal Sepsis Outcome Programme (AESOP) annual report 2017. Commun Dis Intell (2018). 2019;43. doi:10.33321/cdi.2019.43.42.
   Google Scholar
• Bell JM, Gottlieb T, Daley DA, Coombs GW. Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Sepsis Outcome Programme (GNSOP) annual report 2017. Commun Dis Intell (2018). 2019;43. doi:10.33321/cdi.2019.43.37.
   Google Scholar
• Coombs GW, Daley DA, Lee YT, Pang S. Australian Group on Antimicrobial Resistance (AGAR) Australian Staphylococcus aureus Sepsis Outcome Programme (ASSOP) Annual Report 2017. Commun Dis Intell (2018). Sep 16 2019;43. doi:10.33321/cdi.2019.43.43.
   Google Scholar
• Research ICoM. AMRSN_Annual_Report_2018; 2018.
   Google Scholar
• CARSS. 2019 national bacterial resistance monitoring report; 2019.
   Google Scholar
• Monaco M, Pimentel de Araujo F, Cruciani M, Coccia EM, Pantosti A. Worldwide epidemiology and antibiotic resistance of Staphylococcus aureus. Curr Top Microbiol Immunol. 2017;409:21–56. doi:10.1007/82_2016_3
   PubMed Web of Science ®Google Scholar
• Sader HS, Castanheira M, Arends SJR, Goossens H, Flamm RK. Geographical and temporal variation in the frequency and antimicrobial susceptibility of bacteria isolated from patients hospitalized with bacterial pneumonia: results from 20 years of the SENTRY Antimicrobial Surveillance Program (1997–2016). J Antimicrob Chemother. 2019;74(6):1595–1606. doi:10.1093/jac/dkz074
   PubMed Web of Science ®Google Scholar
• Institute CaLS. Performance Standards for Antimicrobial Susceptibility Testing. M100-E302020. Wayne, PA: Clinical and Laboratory Standards Institute; 2020.
   Google Scholar
• Dekter HE, Orelio CC, Morsink MC, et al. Antimicrobial susceptibility testing of Gram-positive and -negative bacterial isolates directly from spiked blood culture media with Raman spectroscopy. Eur J Clin Microbiol Infect Dis. 2017;36(1):81–89. doi:10.1007/s10096-016-2773-y
   Web of Science ®Google Scholar
• Huang WE, Griffiths RI, Thompson IP, Bailey MJ, Whiteley AS. Raman microscopic analysis of single microbial cells. Anal Chem. 2004;76(15):4452–4458. doi:10.1021/ac049753k
   PubMed Web of Science ®Google Scholar
• Song YZ, Cui L, Lopez JAS, et al. Raman-deuterium isotope probing for in-situ identification of antimicrobial resistant bacteria in Thames River. Sci Rep. 2017;7:16648. doi:10.1038/s41598-017-16898-x.
   Web of Science ®Google Scholar
• Tao Y, Wang Y, Huang S, et al. Metabolic-activity-based assessment of antimicrobial effects by D2O-labeled single-cell raman microspectroscopy. Anal Chem. 2017;89(7):4108–4115. doi:10.1021/acs.analchem.6b05051
   PubMed Web of Science ®Google Scholar
• Wang Y, Xu JB, Kong LC, et al. Raman-deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota. Microb Biotechnol. 2020;13(2):572–583. doi:10.1111/1751-7915.13519
   Web of Science ®Google Scholar
• Zhang SH, Guo LZ, Yang K, et al. Induction of Escherichia coli into a VBNC state by continuous-flow UVC and subsequent changes in metabolic activity at the single-cell level. Front Microbiol. 2018;9:2243. doi:10.3389/fmicb.2018.02243.
   PubMed Web of Science ®Google Scholar
• Berry D, Mader E, Lee TK, et al. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A. 2015;112(2):E194–E203. doi:10.1073/pnas.1420406112/-/DCSupplemental
   PubMed Web of Science ®Google Scholar
• Wang Y, Ji YT, Wharfe ES, et al. Raman activated cell ejection for isolation of single cells. Anal Chem. 2013;85(22):10697–10701. doi:10.1021/ac403107p
   PubMed Web of Science ®Google Scholar
• Xu B, Du Y, Lin J, et al. Simultaneous identification and antimicrobial susceptibility testing of multiple uropathogens on a microfluidic chip with paper-supported cell culture arrays. Anal Chem. 2016;88(23):11593–11600. doi:10.1021/acs.analchem.6b03052
   Web of Science ®Google Scholar
• Sun H, Chan CW, Wang Y, et al. Reliable and reusable whole polypropylene plastic microfluidic devices for a rapid, low-cost antimicrobial susceptibility test. Lab Chip. 2019;19(17):2915–2924. doi:10.1039/c9lc00502a
   Web of Science ®Google Scholar
• Amin M, Navidifar T, Saleh Shooshtari F, Goodarzi H. Association of the genes encoding metallo-beta-lactamase with the presence of integrons among multidrug-resistant clinical isolates of Acinetobacter baumannii. Infect Drug Resist. 2019;12:1171–1180. doi:10.2147/IDR.S196575
   PubMed Web of Science ®Google Scholar
• Goic-Barisic I, Hrenovic J, Kovacic A, Music MS. Emergence of oxacillinases in environmental carbapenem-resistant Acinetobacter baumannii associated with clinical isolates. Microb Drug Resist. 2016;22(7):559–563. doi:10.1089/mdr.2015.0275
   PubMed Web of Science ®Google Scholar
• Murugan N, Malathi J, Umashankar V, Madhavan HN. Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient. Gene. 2016;578(1):105–111. doi:10.1016/j.gene.2015.12.022
   Web of Science ®Google Scholar
• Blackwell GA, Holt KE, Bentley SD, Hsu LY, Hall RM. Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore. J Antimicrob Chemother. 2017;72(4):1031–1039. doi:10.1093/jac/dkw542
   PubMed Web of Science ®Google Scholar
• Forsberg KJ, Patel S, Wencewicz TA, Dantas G. The tetracycline destructases: a novel family of tetracycline-inactivating enzymes. Chem Biol. 2015;22(7):888–897. doi:10.1016/j.chembiol.2015.05.017
   PubMedGoogle Scholar
• Deng M, Zhu MH, Li JJ, et al. Molecular epidemiology and mechanisms of tigecycline resistance in clinical isolates of Acinetobacter baumannii from a Chinese university hospital. Antimicrob Agents Chemother. 2014;58(1):297–303. doi:10.1128/AAC.01727-13
   Web of Science ®Google Scholar
• Ostrer L, Khodursky RF, Johnson JR, Hiasa H, Khodursky A. Analysis of mutational patterns in quinolone resistance-determining regions of GyrA and ParC of clinical isolates. Int J Antimicrob Agents. 2019;53(3):318–324. doi:10.1016/j.ijantimicag.2018.12.004
   Web of Science ®Google Scholar
• Nang SC, Han ML, Yu HH, et al. Polymyxin resistance in Klebsiella pneumoniae: multifaceted mechanisms utilized in the presence and absence of the plasmid-encoded phosphoethanolamine transferase gene mcr-1. J Antimicrob Chemother. 2019;74(11):3190–3198. doi:10.1093/jac/dkz314
   PubMed Web of Science ®Google Scholar
• Mlynarcik P, Kolar M. Molecular mechanisms of polymyxin resistance and detection of mcr genes. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2019;163(1):28–38. doi:10.5507/bp.2018.070
   PubMed Web of Science ®Google Scholar
• Moffatt JH, Harper M, Boyce JD. Mechanisms of polymyxin resistance. Adv Exp Med Biol. 2019;1145:55–71. doi:10.1007/978-3-030-16373-0_5
   PubMed Web of Science ®Google Scholar
• Li X, Quan J, Yang Y, et al. Abrp, a new gene, confers reduced susceptibility to tetracycline, glycylcine, chloramphenicol and fosfomycin classes in Acinetobacter baumannii. Eur J Clin Microbiol Infect Dis. 2016;35(8):1371–1375. doi:10.1007/s10096-016-2674-0
   Web of Science ®Google Scholar
• Alcalde-Rico M, Hernando-Amado S, Blanco P, Martinez JL. Multidrug efflux pumps at the crossroad between antibiotic resistance and bacterial virulence. Front Microbiol. 2016;7:1483. doi:10.3389/fmicb.2016.01483
   PubMed Web of Science ®Google Scholar
• Chuanchuen R, Narasaki CT, Schweizer HP. The MexJK efflux pump of Pseudomonas aeruginosa requires OprM for antibiotic efflux but not for efflux of triclosan. J Bacteriol. 2002;184(18):5036–5044. doi:10.1128/jb.184.18.5036-5044.2002
   PubMed Web of Science ®Google Scholar
• Kale P, Dhawan B. The changing face of community-acquired methicillin-resistant Staphylococcus aureus. Indian J Med Microbiol. 2016;34(3):275–285. doi:10.4103/0255-0857.188313
   PubMed Web of Science ®Google Scholar
• Thaden JT, Pogue JM, Kaye KS. Role of newer and re-emerging older agents in the treatment of infections caused by carbapenem-resistant Enterobacteriaceae. Virulence. 2017;8(4):403–416. doi:10.1080/21505594.2016.1207834
   PubMed Web of Science ®Google Scholar