Skip to main content
SpringerLink
Log in

Approaches for Determining Antimicrobial Drug-Resistant Bacteria: The Way Ahead

  • Chapter
  • First Online:
Modern Tools and Techniques to Understand Microbes

  • 1534 Accesses

Abstract

Since the beginning, medical practitioners and veterinarians have employed a vast variety of antimicrobials to treat microbial infectious diseases that were based primarily on past clinical experiences. However, the emergence of resistance among microbial species against traditionally used antimicrobials has made it more difficult for clinicians to empirically select an appropriate antimicrobial agent. As a result, global concern has been deviated toward finding the efficacy of available antimicrobials. Therefore, it is recommended to validate already existing in vitro antimicrobial susceptibility testing (AST) methods. Although a variety of methods exist, the goal of AST is to provide a reliable predictor of how an organism is likely to respond to antimicrobial therapy in the infected host. The selection of a particular AST method is based on many factors such as validation data, practicality, flexibility, automation, cost, reproducibility, accuracy, and individual preference. In the modern methodologies, use of genotypic approaches for detection of antimicrobial resistance genes has also been promoted as a way to increase the speed and accuracy of susceptibility testing. Many DNA-based assays are being developed to detect bacterial antibiotic resistance at the genetic level. These methods, when used in conjunction with phenotypic analysis, offer the promise of increased sensitivity, specificity, and speed in the detection of specific known resistance genes and can be used in tandem with traditional laboratory AST methods. The invention of new molecular technologies in genomics and proteomics is shifting traditional techniques for bacterial classification, identification, and characterization in the twenty-first century toward methods based on the elucidation of specific gene sequences or molecular components of a cell. The new methods can be rapid, offer high throughput, and produce unprecedented levels of discrimination among strains of bacteria and archaea.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Al-Qadiri HM, Lin M, Cavinato AG, Rasco BA (2006) Fourier transform infrared spectroscopy, detection and identification of Escherichia coli O157:H7 and Alicyclobacillus strains in apple juice. Int J Food Microbiol 111:73–80

    Article  CAS  PubMed  Google Scholar 

  • Bons JA, Wodzig WK, van Dieijen-Visser MP (2005) Protein profiling as a diagnostic tool in clinical chemistry: a review. Clin Chem Lab Med 43:1281–1290

    Article  CAS  PubMed  Google Scholar 

  • Cai HY, Archambault M, Gyles CL, Prescott JF (2003) Molecular genetic methods in the veterinary clinical bacteriology laboratory: current usage and future applications. Anim Health Rev 4:73–93

    Article  CAS  Google Scholar 

  • Chen S, Zhao S, Mcdermott PF, Schroeder CM, White DG, Meng J (2005) A DNA microarray for identification of virulence and antimicrobial resistance genes in Salmonella serovars and Escherichia coli. Mol Cell Probes 19:195–201

    Article  CAS  PubMed  Google Scholar 

  • Clinical and Laboratory Standards Institute (CLSI) (2006) Document M45-A. Methods for antimicrobial dilution and disk susceptibility of infrequently isolated or fastidious bacteria; approved guideline. CLSI, Wayne, PA

    Google Scholar 

  • Clinical and Laboratory Standards Institute (CLSI) (2008) Document M31-A3. Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals, approved standard, third edition. CLSI, Wayne, PA

    Google Scholar 

  • Cocconcelli PS, Porro D, Galandini S, Senini L (1995) Development of RAPD protocol for typing of strains of lactic-acid bacteria and enterococci. Lett Appl Microbiol 21:376–379

    Article  CAS  PubMed  Google Scholar 

  • Dare D (2006) Rapid bacterial characterization and identification by MALDI-TOF mass spectrometry. In: Tang Y-W, Stratton CW (eds) Advanced techniques in diagnostic microbiology. Springer, New York, pp 117–133

    Chapter  Google Scholar 

  • Dehaumont P (2004) OIE international standards on antimicrobial resistance. J Vet Med [Ser B] 51:411–414

    Article  CAS  Google Scholar 

  • Edwards-Jones V, Claydon MA, Evason DJ, Walker J, Fox AJ, Gordon DB (2000) Rapid discrimination between methicillin-sensitive and methicillin-resistant Staphylococcus aureus by intact cell mass spectrometry. J Med Microbiol 49:295–300

    Article  CAS  PubMed  Google Scholar 

  • Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71

    Article  CAS  PubMed  Google Scholar 

  • Frye JG, Jesse T, Long F, Rondeau G, Porwollik S, McClelland M, Jackson CR, Englen M, Fedorka-Cray PJ (2006) DNA microarray detection of antimicrobial resistance genes in diverse bacteria. Int J Antimicrob Agents 27:138–151

    Article  CAS  PubMed  Google Scholar 

  • Frye JG, Lindsey RL, Rondeau G, Porwollik S, Long G, Mcclelland M, Jackson CR, Englen MD, Meinersmann RJ, Berrang ME, Davis JA, Barrett JB, Turpin JB, Thitaram SN, Fedorka-Cray PJ (2010) Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information Database. Microb Drug Resist 16:9–19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ge B, Bodeis S, Walker RD, White DG, Zhao S, Mcdermott PF, Meng J (2002) Comparison of Etest and agar dilution for in vitro antimicrobial susceptibility testing of Campylobacter. J Antimicrob Chemother 50:487–494

    Article  CAS  PubMed  Google Scholar 

  • Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P et al (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739

    Article  CAS  PubMed  Google Scholar 

  • He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC et al (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77

    Article  CAS  PubMed  Google Scholar 

  • Hecker M, Engelmann S, Cordwell SJ (2003) Proteomics of Staphylococcus aureus—current state and future challenges. J Chromatogr B Analyt Technol Biomed Life Sci 787:179–195

    Article  CAS  PubMed  Google Scholar 

  • Honisch C, Chen Y, Mortimer C, Arnold C, Schmidt O, van den Boom D, Cantor CR, Shah HN, Gharbia SE (2007) Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing. Proc Natl Acad Sci 104:10649–10654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krader P, Emerson D (2004) Characterization of Archaea and some extremophilic bacteria using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Extremophiles 8:259–268

    Article  CAS  PubMed  Google Scholar 

  • Krishnamurthy T, Ross PL (1996) Rapid identification of bacteria by direct matrix-assisted laser desorption/ionization mass spectrometric analysis of whole cells. Rapid Commun Mass Spectrom 10:1992–1996

    Article  CAS  PubMed  Google Scholar 

  • Lay JO Jr (2001) MALDI-TOF mass spectrometry of bacteria. Mass Spectrom Rev 20:172–194

    Article  CAS  PubMed  Google Scholar 

  • Lin JJ, Kuo J, Ma J (1996) A PCR-based DNA fingerprinting technique: AFLP for molecular typing of bacteria. Nucleic Acids Res 24:3649–3650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu WT, Stahl DA (2007) Molecular approaches for the measurement of density, diversity, and phylogeny. In: Hurst CJ, Crawford RL, Garland JL, Lipson DA, Mills AL, Stetzenbach LD (eds) Manual of environmental microbiology, 3 edn. ASM Press, Washington, DC, pp 139–156

    Google Scholar 

  • Liu WT, Mirzabekov AD, Stahl DA (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3:619–629

    Article  CAS  PubMed  Google Scholar 

  • Logue JB, Bürgmann H, Robinson CT (2008) Progress in the ecological genetics and biodiversity of freshwater bacteria. BioScience 58:103–113

    Article  Google Scholar 

  • Ludwig W, Klenk H-P (2001) Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. In: Boone DR, Castenholtz RW (eds) Bergey’s manual of systematic bacteriology. Springer, Berlin, pp 49–65

    Chapter  Google Scholar 

  • Lundquist M, Caspersen MB, Wikström P, Forsman M (2005) Discrimination of Francisella tularensis subspecies using surface enhanced laser desorption ionization mass spectrometry and multivariate data analysis. FEMS Microbiol Lett 243:303–310

    Article  CAS  PubMed  Google Scholar 

  • Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mellmann A, Cloud J, Maier T et al (2008) Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol 46:1946–1954

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nouwens AS, Cordwell SJ, Larsen MR, Molloy MP, Gillings M, Willcox MD, Walsh BJ (2000) Complementing genomics with proteomics: the membrane subproteome of Pseudomonas aeruginosa PAO1. Electrophoresis 21:3797–3809

    Article  CAS  PubMed  Google Scholar 

  • O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021

    PubMed  PubMed Central  Google Scholar 

  • Ojha S, Kostrzynska M (2008) Examination of animal and zoonotic pathogens using microarrays. Vet Res 39:4–26

    Article  PubMed  Google Scholar 

  • Peng X, Xu C, Ren H, Lin X, Wu L, Wang S (2005) Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Pseudomonas aeruginosa responding to ampicilin, kanamycin, and tetracycline resistance. J Proteome Res 4:2257–2265

    Article  CAS  PubMed  Google Scholar 

  • Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J (2005) Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J Clin Microbiol 43:2291–2302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pieper R, Gatlin-Bunai CL, Mongodin EF, Parmar PP, Huang ST, Clark DJ, Fleischmann RD, Gill SR, Peterson SN (2006) Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin. Proteomics 6:4246–4258

    Article  CAS  PubMed  Google Scholar 

  • Pignone M, Greth K, Cooper J, Emerson D, Tang J (2006) Identification of mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Clin Microbiol 44:1963–1970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poxton IR (2005) Molecular techniques in the diagnosis and management of infectious diseases: do they have a role in bacteriology? Med Princ Pract 14:20–26

    Article  PubMed  Google Scholar 

  • Rathe M, Kristensen L, Ellermann-Eriksen S, Thomsen MK, Schumacher H (2009) Vancomycin-resistant Enterococcus spp.: validation of susceptibility testing and in vitro activity of vancomycin, linezolid, tigecycline and daptomycin. APMIS 118:66–73

    Article  Google Scholar 

  • Redmond C, Baillie LW, Hibbs S, Moir AJ, Moir A (2004) Identification of proteins in the exosporium of Bacillus anthracis. Microbiology 150:355–363

    Article  CAS  PubMed  Google Scholar 

  • Richter D, Postic D, Sertour N, Livey I, Matuschka FR, Baranton G (2006) Delineation of Borrelia burgdorferi sensu lato species by Multilocus sequence analysis and confirmation of the delineation of Borrelia spielmanii sp. nov. Int J Syst Evol Microbiol 56:873–881

    Article  CAS  PubMed  Google Scholar 

  • Sampath R, Hall TA, Massire C, Li F, Blyn LB, Eshoo MW, Hofstadler SA, Ecker DJ (2007) Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann N Y Acad Sci 1102:109–120

    Article  CAS  PubMed  Google Scholar 

  • Seo GM, Kim SJ, Chai YG (2004) Rapid profiling of the infection of Bacillus anthracis on human macrophages using SELDI-TOF mass spectroscopy. Biochem Biophys Res Commun 325:1236–1239

    Article  CAS  PubMed  Google Scholar 

  • Stepanovic S, Hauschild T, Dakic I, Al-Doori Z, Svabic-Vlahovic M, Ranin L, Morrison D (2006) Evaluation of phenotypic and molecular methods for detection of oxacillin resistance in members of the Staphylococcus sciuri group. J Clin Microbiol 44:934–937

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vandamme B, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

    CAS  PubMed  PubMed Central  Google Scholar 

  • Versalovic J, Schneider M, de Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). Methods Cell Mol Biol 5:25–40

    CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Freijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res 21:4407–4414

    Article  Google Scholar 

  • Walker RD (2007) Antimicrobial susceptibility testing and interpretation of results. In: Giguere S, Prescott JF, Baggot JD, Walker RD, Dowling PM (eds) Antimicrobial therapy in veterinary medicine. Blackwell, Ames, IA

    Google Scholar 

  • Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68:2535–2541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • World Organization for Animal Health (OIE) (2010) Chapter 6.9. Responsible and prudent use of antimicrobial agents in veterinary medicine. In: OIE terrestrial animal health code, vol 1. OIE, Paris, France

    Google Scholar 

  • Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1919

    Article  CAS  PubMed  Google Scholar 

  • Zelazny AM, Ferraro MJ, Glennen A, Hindler JF, Mann LM, Munro S, Murray PR, Reller LB, Tenover FC, Jorgensen JH (2005) Selection of strains for quality assessment of the disk induction method for detection of inducible clindamycin resistance in staphylococci: a CLSI collaborative study. J Clin Microbiol 43:2613–2615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgment

Ajit Varma is thankful to Department of Science and Technology and Department of Biotechnology for partial financial funding and to DST-FIST for providing confocal microscope facility.

Author information

Authors and Affiliations

  1. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Pankaj Goyal, Manoj Kumar, Vivek Kumar, Narendra Tuteja & Ajit Varma

  2. School of Biotechnology, Gautam Buddha University, Noida, 201308, Uttar Pradesh, India

    Nim J. Singh

  3. Amity Institute for Advanced Research and Studies, Amity University, Noida, Uttar Pradesh, India

    Rupesh Kumar Basniwal

Authors
  1. Pankaj Goyal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nim J. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rupesh Kumar Basniwal
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manoj Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Vivek Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Narendra Tuteja
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ajit Varma
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pankaj Goyal .

Editor information

Editors and Affiliations

  1. Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India

    Ajit Varma

  2. ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kusmaur, Mau Nath Bhanjan, Uttar Pradesh, India

    Arun Kumar Sharma

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Goyal, P. et al. (2017). Approaches for Determining Antimicrobial Drug-Resistant Bacteria: The Way Ahead. In: Varma, A., Sharma, A. (eds) Modern Tools and Techniques to Understand Microbes. Springer, Cham. https://doi.org/10.1007/978-3-319-49197-4_13

Download citation

Publish with us

Policies and ethics

Search

Navigation