Skip to main content
SpringerLink
Log in

Diagnostics and Resistance Profiling of Bacterial Pathogens

  • Chapter
  • First Online:
Book cover How to Overcome the Antibiotic Crisis

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 398))

Abstract

Worldwide infectious disease is one of the leading causes of death. Despite improvements in technology and healthcare services, morbidity and mortality due to infections have remained unchanged over the past few decades. The high and increasing rate of antibiotic resistance is further aggravating the situation. Growing resistance hampers the use of conventional antibiotics, and substantial higher mortality rates are reported in patients given ineffective empiric therapy mainly due to resistance to the agents used. These infections cause suffering, incapacity, and death and impose an enormous financial burden on both healthcare systems and on society in general. The accelerating development of multidrug resistance is one of the greatest diagnostic and therapeutic challenges to modern medicine. The lack of new antibiotic options underscores the need for optimization of current diagnostics, therapies, and prevention of the spread of multidrug-resistant organisms. The so-called -omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have yielded large-scale datasets that advanced the search for biomarkers of infectious diseases in the last decade. One can imagine that in the future the implementation of biomarker-driven molecular test systems will transform diagnostics of infectious diseases and will significantly accelerate the identification of the bacterial pathogens at the infected host site. Furthermore, molecular tests based on the identification of markers of antibiotic resistance will dramatically change resistance profiling. The replacement of culturing methods by molecular test systems for early diagnosis will provide the basis not only for a prompt and targeted therapy, but also for a much more effective stewardship of antibiotic agents and a reduction of the spread of multidrug resistance as well as the appearance of new antibiotic resistances.

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 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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

  • Ackermann BL, Hale JE, Duffin KL (2006) The role of mass spectrometry in biomarker discovery and measurement. Curr Drug Metab 5:525–539

    Article  Google Scholar 

  • Arnold C, Westland L, Mowat G et al (2005) Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum. Clin Microbiol Infect 11:122–130

    Article  CAS  PubMed  Google Scholar 

  • Balding DJ (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7:781–791

    Article  CAS  PubMed  Google Scholar 

  • Banoei MM, Donnelly SJ, Mickiewicz B et al (2014) Metabolomics in critical care medicine: a new approach to biomarker discovery. Clin Invest Med 37:E363–E376

    CAS  PubMed  Google Scholar 

  • Biomarkers Definitions Working Group (2001) Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin Pharmacol Ther 69:89–95

    Article  Google Scholar 

  • Cai HY, Caswell JL, Prescott JF (2014) Nonculture molecular techniques for diagnosis of bacterial disease in animals: a diagnostic laboratory perspective. Vet Pathol 51:341–350

    Article  CAS  PubMed  Google Scholar 

  • Call DR, Bakko MK, Krug MJ et al (2003) Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob Agents Chemother 47:3290–3295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cegelski L, Marshall GR, Eldridge GR et al (2008) The biology and future prospects of antivirulence therapies. Nat Rev Microbiol 6:17–27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen PE, Shapiro BJ (2015) The advent of genome-wide association studies for bacteria. Curr Opin Microbiol 25:17–24

    Article  CAS  PubMed  Google Scholar 

  • Classen S, Staratschek-Jox A, Schultze JL (2008) Use of genome-wide high-throughput technologies in biomarker development. Biomark Med 2:509–524

    Article  CAS  PubMed  Google Scholar 

  • Collino S, Martin FP, Rezzi S (2013) Clinical metabolomics paves the way towards future healthcare strategies. Br J Clin Pharmacol 75:619–629

    CAS  PubMed  PubMed Central  Google Scholar 

  • Croxatto A, Prod’hom G, Greub G (2012) Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 36:380–407

    Article  CAS  PubMed  Google Scholar 

  • Dellinger RP, Levy MM, Rhodes A et al, Surviving Sepsis Campaign Guidelines Committee including the Pediatric Subgroup (2012) Surviving sepsis campaign: international guidelines for management of severe sepsis and septic shock: 2012. Crit Care Med 41:580–637

    Google Scholar 

  • Didelot X, Bowden R, Wilson DJ et al (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13:601–612

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dittmar G, Selbach M (2015) SILAC for biomarker discovery. Proteomics Clin Appl 9:301–306

    Article  CAS  PubMed  Google Scholar 

  • Dunne WM Jr, Westblade LF, Ford B (2012) Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31:1719–1726

    Article  CAS  PubMed  Google Scholar 

  • Endimiani A, Hujer KM, Hujer AM et al (2011) Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Clin Infect Dis 52(Suppl 4):S373–S383

    Article  PubMed  PubMed Central  Google Scholar 

  • European Commission (2010) Biomarkers for patient stratification. http://ec.europa.eu/research/health/pdf/biomarkers-for-patient-stratification_en.pdf

  • Farhat MR, Shapiro BJ, Kieser KJ et al (2013) Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet 45:1183–1189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fitousis K, Moore LJ, Hall J et al (2010) Evaluation of empiric antibiotic use in surgical sepsis. Am J Surg 200:776–782

    Article  PubMed  Google Scholar 

  • Francis RO, Wu F, Della-Latta P et al (2012) Rapid detection of Klebsiella pneumoniae carbapenemase genes in enterobacteriaceae directly from blood culture bottles by real-time PCR. Am J Clin Pathol 137:627–632

    Article  PubMed  Google Scholar 

  • Garnacho-Montero J, Garcia-Garmendia JL, Barrero-Almodovar A et al (2003) Impact of adequate empirical antibiotic therapy on the outcome of patients admitted to the intensive care unit with sepsis. Crit Care Med 31:2742–2751

    Article  PubMed  Google Scholar 

  • He QY, Chiu JF (2003) Proteomics in biomarker discovery and drug development. J Cell Biochem 89:868–886

    Article  CAS  PubMed  Google Scholar 

  • Hrabák J, Walková R, Studentová V et al (2011) Carbapenemase activity detection by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 49:3222–3227

    Article  PubMed  PubMed Central  Google Scholar 

  • Infectious Diseases Society of America (2011) An unmet medical need: rapid molecular diagnostics tests for respiratory tract infections. Clin Infect Dis 52(Suppl 4):S384–S395

    Google Scholar 

  • Kilianski A, Haas JL, Corriveau EJ et al (2015) Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 4:12

    Article  PubMed  PubMed Central  Google Scholar 

  • Köser CU, Ellington MJ, Cartwright EJ et al (2012) Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8:e1002824

    Article  PubMed  PubMed Central  Google Scholar 

  • Kostrzewa M, Sparbier K, Maier T et al (2013) MALDI-TOF MS: an upcoming tool for rapid detection of antibiotic resistance in microorganisms. Proteomics Clin Appl 7:767–778

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Roberts D, Wood KE et al (2006) Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock. Crit Care Med 34:1589–1596

    Article  PubMed  Google Scholar 

  • Lawn SD, Mwaba P, Bates M et al (2013) Advances in tuberculosis diagnostics: the Xpert MTB/RIF assay and future prospects for a point-of-care test. Lancet Infect Dis 13:349–361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leekitcharoenphon P, Nielsen EM, Kaas RS et al (2014) Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS ONE 9:e87991

    Article  PubMed  PubMed Central  Google Scholar 

  • Liotta LA, Ferrari M, Petricoin E (2003) Clinical proteomics: written in blood. Nature 425:905

    Article  CAS  PubMed  Google Scholar 

  • Livermore DM, Wain J (2013) Revolutionising bacteriology to improve treatment outcomes and antibiotic stewardship. Infect Chemother 45:1–10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacArthur RD, Miller M, Albertson T et al (2004) Adequacy of early empiric antibiotic treatment and survival in severe sepsis: experience from the MONARCS trial. Clin Infect Dis 38:284–288

    Article  PubMed  Google Scholar 

  • Maiden MC, Bygraves JA, Feil E et al (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 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  CAS  PubMed  Google Scholar 

  • Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem 6:287–303

    Article  CAS  Google Scholar 

  • Myers FB, Henrikson RH, Xu L et al (2011) A point-of-care instrument for rapid multiplexed pathogen genotyping. Conf Proc IEEE Eng Med Biol Soc 2011:3668–3671

    PubMed  Google Scholar 

  • Pai NP, Vadnais C, Denkinger C et al (2012) Point-of-care testing for infectious diseases: diversity, complexity, and barriers in low- and middle-income countries. PLoS Med 9:e1001306

    Article  PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60:227–237

    Article  CAS  PubMed  Google Scholar 

  • Rai AJ (2007) Biomarkers in translational research: focus on discovery, development and translation of protein biomarkers to clinical immunoassays. Expert Rev Mol Diagn 7:545–553

    Article  CAS  PubMed  Google Scholar 

  • Randell P (2014) It’s a MALDI but it’s a goodie: MALDI-TOF mass spectrometry for microbial identification. Thorax 69:776–778

    Article  PubMed  Google Scholar 

  • Read TD, Massey RC (2014) Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology. Genome Med 6:109

    Article  PubMed  PubMed Central  Google Scholar 

  • Reinhart K, Hartog CS (2010) Biomarkers as a guide for antimicrobial therapy. Int J Antimicrob Agents 36:S17–S21

    Article  CAS  PubMed  Google Scholar 

  • Rodrigues Ribeiro Teles FS, de Távora Pires, Tavira LA, Pina da Fonseca LJ (2010) Biosensors as rapid diagnostic tests for tropical diseases. Crit Rev Clin Lab Sci 47:139–169

    Article  PubMed  Google Scholar 

  • Schürch AC, Siezen RJ (2010) Genomic tracing of epidemics and disease outbreaks. Microb Biotechnol 3:628–633

    Article  PubMed  PubMed Central  Google Scholar 

  • Soo Hoo GW, Wen YE, Nguyen TV et al (2005) Impact of clinical guidelines in the management of severe hospital-acquired pneumonia. Chest 128:2778–2787

    Article  PubMed  Google Scholar 

  • Sparbier K, Schubert S, Weller U et al (2012) Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based functional assay for rapid detection of resistance against β-lactam antibiotics. J Clin Microbiol 50:927–937

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strauss C, Endimiani A, Perreten V (2014) A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria. J Microbiol Methods 108:25–30

    Article  PubMed  Google Scholar 

  • van Belkum A (2003) Molecular diagnostics in medical microbiology: yesterday, today and tomorrow. Curr Opin Pharmacol 3:497–501

    Article  PubMed  Google Scholar 

  • van Dijk EL, Auger H, Jaszczyszyn Y et al (2014) Ten years of next-generation sequencing technology. Trends Genet 30:418–426

    Article  PubMed  Google Scholar 

  • Wallis RS, Pai M, Menzies D et al (2010) Biomarkers and diagnostics for tuberculosis: progress, needs, and translation into practice. Lancet 375:1920–1937

    Article  CAS  PubMed  Google Scholar 

  • World Health Organization (2004) Mapping the landscape of diagnostics for sexually transmitted infections. http://www.who.int/tdr/publications/documents/mapping-landscape-sti.pdf

  • Zhao YY, Cheng XL, Lin RC et al (2015) Lipidomics applications for disease biomarker discovery in mammal models. Biomark Med 9:153–168

    Article  CAS  PubMed  Google Scholar 

  • Zignol M, van Gemert W, Falzon D et al (2012) Surveillance of anti-tuberculosis drug resistance in the world: an updated analysis, 2007–2010. Bull World Health Organ 90:111–119D

    Article  PubMed  Google Scholar 

  • Zolg JW, Langen H (2004) How industry is approaching the search for new diagnostic markers and biomarkers. Mol Cell Proteomics 3:345–354

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dept. Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany

    Klaus Hornischer & Susanne Häußler

Authors
  1. Klaus Hornischer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Susanne Häußler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Susanne Häußler .

Editor information

Editors and Affiliations

  1. Department Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Niedersachsen, Germany

    Marc Stadler

  2. Dept. Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Niedersachsen, Germany

    Petra Dersch

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing AG

About this chapter

Cite this chapter

Hornischer, K., Häußler, S. (2016). Diagnostics and Resistance Profiling of Bacterial Pathogens. In: Stadler, M., Dersch, P. (eds) How to Overcome the Antibiotic Crisis . Current Topics in Microbiology and Immunology, vol 398. Springer, Cham. https://doi.org/10.1007/82_2016_494

Download citation

Publish with us

Policies and ethics

Search

Navigation