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Bacterial identification with mass spectrometry

Mass spectrometry can make a significant contribution to rapid identification of pathogens by diagnostic laboratories
Jamie Laughlin MSc MA CSci FIBMS
Head, BMS Microbiology and Immunology,
Heatherwood and Wexham Park Foundation Trust Hospital, Slough, UK
The rapid identification of micro-organisms has been a major barrier to clinicians as they struggle to provide appropriate empirical antimicrobial treatment while waiting, sometimes days, for a definitive identification of the pathogen. Identification is of great value for the selection of optimal antimicrobial management and improves clinical outcomes. This is particularly true for patients with bloodstream infections (BSI), where prompt and aggressive initiation of antimicrobial therapy is the mainstay of treatment.(1)
In broad terms, it allows the expedient de-escalation from board spectrum antibiotics to a more targeted one. Defensive medicine that usually involves prescribing a broad spectrum antibiotic is commonly practised. Anywhere between 20% and 50% of antibiotics prescribed in the US are probably unnecessary, highlighting the importance of antibiotic stewardship.(2) Increasing rates of drug resistance have forced clinicians to expose patients with presumed bacterial infection to treatment with empiric combinations of broad spectrum antibiotics.(3)
The empirical use of broad-spectrum antibiotics increases, by selection, the prevalence of bacteria resistant to antibiotics. The switch to a more narrow-spectrum antibiotic minimises the risks of the antibiotic, that is, disruption of normal flora, toxic side effects and selective pressures. Additionally, it can influence the length of hospital stays, and reduce associated mortality rates. Early identification also makes the management of any infection control matters easier, as appropriate measures can be initiated much sooner. 
The need for new technologies
There has been a critical need for new technologies in microbiology, which has historically been manual and conservative in its approach. This has been true, in particular, for BSIs where associated mortality is high. Interventional-based microbiology must be embraced. New technologies can not only offer speed but also improved quality and accuracy, which are qualities instilled in a diagnostic environment. 
Today, diagnostic laboratories can make a significant contribution to rapid identification of pathogens by utilising mass spectrometry (MS). Conventionally, identification has been achieved using macro- and microscopic observation of morphology and biochemical/serological reactions.(4) Matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) MS is a technique that, broadly speaking, characterises the protein material of bacteria and fungi. More importantly, the technical complexity of the workflow is minimal. The technology is characterised by requiring only minimal reagents and sample size. Running costs are also minimal and a less-specialised knowledge of microbiology is required.(5)
In addition, reducing the number of steps in the identification process reduces the possibility of error. It is a technique used to screen simultaneously a multitude of molecules and determine their identity by analysing their individual mass-to-charge ratio. These molecular ‘signatures’ can be used for rapid bacterial and fungal identification from isolated colonies. Dominant spectral peaks are from conserved areas of proteins that are highly stable under different growth conditions, thus avoiding bias from different culture methods and assuring reproducibility.
Initially this technology was used to identify bacteria and yeasts grown on agar plates; however, more recently it has been used to identify organisms directly from blood culture bottles with the greatest success being achieved with the Gram-negative isolates. MALDI-TOF has been described as the fastest of all techniques for bacterial identification directly from blood cultures,(6) thereby allowing for real-time diagnosis and a more targeted antibiotic therapy. A number of authors(3,7) have tested the hypothesis that patient care would be enhanced by utilising MS technology with real-time clinical interpretation and intervention with regard to antibiotic therapies. Perez et al demonstrated earlier initiation of a more targeted antimicrobial therapy, informed by more rapid identification utilising MS, improved patient outcome and reduced hospital expenditure.
Available systems
Systems currently available on the market are the Bruker Microflex and Biomerieux Shimadzu systems (Figures 1 and 2). While the technology in these platforms is very similar, their scoring algorithm and signal processing differ. 
To realise the full benefits of these systems, the end-to-end capabilities and integration in existing workflows must be assessed. Looking at these systems in isolation is short-sighted and naïve. To achieve the significant benefits that this technology can provide, communication with the end-users, predominately the clinicians, must be improved. Changes in workflow in the laboratory must also be assessed to maximise the benefit of a rapid identification for the patient. Once the bacteria or fungi are identified, the lab and, more importantly, the clinicians have an understanding of the type of organism, which allows for the more targeted therapy.
Information is power and equipped with better data, clinicians can avoid empirical prescription, a major factor in reducing antimicrobial resistance. To make a real impact on the antibiotic usage within the hospital environment, resources must be made available for clinicians to view the results as they become available. Patient care can be enhanced with rapid methods to obtain identification results with real-time clinical interpretation and action. Central to improved patient outcomes is fast reliable information flow and inter-disciplinary collaborative work between pharmacy, pathology and clinicians.
Barenfanger et al. demonstrated clear benefits from improved intervention involving antimicrobial therapy. Interventions were achieved utilising a computer software program (TheraTrac 2) that links pathology results immediately to pharmacy, and thus any potential problems with a patient’s antimicrobial therapy.
New software can now enable pharmacists to access data in real time and in turn can link this to their knowledge of patients’ current antimicrobial therapies to improve their care. There is ample evidence to suggest pharmacological interventions involving antimicrobial therapy have demonstrated financial savings, and improved patient outcome.(8)
It is unfortunate that in many hospital Trusts the link between ever-improving and rapid technology in microbiology, that is, MS and antimicrobial intervention, is still not as robust and forward-thinking to gain real tangible benefits. Investment in software that improves connectivity, workflow and information management is imperative. Software such as Myla® (Biomerieux) enhances the capabilities of MS technology because the concept is about improved connectivity and information management. The idea is that ‘critical results’, i.e. the most relevant information, is made readily available to clinicians and pharmacists so that ‘interventions’ can become more of the norm.
Future prospects
MS to all intents and purposes in microbiology is still in its infancy. Future prospects are exciting and have opened up new avenues for both clinical and experimental microbiology. Research is constantly pushing the boundaries, with the detection of resistant mechanisms determinants through proteomics of multi-resistant bacteria well underway.(9) MALDI-TOF also holds the potential in the future to directly identify pathogens from biological fluids such as urines. Its greatest potential certainly arises for antibiotic resistance profiling within minutes,(10) which would revolutionise antibiotic stewardship and certainly have an immense effect on the fight against emerging resistant populations.
MS results are promising and strongly indicate that MALDI-TOF-MS will have a significant role to play in the future of modern diagnostic microbiology along with improved communication software and the adoption of a more interventional-like strategy by clinicians/pharmacists.
  1. Ibrahim EH et al. The influence of inadequate antimicrobial treatment of bloodstream infections on patient outcomes in the ICU setting. Chest 2000;118:146–55.
  2. Paxton A. Antibiotic program supersizes impact of molecular testing. CAP Today 2011;25:49–52.
  3. Perez KK et al. Integrating rapid pathogen identification and antimicrobial stewardship significantly decreases hospital costs. Arch Patol Lab Med 2013;137:1247–54.
  4. Anderson NW et al. Effects of solid-medium type on routine identification of bacterial isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2012;50:1008–13.
  5. Emonet S et al. Application and use of various mass spectrometry methods in clinical microbiology. Clin Microbiol Infect 2010;16:1604–13
  6. Ferroni A et al. Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2010;48:1542–8.
  7. Huang AM et al. Impact of rapid organism identification via matrix-assisted laser desorption/ionization time of flight combined with antimicrobial stewardship team intervention in adult patients with bacteraemia and Candidemia. Clin Infect Dis 2013;57:1237–45.
  8. Barenfanger J, Drake C, Kacich G. Clinical and financial benefits of rapid bacterial identification and antimicrobial susceptibility testing. J Clin Microbiol 1999;37:1415–8.
  9. Hrabak J, Chudackova E, Walkova, R. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis. Clin Microbiol Rev 2013;26:103–14.
  10. Steensels D, Verhaegen J, Lagrou K. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of bacteria and yeasts in a clinical microbiological laboratory: a review. Acta Clin Belq 2011;66:267–73.