Elsevier

Mayo Clinic Proceedings

Volume 91, Issue 10, October 2016, Pages 1448-1459
Mayo Clinic Proceedings

Review
New Developments in Clinical Bacteriology Laboratories

https://doi.org/10.1016/j.mayocp.2016.06.020Get rights and content

Abstract

There are a number of changes underway in modern clinical bacteriology laboratories. Panel-based molecular diagnostics are now available for numerous applications, including, but not limited to, detection of bacteria and select antibacterial resistance markers in positive blood culture bottles, detection of acute gastroenteritis pathogens in stool, and detection of selected causes of acute meningitis and encephalitis in the cerebrospinal fluid. Today, rapid point-of-care nucleic acid amplification tests are bringing the accuracy of sophisticated molecular diagnostics closer to patients. A proteomic technology, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, is enabling rapid, accurate, and cost-effective identification of bacteria, as well as fungi, recovered in cultures. Laboratory automation, common in chemistry laboratories, is now available for clinical bacteriology laboratories. Finally, there are several technologies under development, such as rapid phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis for the detection of bacteria in clinical specimens. It is helpful for clinicians to be aware of the pace of new development in their bacteriology laboratory to enable appropriate test ordering, to enable test interpretation, and to work with their laboratories and antimicrobial stewardship programs to ensure that new technology is implemented to optimally improve patient care.

Section snippets

Advances in Traditional Molecular Diagnostics

Nucleic acid amplification tests, such as polymerase chain reaction (PCR), have become part of daily clinical practice. They allow rapid and sensitive detection of microorganisms, including bacteria, as well as viruses, parasites, and fungi, directly from clinical specimens. Until recently, they have been the domain of large, sophisticated laboratories and have typically been ordered and performed one by one. An advantage of bacterial culture is that it enables growth of many different organism

Point-of-Care Molecular Testing

Although rapid panel-based molecular diagnostic tests are not currently CLIA-waived, there are now CLIA-waived rapid point-of-care nucleic acid amplification tests available. These assays take the expert testing traditionally offered in clinical microbiology laboratories and bring them closer to the patient. For example, assays are now available for Streptococcus pyogenes (group A streptococcus) as well as influenza on the cobas Liat System (Roche Diagnostics) and the Alere i system (Alere

Proteomics Revolutionize Identification of Cultured Bacteria

This section is based, in part, on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in clinical microbiology.16

Despite the advent of an increasing number of molecular diagnostics, such as those discussed above, it is unlikely that cultures will disappear anytime soon.17 Cultures detect various types of organisms, making it nearly impossible to completely replicate their utility on the basis of current technology, price, and turnaround time, with

Laboratory Automation

Laboratory automation, involving robotic specimen aliquoting, testing, and reporting, is the standard in chemistry laboratories today. These innovations have been slowly implemented in clinical bacteriology laboratories because of the need for a large number of diverse human activities not easily amenable to automation and because of various specimen types and specimen collection containers used.31 Several companies have developed and are continuing to refine automation systems for use in

Looking Ahead

In the present era of antimicrobial resistance, a clinical need not completely addressed by these aforementioned strategies is rapid phenotypic antimicrobial susceptibility testing. For some resistance mechanisms, such as methicillin resistance in staphylococci, or vancomycin resistance in enterococci, molecular methods may be fairly easily applied, providing rapid susceptibility results, albeit of a limited spectrum. But for many other types of bacteria and most other types of antimicrobial

Conclusion

A number of new technologies have recently been introduced in modern clinical bacteriology laboratories, including panel-based molecular diagnostics for numerous applications, rapid point-of-care nucleic acid amplification tests, MALDI-TOF MS, and laboratory automation. Several new technologies are also under development, including rapid phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis for the agnostic detection of bacteria (and other

Acknowledgments

I thank Nancy L. Wengenack, PhD, Bobbi S. Pritt, MD, Matthew J. Binnicker, PhD, Priya Sampathkumar, MD, Ritu Banerjee, MD, PhD, Scott A. Cunningham, MS, and Emily A. Vetter, Brenda L. Dylla, and Sherry M. Ihde for their thoughtful reviews of this article.

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    Grant Support: This work was supported by the Antimicrobial Resistance Leadership Group of the National Institutes of Health (award no. UM1 AI104681) and the Mayo Clinic Center for Individualized Medicine.

    Potential Competing Interests: Dr Patel receives grants from BioFire, Check-Points, Curetis, 3M, Merck, Hutchison Biofilm Medical Solutions, Accelerate Diagnostics, Allergan, and The Medicines Company. She is a consultant to Curetis, Roche, Qvella, and Diaxonhit; monies are paid to Mayo Clinic. In addition, she has a patent on Bordetella pertussis/parapertussis polymerase chain reaction issued, a patent on a device/method for sonication issued, with royalties paid by Samsung to Mayo Clinic, and a patent on an antibiofilm substance issued. She serves on an Actelion data monitoring board. She receives travel reimbursement and an editor's stipend from American Society for Microbiology and Infectious Diseases Society of America and honoraria from the United States Medical Licensing Examination, UptoDate, and the Infectious Diseases Board Review Course.

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