Art and Science of Laboratory Medicine

Art and Science of Laboratory Medicine

Friday, December 9, 2016

Fungal Snowman

Beautiful petri plate snowman by Michelle Travis, UK


Original image:
Getting into to the Christmas spirit in York, UK

 Source: Facebook via Michelle Travis


Whole genome sequencing cannot yet be used to determine antimicrobial susceptibility

EUCAST experts publish report where they show that whole genome sequencing (WGS) cannot yet be used to determine antimicrobial susceptibility of many important bacterial species.

Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST).

The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values (ECOFFs) in order to improve differentiation of wild type from non-wild type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretative criteria for WGS-based predictive AST. Only datasets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. In order to facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical labs remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on prior culture since analysis directly on specimens remains challenging.

For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.

Read the report:
EUCAST_publication_WGS-AST.pdf

CMI, Clinical Microbiology and Infection

Thursday, December 8, 2016

Study indicates a genetic test may show which chemotherapy patients are at risk for serious blood clots

Chemotherapy is known to carry a risk of venous thromboembolism in cancer patients, a particularly common risk in frequent cancers like breast cancer. But a genetic test may predict which of these patients are most likely to develop such serious blood clots, researchers report.

VTE is preventable through prophylaxis treatment with heparin, an anticoagulant. But because a side effect is less controllable bleeding, the drug is not routinely recommended to patients undergoing chemotherapy.

Researchers examined 4,261 Swedish women diagnosed with primary invasive breast cancer between 2001 and 2008. Risk stratification was based on chemotherapy use and genetic susceptibility, which was determined by a risk score assessing nine genes involved in VTE. Patients ranked in the highest 5 percent were classified as having a high genetic susceptibility.

Patients were followed for a median of 7.6 years, and 276 experienced a VTE during that time.

Read more:
Blood Clot Risk in Breast Cancer Patients Seen via Gene Test

Source: Breast cancer news

Wednesday, December 7, 2016

The good and bad of microbiology lab automation

Here is a summary of the potential quality benefits of “Total Lab Automation” (TLA) systems (e.g. Kiestra, Biomeurieux, Copan Wasp). You might be involved in a business case for one for your own laboratory.

Main advantages:
  • Plate tracking
  • Less menial tasks
  • Better plate spreading
  • Less plate contamination
  • Storage of digital images of plates
  • Standardised incubation times
  • Less time out of the incubator
  • Remote plate reading
  • Plate checking
  • Plate interpretation
Disadvantages:
  • Redundancy of staff
  • What happens if it breaks down<
Read more:
“The good and bad of lab automation….

Source: Microbiology matters
Image: Michael

Tuesday, December 6, 2016

MALDI-ToF - Benefits and Limitations in Microbiology

Helping clinicians quickly and effectively address the medical concerns of their patients should be the ultimate goal of any clinical microbiology laboratory. Delivering on this goal can be especially important when a patient presents with a bacterial or fungal infection. MALDI-ToF can help improve patient outcomes by speeding diagnosis and improving the quality of care.

There are many benefits to incorporating MALDI-ToF to aid in identification of microorganisms. Identification with MALDI-ToF is a relatively simple process. The process can reduce the time needed for identification and diagnosis from days to hours. There are, however, some limitations to MALDI-ToF. Some organisms may require repeat analysis and additional processing, and some closely related organisms are not differentiated and may cause challenges with identification. Also the initial purchase price of the equipment is high, which may limit the types of labs that can adopt it.

While not all laboratories are capable of widely adopting MALDI-ToF, those that can, probably should. MALDI-ToF may promote better patient outcomes through speedier diagnosis and information to influence efficacious treatment for many bacterial, yeast, and mycobacterial infections, greatly improving the quality of clinical management and patient care.

Read more:

MALDI-ToF is poised to speed diagnosis for bacterial and fungal infections(MLO)

MALDI-ToF principle (Frontiers Microbiology)

Source: MLO
Image: Juha Wahlstedt

Syphilis is coming back

Over the last few decades, an age-old infectious disease has been re-emerging globally: Syphilis. Using techniques to analyze low levels of DNA, an international research team headed by the University of Zurich has now shown that all syphilis strains from modern patient samples share a common ancestor from the 1700s. Furthermore, their research demonstrates that strains dominating infections today originate from a pandemic cluster that emerged after 1950, and these strains share a worrying trait: Resistance to the second-line antibiotic azithromycin.

Infection with the bacteria Treponema pallidum subsp. pallidum (TPA) has been re-emerging globally in the last few decades; more than 10 million cases are reported annually. Yet the reason for the resurgence of this sexually transmitted infection remains poorly understood.

Philipp Bosshard from the University Hospital Zurich is continuing to collect Swiss patient samples in order to further study the clinical aspects of the work. The researchers are convinced that this type of analysis will open new opportunities to develop a comprehensive understanding of the epidemiology of syphilis – a devastating disease that persists to this day, despite the availability of treatment.

Read more:
Re-emergence of Syphilis Traced to Pandemic Strain Cluster

Source: University of Zurich
Image: Microbeworld

Monday, December 5, 2016

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