Tag Archives: malditof

“Nothing is perfect..”

Confessions of a Microbiologist,

Apologies for the paucity of posts recently. I have had an unwell child.

MALDI-TOF (Matrix Assisted Laser Desorption & Ionisation- Time Of Flight) has revolutionised microrganism identification in the past decade, and in particular bacterial identification in the microbiology laboratory. It will continue to evolve into fields such as filamentous fungi, mycobacteria, antimicrobial resistance etc.

Rarely has such an innovation been so rapidly and comprehensively adopted by the laboratory community. And you can see why. It’s quick, it’s easy, it’s cheap (the consumables are anyway) and it’s reliable.

But it’s not perfect….

Some well known identification limitations are listed below where MALDI-TOF struggles to give the microbe a label, or at least one which fits in with our pre-defined beliefs.

Take the following well known, and not so well known examples…

  • E. coli and Shigella species
  • Streptococcus pneumoniae and Streptococcus mitis
  • Bordetella pertussis and Bordetella bronchiseptica
  • Klebsiella oxytoca and Raoultella ornitholytica
  • Shewanella putrifaciens and Shewanella algae
  • Proteus vulgaris and Proteus penneri
  • Klebsiella pneumoniae and Klebsiella variicola
  • Haemophilus haemolyticus and Haemophilus influenzae
  • Serratia ureilytica and Serratia marcescens

There are many more. Please feel free to suggest others that you have come across. There will be even be differences between different MALDI-TOF platforms, e.g. Bruker and VITEK MS.

Most of the time it does not matter too much from a clinical point of view. Some of the time, it does, and we need to try and clarify with molecular or biochemical means.

It shouldn’t surprise us however that the identification is not perfect. All identification systems are essentially typing systems in disguise, and they all have databases or libraries at the core of their function..

  • “APIs” are a typing system based on biochemical reactions.
  • MALDI-TOF is a typing system based on proteonomics.
  • 16SRNA sequencing is a typing system based on nucleic acid sequences.

Identification systems therefore suffer from the inherent problems of all typing systems. No typing system can be matched exactly against any other typing system.

For all typing systems the ability to group isolates and the ability to discriminate them is a trade-off of sorts. For MALDI-TOF, the bigger the databases get, the more the system can discriminate, and thus the more it can potentially differ from the original (textbook) identification.

So no system is perfect, including MALDI-TOF.

But it’s very, very good….

Michael

“Too soft, too generous, too nice, and too slow…”

Antimicrobial Resistance, Confessions of a Microbiologist, The Art of Microbiology, , ,

Guidelines for antimicrobial stewardship often include only a cursory mention of the role of the clinical microbiology laboratory, which is a shame, because in my opinion it is one of the key areas where real change to anti-microbial stewardship can be effected. (The other key area is in the writing of sensible narrow spectrum empiric antibiotic policies.)

But we don’t help ourselves…. Speaking generally, I think clinical microbiology laboratories are notoriously bad at antimicrobial stewardship.

Why?

Several reasons actually.

Because we are too soft: We often release antimicrobial susceptibilities from the laboratory even when we have no idea what is going on with the patient. I.e. no clinical details have been provided. Therefore we think nothing of releasing a range of antibiotics to the clinician when we don’t actually know what is wrong with the patient, whether they have an infection, and how severe it is.

Antibiotic susceptibilities should not be released unless the laboratory has reasonable evidence that they are required.

Because we are too generous: We are happy to test a whole range of antibiotics (often up to 20 for the one isolate!), “just in case” one of them might need to be used. This range often includes both narrow spectrum and broad spectrum agents. Probably over 95% of all the susceptibilities that we test and report are never utilised.

We need to dramatically reduce the range of antibiotics that we test for and we need to focus our reporting to the narrowest spectrum antibiotics that we can get away with.

Because we are too nice: We have a low threshold for releasing antibiotic susceptibilities on “putative pathogens“. By doing this, we have just given the green light for the clinician to classify a putative pathogen as an actual pathogen, and therefore start/continue antibiotics.

If we have isolated a putative pathogen, let’s keep it putative. Report the organism, and ask the clinician to make a clinical assessment, and then to get back to the laboratory if susceptibilities are required.

Because we are too slow: We are certainly quicker than we used to be, thanks to MALDI-TOF, smart incubators, and increasingly rapid PCR platforms, but we need to be quicker still… We need to get rid of self-congratulatory, retrospective infectious serology testing and channel our test budgets into real-time diagnosis with PCR or similar, and on patients who fulfil well defined clinical criteria for testing. We need to get rapid molecular platforms for STDs into Sexual Health clinics so they are not required to prescribe an antibiotic for everybody who walks through the door. We need to increase Influenza and RSV testing during the winter season to try and reduce unnecessary antibiotic prescribing for viral infections.

Not only do we need to be quicker, we also need to be smarter…

The clinical microbiology laboratory doesn’t score very well in the antimicrobial stewardship report card. We need to be bold and innovative to change things for the better.

But it is entirely up to us…

Michael

“In a world of its own…”

Confessions of a Microbiologist, ,

Onychomycosis_due_to_Trychophyton_rubrum,_right_and_left_great_toe_PHIL_579_lores

Dermatophyte mycology I have always found a bit of a mystery, and even as a clinical microbiologist it has never really ignited my passion. All those microconidia and macroconidia are completely lost on me. I am comforted however by the fact that there are people within my laboratory who are excited by this subject and take pride in being good at it.

The thing which intrigues me about this area of microbiology is how long it takes to get a culture result from the skin scrapings and nail clippings….Nothing to do with the lab staff of course, that is just the way it is for this branch of microbiology, which has not changed much in decades.

Two weeks, three weeks and counting, with no real sign of this turnaround time coming down. (Maldi-tof of filamentous fungi may help a little in the future with regards to this.)

Having said this, I have never ever had a complaint from a clinician about the length of time it takes to produce a mycology result from a skin scraping or nail clipping, and this in itself says a few things to me about mycological culture and its clinical implications. In a smallish proportion of cases the culture result does have an impact on diagnosis and subsequent management of the patient, but this cohort of patients is small and generally as a group are not “sick” in the more traditional sense of the word.

As Bacteriology Automation systems begin to become commonplace, dermatophyte mycology is starting to become an increasingly isolated sub-speciality, requiring a different skill set from most of the other samples.

I sometimes wonder if all the skin scrapings and nail clippings in the country (what a thought!) should be packaged up and processed at the one laboratory. To be frank, a day transporting the samples makes little difference when your average turnaround time is three weeks…..

But then again, maybe not. I go back to my first paragraph, “some people are excited by this area”, and all clinical microbiology laboratories need people that are impassioned by their work…..

Michael