99. AST: Automated Identification & Sensitivities - the Vitek2 with BioMérieux

This week Jame is joined by Nick and Dal from BioMérieux as they take a deep dive into the Vitek2, one of the machines available for performing Automated Antimicrobial Susceptibility Testing.

Note: This episode was produced in collaboration with BioMérieux. An honorarium received from them will be donated directly to charitable causes.

Message from BioMérieux: Every effort has been made to ensure the accuracy of information shared during our podcast appearances. The views expressed by our representatives are in good faith and based on the information available at the time. We accept no liability for any errors, omissions, or discrepancies. For the most accurate and up-to-date product details, please refer to our official website or contact us directly

Transcript

Jame: 0:00

Hi everyone, welcome to The Idiot's Podcast. That's infectious disease insight of The Specialists. I'm James, that's Kate, this is Dal, and over there's Nick, and we're going to tell you everything you need to know about infectious disease.

Intro: 0:11

Soon may the editing come to discontinue the taso, son. One day when the CRP's done, we'll take our leave and go.

Jame: 0:22

Dal, how are you doing?

Dal: 0:24

Yeah, very well. Thank you.

Jame: 0:25

Nick?

Nick: 0:27

Surprisingly well, yes, lack of sleep, but doing good.

Jame: 0:30

Good. So, you guys both worked for BIMERIU. Can you tell us a little bit about yourselves?

Dal: 0:37

Yeah. So well, before joining by Mary, I actually did a biomedical science degree which included a placement year in a microbiology lab. And that's when I first really was out there with the microbiology side of things in the real life. Then I finished my degree, did a couple of years NHS. And then I said I want to see what else is out there. Sort of a vacancy going for biomeria as a field application specialist applied for it and yeah managed to succeed as well. So yeah, now been a field application specialist for four years.

Jame: 1:13

that's what you do now? Yeah, Okay. And Nick?

Nick: 1:17

Very similar to Dal studied for a biomedical science degree up at the university of Aberdeen, Dundee didn't manage to get placement because it was a few years before Dal. So financially NHS couldn't handle placement students, which was unfortunate. So I ended up getting a job really luckily in the virology department down at the Edinburgh Royal infirmary,

Jame: 1:41

and you were there until a few years ago and then you came to Byron Mary II, is that right?

Nick: 1:46

Yes, that's correct. And I've been with Biomerio ever since.

Jame: 1:49

And what's your official title?

Nick: 1:51

Field application specialist, regional team leader.

Jame: 1:55

Oh, so you're Dal's boss.

Nick: 1:58

No I was but now he, is on the same level as me. He has his own regional area to manage to.

Jame: 2:05

Oh, I see. He's snapping at your heels. Okay. And Kate, who I am recording with later, is working for Byron Mary II and she will introduce herself in the next episode. So why are we talking to you today? Well, we would very much like to talk to you about the Vitek 2. And to give a quick introduction, there are some machines used in the microbiology lab which are used for antimicrobial susceptibility testing in an automated sort of high throughput fashion. The Vitek 2 from BioMérieux, the Phoenix. From Becton Dickinson or BD and the micro scan as well and the idiots podcast has done a couple of episodes on how the lab identifies and does sensitivity testing gets pathogens. We've had an episode on the Maloff. It's not our area of expertise, so we tend to leave this to the likes of Louis Plaza from the Let's Talk Micro Podcast. But when bio Mario got in touch, I couldn't resist the opportunity to create a little episode about the Vitech. This is the one that I was trained on in the lab. And so, that led to the creation of this episode today. So, why don't we start by talking about what the Vitek platform is in general, and then we'll talk about the Vitek too. Dal?

Dal: 3:39

Yeah. So, to put simply the VITEC2 system is a identification and a antimicrobial susceptibility testing system. So in terms of ID. It looks at biochemicals and in terms of obviously the AST side of things, it looks at antibiotics at different gradients for MIC testing.

Jame: 3:58

So you can look at both And unlike the other systems, you can use it for ident as well. So the other two just do sounds. And I suppose that the ID sort of facility, a lot of places will have moved over to Moldatov testing now for kind of reasons of high throughput and ease of use. But until the Moldy was popularized in the 2010s your options really for identifying an organism were the old fashioned way, or using the biotech. Did the Vitek 1 do ID, or did it just do sends?

Nick: 4:35

It also did ID as well.

Jame: 4:38

And what's the sort of timeline for when these systems were developed?

Nick: 4:41

So Vitek itself was originally a project, a joint project with NASA. It was said developed as a system to go into the International Space Station to look at a micro organism growth in space

Jame: 4:59

wow.

Nick: 5:00

and it's a bit before my time and there is a couple of articles out there about this research that they did and but soon after that it was realized that it's incredibly useful in a microbiology setting within a laboratory in the hospital. Yes,

Jame: 5:17

So it was then commercialized, and the second sort of generation of these machines is the the Vitek 2, which is the one that's seen more widespread use. And in particular, I know that in Scotland, all the microbiology labs got together and they all decided on one system they were going to adopt, and they all adopted the Vitek 2. I don't know how widespread it is throughout the rest of the UK or the world.

Nick: 5:43

and I mean, down in England we've seen a lot more uptake in Vitech two, especially over the past 10, 15 years. You could probably go round the majority of microbiology labs and either see our small system, which is the Vitech two compact a normal Vitech two, which has got the capacity for 60 samples, or a ATE two xl, which is 120. In some labs, you might even be lucky to have four Vita, two xls. You have some labs that. really put a lot of samples through these.

Jame: 6:16

Yeah. And that's interesting, I didn't realize that it came in different sizes. It makes me wonder Enbra's got.

Nick: 6:23

So they, yeah, they've got three Vitae 2XLs, so they've got capacity for 360 samples at a time.

Jame: 6:30

wow, that's yeah, that's a lot. The Vita 2 Compact, how many samples can that hold at any one time?

Nick: 6:40

That's up to 60.

Jame: 6:43

Also the Compact and the normal one, they both have capacity for

Nick: 6:46

yes, they just have different different settings, whereas the Vitek 2 itself has a automatic saline dispenser for doing your dilutions. The Vitek 2 Compact, you have to do that manually off the system.

Jame: 6:59

Yeah

Nick: 7:00

And we tend to find that the vitae two compacts going back to your earlier conversation about smaller hospitals and laboratories, they tend to have the vitae two compacts. So your Highlands and Islands, your Stornoways, your Shetlands, your Orkneys, or even down south in Lancaster, Furness, these places used to have. Smaller systems as we're seeing now, there's more and more needs and more uptake of use of these systems. So we are seeing places move away to the gradually the bigger systems.

Jame: 7:30

I see. As More and more samples are taken, which is a double edged sword, but a conversation for another time. Okay. Fine. So for those of you that haven't seen it in real life, it looks. From the outside like a big box and there's an intake port and there's a port that puts out and this will link up to a computer which will spit out the results onto your onto your limbs, your lab information management system. But let's talk about how you go about prepping a sample for for use. So the Vitek 2 uses a cartridge system, is that right? And let's talk about the ID sort of cartridge. Whenever I've seen these things, I've seen a cartridge that got a bunch of little windows, and I know that something's happening to those windows, but I know not what. So Dal, why don't you take us through what's going on after you've prepared the sample and how you would prepare a sample for loading into the system.

Dal: 8:34

Yeah. So essentially with your followup work after a biomedical scientist has done their plate reading the next step to that would be obviously to do the identification and AST testing. So with the Vitek 2, we've got enclosed cards. And these cards are basically the size of a debit card. And they've got a range of different wells, as you mentioned. And for the ID side, you've got biochemicals in there. It's exactly the same as how like an API works, but it's more in a card

Jame: 9:00

Okay, so it's exactly the same. So if you're like looking at a gram positive card, would it have inside it catalase, coagulase Lansfield

Dal: 9:13

All the different sugars and biochemicals and metabolites that the ID would require would be in those cards yet.

Jame: 9:21

Is there like chemical reagents which will let you know, do a color change depending on what's positive and what's negative or does it not work like that?

Dal: 9:29

So there are color changes in there, but it's more to do with the turbidity of the actual wells itself when the microorganisms grow in. And inside the vitecta, there's something called the optics, but the way I explain it, In terms of simple terms, it's like a pair of eyes, which are basically looking at the microorganism and how it's growing in each. Well, so especially when it comes to antibiotics as well, the more turbid it is, that means obviously there's growth there, but we want to make sure that growth isn't there. So we know what the minimum inhibitory concentration of the antibiotic is to minimize the infection and eradicate it.

Jame: 10:02

So I guess that's for the SENS cards. That's it. It's just literally turbidity, implying growth in a, in certain antibiotic rich liquid media. Yeah. But for the ID, is there any more complexity to it? So say you've got a little window and it's got coagulase in it. Is it sort of looking at a color change or is it doing anything different?

Dal: 10:25

Just the color change. That's all positive and negative. Yeah.

Jame: 10:29

So and in terms of different kinds of cards for ID, Am I right in thinking that it's a gram positive card which will do your staphs and streps and what have you, a gram negative card for your enterobacteriales and others, and a separate non fermenters card, or am I misremembering that?

Dal: 10:45

Yeah. So there is obviously, like you say, the gram negative gram positive card. There is also a yeast card as well for ID. And then we've also got the NH ID card and that involves like Neisseria, Haemophilus and other fastidious gram negative organisms as well. And then finally, we've also got an ANC ID card, which is more your anaerobic IDs and criniform bacterias as well.

Jame: 11:08

Gotcha. And so the NH card, Neisseria haemophilus and other hassex, or just a weird smorgasbord of other

Dal: 11:17

Yeah. Yeah, that's right. So just other kind of weird and wonderful fastidious organisms, but the most common ones tend to be your gram negative, gram positive and the yeast ID cards really.

Jame: 11:27

Yeah, and non fermenters are done on the gram negative in the cards, is there different sort of media to aid growth, what are the different cards that are commonly used, let's say?

Dal: 11:39

Yeah, so for the SEND cards, they're all again just Muller Hinton kind of agar wells in them. But again, for the, Sensitivity, it's a bit more complex because it depends on the scenario of the isolate that you have. So we've got multiple gram negative AST cards, and it could be that, oh, if you're dealing with a urine, there's a specific gram negative AST card that you would use. But if there's a different scenario that you're using in terms of the source. of the isolate, then there'd be a different gram negative AST card. And the same rule applies for the GP card as well, because obviously these are the size of a debit card. So it depends on what antibiotics are required. And that's something that we tend to go through with the customers right at the start in terms of what their requirements are, what the medics need, these are the antibiotics we have in X, Y, and Z cards, and this is what you'd use in that scenario as well.

Jame: 12:22

Yeah. And although we aren't really touching on it, the The sensitivity cards can be tweaked in terms of what's on there for a particular customer. So Scotland uses the same cards for the whole country, but those cards are determined in consultation with Bimeria.

Nick: 12:40

Yes, they are. And we've got vast customers across the globe that have that exact same arrangement grouped together and work with us to develop a card that suits their needs best.

Jame: 12:53

because after all different antibiotics are available in different countries and there are different patterns of usage which might mean that a gram negative testing arm which is suitable for use in Norway might not be necessarily suitable for use in Scotland or the rest of the UK.

Nick: 13:08

Exactly. The epidemiological factors start to come in.

Jame: 13:11

Yeah, particularly, yeah, I wasn't even thinking of that, but particularly if you're in a place where there's lots and lots of ESBL or other resistance patterns that you need to. Worry about. Okay, yeah, and so in terms of preparing the sample, you will have, say if it's a blood culture, you've done initial tests. initial read and now you've grown a colony up on a blood agar plate. You'll then take a sample of that and put it in a saline solution and get a predetermined turbidity. I think it's 0. 5 McFarland point, and there are special optical reader. Devices that can look at your test tube and calculate that for you and you will put a set amount of that into a Vita card and then it goes into the machine and am I right in thinking for the first few hours the machine is just incubating it at a set temperature?

Dal: 14:06

Yeah, that's right. So it's just that that 37 degrees. And it's just in there just spinning in the carousel itself. And then by then every 15 minutes, the Vitek will then take a reading inside the system. So that's, it's again, all enclosed. You would not have to get involved with it. It's all automated.

Jame: 14:27

And so from time going in to first readout, what's the sort of average time that you will, a point which you will start to get results for ID and sense?

Dal: 14:38

So in terms of ID, it can be as little as three hours for the gram negative and the gram positive ID cards on the AST. It's a little bit longer, but again, it just depends on the organism that you're dealing with. And obviously the antibiotics of question as well. So we tend to say 3 to 10 hours for the ID and then maybe 4 to 18 hours for the AST side of things.

Jame: 15:01

I mean, that's pretty quick, for IDE in particular, that's pretty quick compared to the methods that it was replacing. The more traditional methods and even the sort of API, you would be still thinking about about six hours or something like that.

Nick: 15:16

And you'd also have all the manual. Manipulation as well.

Dal: 15:20

Yeah.

Jame: 15:21

Yeah, okay, let me, let's talk a little bit about sensitivity now. So let's take the gram positives and the gram negatives. Is there any antibiotic sensitivity testing that's particularly problematic with the Vitek 2? Any ones that you need to watch out for?

Nick: 15:41

So yeah, from a breakpoints point of view with yeasts, it can be quite problematic from a European based perspective, because quite often or not, UCAS doesn't provide breakpoints for this. So we just get an interpretation when really from a treatment point of view, we want to actually have that minimum inhibitory concentration. We do find a lot of customers will then look to use CLSI guidelines, which as a company in the clinical setting, we favor. And it's what we are trained to deal with in Europe. And whereas our American counterparts for bio Mario, they will solely deal with CLSI.

Jame: 16:19

Yeah, but that interpretation, problem. I mean, we run into all the time really the, I think that when it comes to the actual, once you've got the MIC, unless you cast of state of the interpretation lies with the microbiologist. That's what they're paid for. You're asking an expert opinion. And so, yeah. The, natural temptation is always if you cast haven't issued a M. I. C. is to just see what C. L. S. I. said about about the matter and then take if they say, Oh, yes, actually, this M. I. C. we consider to be sensitive. That gives you more confidence to use it. And it's not that you're horse trading against each of them, but it's just something that you have to do., So fungal antibiotic sense, that's an issue. And we've yeah, talked about turnaround time. The gold standard that it was being referred against historically was, disk testing on a, on an agar plate. So was that what it was initially compared against?

Dal: 17:30

Yeah, initially it would have been compared to agar dilution. And I think with a lot of our older kind of drug formulations and our older cards, that's what the reference method would have been. But now it's obviously compared to the broth micro dilution and a lot of our referencing now, especially with the new drug formulations and the new cards that we've got coming out, the reference is against the broth micro dilution.

Jame: 17:52

Oh do you have card, do you have card updates that are coming

Dal: 17:56

Yes. So every so often we look at our cards, we look at what UCAS and CLSI guidelines have, and we make sure that the break points fits within the wells of what the current cards have. And if they don't, we make those changes then obviously from an R& D perspective and then obviously have them released for customers as well.

Jame: 18:15

Okay, I see, yeah. And as time goes on, is the number of cards increasing? Or are you trying to consolidate and get more done with one card?

Nick: 18:24

I think very much there's been somewhat of a consolidation and especially in the past five years, there used to be a lot of cards for so many different people for different scenarios. There has been consultation to consolidate. We have had a development where they were looking at increasing the card size so there was more wells on a card. And

Jame: 18:49

Not physically increasing the size, Do you just mean increasing the actual number of wells?

Nick: 18:54

so it would go from the number of wells, I think, correct me if I'm wrong, Dale, it'll go to 102 wells, is that

Dal: 18:59

Yeah, that's right.

Nick: 19:01

So yeah, you'd be able to fit a lot more on the one card.

Jame: 19:04

And so each well is a different sort of bug drug sensitivity with the drug at a certain concentration. Let's say if you were testing Staph aureus against flu clocks, do you, how many wells would you have? Would you have one at the S breakpoint, one at the R breakpoint, and one either side? Or how would you set it up?

Dal: 19:26

So it's all to do with the, basically the Dublin dilutions. So, I mean, each card. In terms of antibiotics can have anything between 15 to maybe 20 antibiotics on there, but it would be to ensure that even the lowest well is still being tested just to make sure that the sensitivity is there or the resistance is there as well. So there are multiple multiple wells per antibiotic just to make sure that the result is accurate and and precise as well

Jame: 19:55

And so yeah, Nick, is there any issues with up because you cast, of course, update their bug drug big points every year? Are the stuff that's in the Vitek database easy and quick to update? Are there any issues with that on the back end?

Nick: 20:10

So as a company we obviously will always want to make sure we fully validate and verify this every single year and as you can imagine there's tens of thousands of different drug bug combinations that come out every single year and being an IVD company this has to go through a rigorous R& D process and it can take time. So we do sometimes have with a validated breakpoint set from the company a little bit of a delay. Now what DAL and some of our other fantastic colleagues have been working on the UK and Ireland is providing what we deem a current UCAST set. And this is Not a globally validated set in terms of it hasn't been through our R and D process, but it's to allow our customers to be on the most up to date breakpoints as soon as they're available for the customer to validate and verify these in house, whilst acknowledging that as they are not validated by the company for use on the system, that this then goes on their validation and verification protocol. And Dal knows a lot about this, so I could potentially hand over to him for a little bit more on that.

Jame: 21:22

Yeah, done.

Dal: 21:23

Yeah, no, just, yeah, just to echo what Nick said, but I think the problem is maybe 10, 15 years ago, there weren't that many UCAS breakpoints available. So a lot of our labs in the UK and Ireland looked up what CLSI breakpoints there are available, what FDA breakpoints are available. I think we are at that transition stage now where there's so many UCAS breakpoints out there now. labs are like, okay, what do we do now? How do we transition to those? It's a lot of time and effort that needs to go into there. But obviously what we can do as a team and as a company is help those customers get something implemented straight away so they can transition to what they were on and what they are to now as well. And obviously another curveball to that is obviously all these source specific break points as well. So you've got urines, you meningitis, pneumonia, specific source break points, and that adds a little bit of complexity as well. But that's something that we're able to do, and we can work with labs about that as well, especially if there's a local decision that they want from the medics on board too.

Jame: 22:21

Gotcha.

Nick: 22:22

Was just going to quickly say, believe it or not, we have had some customers who have still been using old BSAC guidelines.

Dal: 22:28

Yes.

Jame: 22:30

Good. That is back in the day. Yeah. And so and lastly, Dal, let me ask you, what do you guys do for the, those bug drug combinations where the aspirate point is set at 0. 001? Think staph, staph aureus and quinolones they always want you to use the higher doses dosage. Is that an interpretation that just goes on in the computer or is there anything that happens in the Vita to itself?

Dal: 23:00

Yeah. So with those arbitrary breakpoints that you're referring to, UCAS are basically saying we don't want you to use the S category. It's only the I and the R category that we want you guys to use. And we can configure that within the system as well. So again we can implement that, so it's only the I and the R you get to use

Jame: 23:17

I suppose that's a post analytic sort of interpretation, but it's fairly easy, I suppose, as long as you're on the latest version of UCAS to update, which kind of feeds back to what you were saying, Nick. And then in terms of detection of resistance, because you're just checking for phenotypic resistance, you're not checking for the presence of an ESBL or carbapenemase gene. Taking meropenem, for example, if the MIC is two or above, you're flagging that up on the computer side and saying this should go for an e test to make sure that there's no resistance present. Is that about the size of it?

Dal: 23:57

Yeah. So with the Vitek 2, the beauty of it is that it does also have a feature called the advanced expert system. So ultimately basic terms is basically just got a microbiologist within the PC itself, that's giving the lab staff a helping hand. So every result that goes through the Vitek 2 gets compared to the knowledge base within the actual software. And this is also getting updated as every software version that we update without in the field as well. So it's real information, a real database and. Traditionally, the the rule based method was obviously great because there were only a few mechanisms out there years and years ago, and obviously my lab staff knew what they were looking for, but obviously now there's a lot more out there, novel mechanisms, and it's obviously ever growing as well. And that traditional method doesn't really work. So we've got that advanced expert system to make sure. Okay. Also, the lab staff are putting through, it matches with what we've got. In the knowledge base as well. And if it doesn't, it'll flag that up to say, Oh, hang on a minute. Is what you have is actually a pure colony. Is it pure growth? Maybe you need to do some repeat testing there or even confirmation as well.

Nick: 25:04

Dal's saying, we do also have that within that portfolio of that library of different phenotypes. And we have the ability for our customers to submit strains to us if they get a result on their system that hasn't been flagged in the library that's present in the advanced expert system. And we're more than happy as a company to take that information on to help people Increase and improve that library so that it's very much like a community based effort from health care providers around the globe to better health care for everyone.

Jame: 25:41

Yeah, so I think that just about wraps it up. We've talked about the Vitek 2, how it works, what people are using for these days, which is, I think, more and more for high throughput sensitivity testing. But it has this ID function, which made it was very useful in the pre Molotov world. But I suppose what you're saying now is that most people are using it for sensitivity testing. And for that it is reasonably accurate And at least allows for the phenotypic detection of resistance, which you can then go on and examine and further through other methods such as perhaps Carbapenemes, PCR, and Merapenemoeic to give an example and other things like that. Brilliant. Guys, thanks very much for coming on the show.

Dal: 26:28

Thanks for having us.

Nick: 26:29

Thank you very much for having us.

Outro: 26:31

Thank you for listening to the Idiots Podcast, the UK's premier infectious disease podcast. We are supported by the British Infection Association, but they do not have creative control over the episode content, so please don't blame them if we get something wrong. Questions, comments, suggestions, why don't you send them in to idiotspodcasting at gmail. com. Have a five star review in your pocket? Kalman, I would love to have it. Please drop it in your podcast player of choice. We tweet. And if you want to donate to support the show, there's a link to do so in the description, but until next time, I'm Jayme. I'm Callum. See you then. Now that the episode's done, we hope you learned and had lots of fun. So go forth and treat people with some of what you now know.