Testing and Treating Infections – and the New Cyrex 12 Autoimmune Pathogens Test


The new Cyrex 12 PAIRS test was released this weekend. It stands for Pathogen Associated Immune Reactivity Screen. In other words, it is looking for infections of various kinds that trigger or exacerbate autoimmunity. Useful. And it got me thinking about testing and treating infections generally.

First,let’s look at the autoimmunity link briefly. We know that there are several triggers or exacerbators of autoimmune disease – some major ones being..

a gluten related disorder (see the TGF site for more on this) and

pathogens such as bacteria, viruses, yeasts and parasites.

Often, these pathogens can lay dormant in your system – you may feel no symptoms either when you got them or when they’re dormant – but you can still be reacting immunologically to them and even have cross-reactions to tissues going on. I’ve talked a lot more about this on the TGF site and in the Gluten Plan, where I have put my whole treatment protocol for autoimmunity for you.

Ages ago, I did a big list of which pathogens are linked to which types of diseases. I never got chance to finish it – I have a massive file in my cupboard! – but now Cyrex have done it for me – and I’ll come back to that a bit later:)

Suffice to say, part of the autoimmune – and chronic disease – puzzle should be to try and identify if a pathogen is causing problems for you. The question is just how you do that.

Best Tests for Infections

First, it can be useful to have a general blood test to look if an infection could be a factor for you.

The usual indicator is what’s going on with your white blood cells. A long time ago, I was taught to take note particularly of what the neutrophils are up to. They tend to go high if a bacterial infection is present and low if there is a chronic virus somewhere.

Eosinophils tend to go up in parasitic infections and allergy.

Basophils contain histamine so, if high, are often a sign of allergy or high histamine reactivity.

Monocytes go up in acute infections.

Obviously, it is a lot more complicated than that but useful stuff I’ve always found – amazing actually what you can get from a blood test at your docs or via the much more comprehensive Functional Blood Chemistry test we do here.

I also advise you get your IgA levels tested. IgA is a good marker of immunity strength generally – as is SIgA which measures mucosal immunity (ie. in the gut, lungs, skin etc. I can’t tell you the number of times I’ve found someone’s low IgA levels have been at least part of the real issue – you can go off killing baddies all you like with protocols etc, but get your immune system in tip-top shape and let it do it for you if it can, then give it some help if it needs it!

You can read more about IgA deficiency here, although note a lot of people have sub-optimal levels rather than an outright immune deficiency disorder, which is what mainstream medicine recognises – as usual.

The docs should be able to check your IgA levels or we can do a Total Immunoglobulins test for you, and we can do stool or salivary SIgA here if you need that.

Then, if you suspect something is going on, there are several ways to check for ‘baddies’.

Finding the Baddies

Can we see them in the gut?

We can do the usual gut stool tests including our favourite DD CSAP2 which acts as an overall gut screen for us, not just for pathogens like bacteria, yeasts or parasites present but inflammation markers, digestive ability, gut immune strength and much more. We often start with that and use it for treatment as is.

Sometimes, we might need to confirm or double-check a pathogen. For example, we might do the Candida SAPS Test to check again for candida and whether it is SAPS positive (ie pathological and not just in your gut).

We might need to look in the small intestine rather than the colon for issues like SIBO (Small Intestine Bacterial Overgrowth), which again you can see in the Gut Tests section and read more about here in my SIBO Factsheet in the A-Z.


Can we find them using DNA testing?

We might also want a different kind of pathogen test, maybe one that includes PCR DNA testing like GI Effects, which is a completely different way of screening and might pick up or confirm something missed in the CSAP3.

The fact of the matter is that no screen is perfect so it is often a combination – if you really need to know! – that works best. I wish it weren’t so, but it is.


Could it be a virus?

Viruses are a bit different in that we don’t tend to pick those up on stool tests. For those, you need specific testing like the Virus Test here or maybe the Cyrex 12 below.

How about Lyme or Borrelia?

Same goes for ticks and spirochete like Lyme, also on that page – the Lyme Test – and we can do any number of co-infections tests too – again the Cyrex 12 below includes some of these markers.

What if they are hidden or we can’t find them?

You can get some infection markers in the various metabolic tests such as the OAT or ONE tests here. These can be quite useful for finding clues in complex cases and then we use follow up testing as needed to confirm or rule out anything suspect. For example, certain markers can suggest a yeast overgrowth or bacterial dysbiosis at the very least.

This is also where the new Cyrex 12 comes in. This is a different approach in that we are looking here for antibody markers – IgG – to pathogens. Is your body reacting immunologically to something somewhere and could that be acting as a trigger, a cross-reactor or an exacerbator of an illness that won’t shift?

Finding an antibody does not mean you have a current infection, but it does suggest you’ve had contact with it at some point and it may be latent and acting as a trigger or cross-reactive. That could be very useful, especially if the usual tests have come up negative to finding any actually present in the body, or the lab’s not been able to culture any. I think it will turn out to be a useful addition to our infection-testing armoury!

I’ve added it to the shop here and given some info in the Overview as usual for you.

So, all in all: it’s not as easy to find infections as you might think, is it?

icon of man with germs attackingTreating Infections Naturally

The whole point of testing for pathogens and infections is to identify an important factor in what’s causing an illness.

In chronic disease: is the body too busy having to cope with a pathogen to be doing its job properly elsewhere in the body and leaving you vulnerable?

Or, as helminth therapy suggests, in some cases, are the presence of certain pathogens in fact helping to keep our over-egged immunity in check?

In autoimmune disease, could a pathogen have been the trigger for the disease or be the nub of a cross-reactivity with body tissues – the body is somehow confusing the pathogen or products from the pathogen’s presence with certain body tissues and attacking it in confusion? This is thought nowadays to be a very likely scenario.

It would be fascinating to know, wouldn’t it, if a pathogen were present and triggering you?

But, controversially, do we ultimately need to know? Only if it helps treatment or answers some questions for you – ie. you’re not going mad at all!

Candida Plan In many cases over the years, I have assumed infection and treated anyway using a combo of immune-regulating, anti-bacterial, anti-parasitic, anti-fungal and anti-viral remedies, much like the Candida Plan or the simpler Gut Plan. It normally sorts most people out.

But, sometimes you do need to know more so you can tweak or treat specifically.

For example, if we have a positive leaky gut test, we might want some info on whether bacterial infection is causing it or food antigens. That’s where we would do Cyrex 2 to look for LPSs – the clues to it being a bacterial infection. We might then go on to do the CSAP3 or GI Effects test if we want to try and see what the bacteria is or confirm the LPS problem.

If someone’s not responding to usual interventions, then we might need to dig a bit deeper.

Importantly, many never even consider that their thyroid autoimmune disease might be related somehow to yersinia, or their gluten related disorder or leaky gut be something to do with cryptosporidium or giardia. But they can be. And that’s where the Cyrex 12 stuff might come in. It’s fascinating and I’ve popped the list of pathogens/diseases into a DropBox doc for you so you can see that here. Note that it also includes Lyme and co-infection markers as well as moulds (molds) – useful.

To summarise testing and natural treatment for infections..

In short: test if you think you need to know and/or you think it will help you treat more effectively. Then, it’s a question of working out how. This is my sort-of thought process in infection cases:

Is infection likely? Blood test for white blood cell counts, IgA and SIga and treat to regulate immunity/get rid of the pathogens, or dig deeper.

Check for presence of pathogens using a stool test (DD CSAP3), Candida SAPs and/or a PCR test (GI Effects). Use other for specifics if needed eg. the Lyme or Virus tests. If your case is complex, you may prefer to start with an overall test like the ONE, OAT or Nutreval as you’ll get markers on loads of different issues then, not just pathogens.

Check for antibody markers, especially if you have autoimmune disease or the risk of one (Cyrex 12) or your illness is not responding to normal interventions – what’s behind it?

For treatment, I’ve put my favourite individual products I recommend all the time on the Infections factsheet in the A-Z here. (In fact, I may use this post to augment that page now I think of it!).

Or, I often recommend people use the Candida Plan with a few tweaks as it sorts the most common issues out.

Use it with the diet if a yeast issue is present, or without the diet if some other type of infection.

The two-stage protocol in it works to prepare and support the body – it’s not just about killing something off. The most usual tweaks are to add an anti-inflammatory such as KapArrest or add something extra for a specific thing found – eg monolaurin for a virus, HCl for low stomach acid etc.

Alternatively, work on something more complex or specific such as SIBO with your chosen health practitioner.

I hope that helps – that started off as a simple new test type post and morphed into a treatise on infections 😉 I’m off for a lie down!





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