Legionella PCR vs Culture: Which Test Do You Need?
For routine compliance in the UK, culture is the method that counts. It grows live Legionella from a water sample in a UKAS-accredited laboratory and reports a count you can compare with the action levels in HSE guidance. PCR is faster and very good at ruling Legionella out, but it detects DNA from dead bacteria as well as live ones, so it supports a culture result rather than replacing it. This guide explains how each method works, what the numbers mean, and how to decide which one fits a given problem on your site.
TL;DR
Culture (ISO 11731) is the method behind compliance testing in the UK. It counts viable bacteria, but results take around a week or more.
qPCR returns results much faster and is highly reliable when it comes back negative. A positive does not prove live, infectious bacteria are present.
Use PCR as a supplement: screening, checking whether a disinfection worked, and tracking trends. Keep culture as your formal record.
Testing is not a control. Temperatures, flushing, cleaning and a current risk assessment come first. Sampling checks that they work.
Whichever method you use, the laboratory must be UKAS-accredited for Legionella in water.
Table of Contents
What each method actually measures
The two methods answer different questions, and most confusion comes from treating them as two routes to the same answer.
Culture asks: is there Legionella in this water that can grow? The laboratory filters or concentrates the sample, spreads it on selective agar, incubates it and counts the colonies that appear. The result is given in colony-forming units per litre (CFU/l). Because only living bacteria form colonies, the count is a direct measure of viable organisms. The standard method is ISO 11731, and results can take up to 15 days from the start of the analysis in the worst case.
qPCR (quantitative polymerase chain reaction) asks: is there Legionella genetic material in this water, and how much? The laboratory extracts DNA from the sample and amplifies target sequences. The signal tells you how many gene copies were present, usually reported as genomic units per litre (GU/l). It cannot tell by itself whether the cells those genes came from were alive.
That single difference explains almost everything else in this comparison: speed, sensitivity, false alarms and legal standing.
Culture and PCR compared
Criterion | Culture (ISO 11731) | qPCR |
What it detects | Viable, culturable Legionella | DNA from live and dead cells |
Typical turnaround | Around a week or more of incubation | Hours to a day or two in the lab |
Result unit | CFU/l | GU/l |
Reading a negative | Not detected at the lab’s detection limit | Very reliable indicator that the sample is also culture-negative |
Reading a positive | Live bacteria were present | Needs context: may include dead cells |
Matches HSG274 action levels | Yes | No, system-specific levels are needed |
Cost | Lower per sample | Higher per sample |
Isolate for typing in an outbreak | Yes | No |
The cost point is supported by a review of PCR, culture and antigen methods, but the exact price gap depends on the laboratory, so ask for both quotes rather than assuming.
What UK compliance expects
The HSE’s guidance on testing and monitoring your water system is clear on two points that matter here. Samples should be analysed by a UKAS-accredited laboratory, and the laboratory’s culture method must be able to detect at least 100 Legionella bacteria per litre. In practice that means ISO 11731 culture, which is why it remains the reference method for duty holders.
The action levels in HSG274 are written in CFU/l. A qPCR result in gene units does not map onto them one for one. If you receive a qPCR figure, you cannot simply read it against the culture thresholds and decide you are compliant or in breach.
Two practical consequences follow:
Your formal monitoring record should be culture. If an inspector, insurer or investigator asks for your sampling history, it should be accredited culture results with the method named on the certificate.
Check the accreditation scope. A laboratory can be UKAS-accredited for some tests and not for Legionella in water. Our guide to a five-minute UKAS check shows how to verify this before you book.
Why PCR is attractive, and where it misleads
The speed and the reliable negative
A UKHSA evaluation of real-time PCR against culture on routine and public health water samples found that the negative predictive value of qPCR was between 97.4% and 100%. In plain terms, when qPCR says there is no Legionella, culture almost always agrees. That makes it a strong screening tool. If you need to know quickly whether a set of outlets is clean, a negative PCR gives you confidence days before culture would finish.
The overestimate
The same evaluation found that the positive predictive value was far lower, between 0% and 50%. Many PCR-positive samples were culture-negative. The reason is DNA persistence: dead bacteria, for instance after a thermal or chemical treatment, still carry detectable genetic material. The average difference between qPCR and culture counts was around one log10 higher for qPCR, so PCR typically reads about ten times above culture.
Researchers writing in PLOS Water describe the same limit and note that viability PCR, which tries to exclude dead cells, is still an emerging technique and not yet a routine compliance standard. A multicentre study of viability PCR using propidium monoazide shows the idea has promise, because the dye blocks DNA from damaged cells, but it is not what most commercial laboratories will report to you today.
What this means for a worried duty holder
Imagine a PCR-positive result on a shower outlet. It does not prove that infectious bacteria are present, and it does not prove they are absent. The right response is to look at the system history: recent disinfection, temperatures, stagnation, previous culture results. Then confirm with culture. A PCR-positive that follows a disinfection a few days earlier may just be dead cells. A PCR-positive on an outlet that has run at 30 °C for months is a different story.
Where PCR genuinely earns its place
A UK-led international trial of qPCR for monitoring Legionella in artificial water systems concluded that qPCR is a useful addition to culture, particularly for large or high-risk systems such as cooling towers. Three uses stand out.
Screening many points quickly. If most results come back negative on PCR, you can concentrate culture on the few doubtful outlets.
Checking a disinfection. A sharp fall in PCR counts after treatment gives early evidence that the work has had an effect, well before a full culture incubation finishes. Duty holders need to agree system-specific alert and action levels with their consultant, because HSG274 thresholds do not translate directly.
Trend monitoring in complex systems. A study comparing culture and qPCR on samples before and after two interventions in a residential area found qPCR useful for monitoring and risk assessment, provided results were interpreted with the context of the system.
None of these uses removes the need for culture. They add speed to decisions you would otherwise make blind for a week.
Clinical testing is a different question
Search results on this topic mix two separate worlds. Testing people for Legionnaires’ disease uses urine antigen tests, PCR and culture on patient specimens. Testing a building’s water uses the methods above. UKHSA’s guidance on referring specimens explains that diagnosis needs confirmation, and that typing data are needed to help identify the likely environmental source. PCR gives a rapid answer on a patient sample. Culture provides an isolate that can be typed and matched to a water system.
This is the strongest argument for keeping culture in your programme. If a case is ever linked to your premises, an isolate from your own water, with a clean accredited chain of custody, is what lets investigators confirm or rule out your site. That is a matter for your responsible person, your public health contacts and your laboratory. If anyone on your site has symptoms, they should see a doctor, not rely on a water test.
Swab or water sample?
People often ask whether to take a swab or a water sample. They are not alternatives for the same job. A water sample, taken from an outlet after the correct pre-flush or non-flush procedure for the question being asked, gives a count per litre that can be compared with action levels. A swab takes material from a surface such as a shower head, tap aerator or the inside of a tank, and tells you whether Legionella is living in the biofilm there. It is useful as investigative evidence, for example when you suspect a fitting is a source, but it does not give a per-litre figure. Either can be analysed by culture or PCR, and the method question is separate from the sampling question.
Our article on UK Legionella testing methods and BS 7592 sampling covers how sampling should be done, since a poorly taken sample gives a poor result whichever technique follows.
How to choose: a practical decision guide
Start from the question you need answered, not the method.
Routine monitoring set by your risk assessment: accredited culture. This is the record that supports your compliance.
A one-off urgent check, such as a suspected problem before reopening a building: consider PCR for a fast first look, with culture running in parallel.
Verifying a disinfection or remedial job: culture for the formal clearance, PCR if you need early evidence of a trend.
Cooling towers and other high-risk systems: agree a combined plan with your consultant, including PCR alert and action levels set for that system.
Suspected link to a case or outbreak: culture is essential for typing. Talk to your laboratory and public health contacts before disinfecting, because treatment can destroy the evidence.
Before any of this, ask whether testing is what you need at all. HSE makes clear that how often you test depends on your system and your risk assessment, and the Government’s ten-point approach to reducing Legionnaires’ disease risk puts the weight on controlling the system: temperatures, cleaning, flushing and records. If those controls hold, the need for routine microbiological sampling falls. A new test method does not change that.
Our view: what we tell site managers
We are asked about PCR most often after a bad result, when someone wants an answer today instead of in ten days. We understand the pressure. Our advice is the same each time.
First, a fast result is only worth having if you can interpret it. A negative PCR is good news you can act on. A positive needs the system history beside it, and that is where a site-specific risk assessment and good logbooks pay off. We write bespoke logbook and control programmes precisely so that when a number arrives, someone can say what it means for that building.
Second, do not let a PCR figure become your compliance document. Duty holders are judged against HSG274 and L8, and the thresholds in those documents are culture-based. Keep accredited culture as your formal record and use PCR to speed up decisions around it.
Third, fix the cause. We regularly see repeat positives on sites where low-use outlets, dead legs or tepid cold water are the real problem. No test method, however sensitive, fixes those. Remedial work and a tighter monitoring routine do.
The method matters less than the question, the sample point, the laboratory’s accreditation and what you do with the result.
— Sammi
Getting accredited testing for your sites
We arrange Legionella water sampling and analysis for sites across the UK, with results reported by UKAS-accredited laboratories. Legionella water testing and analysis starts from £55 per sample, and a Legionella risk assessment starts from £185. The assessment decides where and how often to sample, so it is usually the sensible first step if your last one is out of date. Our guide to interpreting Legionella water samples is also worth keeping for the day results arrive.
What to do when a result comes back positive
Whichever method produced it, the sequence is similar.
Do not ignore it, and do not panic. Check which outlet, which method and what the unit is.
Compare culture results with the action levels in HSG274, and ask your consultant to interpret PCR values for your system.
Review recent events: disinfection, temperature failures, building use changes, long closures.
Act on the cause: flushing, cleaning, disinfection or repairs, then resample. Our system disinfection and flushing service covers tank cleaning, disinfection and ongoing maintenance.
Record everything in the logbook, including the decision and the follow-up sample.
If the positive involves showers used by the public, our article on what dutyholders should do after suspected Legionella in showers sets out the steps in more detail.
FAQ
What is the difference between a PCR test and a culture?
Culture grows live bacteria from a water sample and counts them, so it measures viable Legionella. PCR detects and counts Legionella DNA, which includes dead cells. Culture is slower but is the method that matches UK action levels, while PCR is faster and best used for screening and trend checks.
Can PCR replace culture for compliance testing?
Not at present. The HSE expects samples to be analysed by a UKAS-accredited laboratory using a culture method with the required detection limit, and HSG274 action levels are expressed in CFU/l. Researchers describe qPCR as a supplement to culture, not a replacement.
How long does a Legionella culture test take?
Plan for around a week or more. The incubation alone can run for up to 15 days under ISO 11731, and transport to the laboratory adds time. If you need an earlier indication, ask your consultant whether PCR alongside culture is appropriate.
Is a swab better than a water sample?
They do different jobs. A water sample gives a count per litre that you can compare with action levels. A swab examines a fitting or surface for biofilm and is mainly investigative. Your risk assessment should say which you need and where.
Why is my PCR result positive when culture is negative?
PCR picks up DNA from dead bacteria as well as live ones, so it can read higher than culture, especially soon after disinfection. UKHSA research found PCR positives were often not confirmed by culture. Review the system history and confirm with culture before drawing conclusions.
Sources
Testing and monitoring your water system for legionella, HSE
Evaluation of Legionella real-time PCR against traditional culture, UKHSA
Comparison of the culture method with multiplex PCR for Legionella confirmation
An international trial of quantitative PCR for monitoring Legionella
Detection of Legionella by qPCR for monitoring and risk assessment
Referral of specimens for confirmation of Legionnaires’ disease, GOV.UK
Ten-point approach for reducing the risk of Legionnaires’ disease
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