Best use of common microbiology tests

Best use of common microbiology tests

This section has flowcharts and background information to help referrers provide optimal testing for the commonest tests, according to current best practice.

Urine culture

Flowchart for UTI diagnosis:

The diagnosis of UTI rests primarily on the presence of new
onset urinary symptoms
, with culture confirmation in certain situations:
  • Treatment of asymptomatic bacteriuria is not recommended*, and has been shown to increase the risk of subsequent symptomatic UTI in women (by causing imbalance in the vaginal microbiome)

* Pregnancy and pre-operative urology are exceptions

Nitrofurantoin resistance is rare amongst uropathogens in our population:

It is therefore highly likely to be effective in people with symptoms of uncomplicated UTI, without the need for culture and susceptibility testing

  • Resistance to other antibiotics is more common, so if nitrofurantoin cannot be used then culture is recommended
Urine dipsticks have limited usefulness:
  • Good sensitivity: negative leucocyte result makes UTI unlikely
  • Very poor specificity: a positive result does not necessarily indicate UTI

A high proportion of elderly patients will have positive leucocytes in the urine under normal circumstances.

Many urine samples are contaminated by perineal flora, meaning:

Uropathogens may be missed due to overgrowth of contaminants (underdiagnosis). Contaminants may be mistaken for uropathogens (overdiagnosis).

  • Encourage patients to provide good quality MSU samples
  • An in-out catheter can be used to provide a good quality urine sample** in patients who find it difficult to provide an uncontaminated sample e.g. cognitive or neurological impairment.

** It is important to state on the request form that a clean catheter has been used to sample, as the lab will treat these samples differently.

Diagnosis of catheter UTI is difficult:

All catheters, unless freshly inserted, will be colonised with bacteria, making urine cultures very difficult to interpret.

  • The most accurate way to diagnose catheter UTI is to remove the existing catheter and obtain either an MSU, or a sample from a freshly replaced catheter**

** It is important to state on the request form that a clean catheter has been used to sample, as the lab will treat these samples differently.

Wound swab culture

Flow chart for use with wound swabs

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Beta-haemolytic streptococci and Staph. aureus are the main causes of skin and soft tissue infection and are susceptible to empiric treatment most of the time, without the need for culture confirmation.

Flucloxacillin and cefalexin are 100% active against beta-haemolytic streptococci and ~90% active against Staph. aureus in our community.

  • Empiric flucloxacillin/cefalexin treatment will therefore be effective for the vast majority of people with skin and soft tissue infections, and a wound swab to confirm the bug is not necessary.
However, in certain situations the risk of resistance to empiric treatment is higher.

Due to a different spectrum of potential bugs causing infection (e.g. bite wound, wound sustained in water or contaminated with soil, surgical wound), or;

Due higher risk of drug resistance (e.g. history of MRSA, not responding to empiric treatment).

  • In these situations a wound swab may be of use to look for bugs that may not respond well to empiric antibiotics.
Wound swabs are often taken to ‘check for infection’ – this is not the correct use of a wound
swab, as it cannot answer that question.

Unfortunately a wound swab cannot tell you whether a wound is infected or not, it can only tell you if there happen to be bugs there.

  • All wounds will be contaminated to some degree with bugs, whether they are infected or not, and a positive wound swab simply reflects this.
A positive wound swab culture does not necessarily mean the wound is infected or that antibiotics are required.

This is a commonly held misconception. Determining whether a wound is infected relies on the clinical assessment of the wound and looking for clinical signs of infection e.g. spreading redness, increased swelling, exudate.

  • A wound swab does not help with this decision.

If there is clinical uncertainty as to whether a wound is infected, it is better to arrange repeat assessment of the wound to try to decide if it is infected, rather than take a swab.

  • We can all do our part to reduce unnecessary antibiotic use by not swabbing wounds that don’t have clinical signs of infection.
Throat swab culture

Flowchart for patients presenting with sore throat

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Most sore throats are due to viral infection.

Around 10% of people have throat colonisation with Group A Streptococcus, so if ten people with viral sore throats have a throat swab performed, on average, one will be incorrectly diagnosed with ‘Strep throat’.

  • Considering how common sore throats are, this represents a lot of misdiagnosis!
  • The flow on effect of this is a lot of unnecessary antibiotic use.
  • Antibiotic prescribing in response to sore throats represents a significant proportion of overall antibiotic consumption in the community.
The focus for throat swabbing should be in those with risk factors for rheumatic fever, and in those with severe symptoms who are at risk of suppurative complications (e.g. quinsy).

All attempts should be made to reduce throat swabbing and antibiotic prescription in people not in these groups.

The laboratory doesn’t routinely do susceptibility testing for Group A strep (Streptococcus pyogenes) because it is always susceptible to penicillins and other beta-lactams.

If your patient is allergic to penicillins, be sure to put this on the request form, as this will prompt the lab to test susceptibility to alternative antibiotics.

Faecal pathogen testing

Flow chart for use with faecal PCR

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Both viruses and bacteria commonly cause acute gastroenteritis in New Zealand.

The vast majority of cases are self-limiting and do not require antimicrobial treatment.

  • In some cases antimicrobial treatment can be harmful.
In most instances, regardless of the cause of gastroenteritis, the appropriate management is supportive and aimed at preventing dehydration.

Therefore, faecal testing is aimed at people or situations where a result may prompt some kind of different action to standard supportive care. These include:

Situations where there may be a lower threshold for treatment, either due to disease severity or patient vulnerability:

  • Diarrhoea not improving after 5-7 days
  • Aged under 5 or over 70 years
  • Bloody diarrhoea
  • Immunocompromised

Situations where different organisms may be implicated, which may require specific treatment:*

  • Rural residence/exposure
  • Recent overseas travel
  • Raw seafood ingestion

Situations where there may be Public Health implications:

  • Patient is a food handler
  • Patient is part of a possible cluster or outbreak

* It is particularly important to include this information in the clinical details, as the laboratory may do additional testing to detect organisms that aren’t detected by the standard PCR e.g. Vibrio infection from shellfish ingestion.

Faecal pathogen testing is now done by PCR (polymerase chain reaction), rather than culture.

Testing is highly sensitive and detection of a pathogen does not always imply it is the cause of a patient’s symptoms.

  • Asymptomatic carriage of organisms is common, especially in pre-school children.
Sputum culture

Flowchart for use with sputum culture

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The upper airways and mouth are very heavily colonised by bacteria under normal circumstances.

Many of these bacteria are the same organisms implicated in community-acquired pneumonia (CAP) and other respiratory tract infections.

Sputum samples tend to become contaminated by these organisms when they pass through the upper airways and mouth to be collected. It can be very difficult to tell if growth of an organism represents oropharyngeal contamination vs lower respiratory tract infection.

  • For this reason, sputum samples have very limited usefulness for informing management decisions, and should usually be avoided.
Sputum samples are often sent on patients to ‘check for bacterial infection’ in the setting of a productive cough.

Because of the difficulties in interpreting colonisation vs infection, sputum samples are very rarely useful for this purpose.

  • The predictive value for bacterial lower respiratory tract infection is low.

Clinical assessment, rather than sputum culture,is required to make this determination e.g. looking for evidence of consolidation to indicate CAP.

  • A productive cough with a positive sputum culture is not in itself an indication for antibiotic treatment.
Due to the limitations of sputum culture, it is not recommended as part of the routine assessment of community patients with acute or chronic productive cough, exacerbations of COPD or asthma.
  • It also has a limited role in patients with CAP, and should only be requested if there is a lack of response to first line treatment.
In those with cystic fibrosis or non-CF bronchiectasis, sputum culture may be of more value.
  • This is to monitor for changes in colonising organisms, which may affect prognosis or alter empiric antibiotic treatment of exacerbations.
In patients with chronic cough and other systemic features (e.g. weight loss, night sweats) or
x-ray changes, consideration should be given to tuberculosis if they were born in areas where TB is more common (e.g. the Pacific, South or South East Asia, NZ in the earlier stages of the 20th century) or have a known contact history.
  • TB/mycobacterial culture needs to be specifically requested on the form.