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Hospital-acquired infection (HAI)

A hospital-acquired infection (HAI) is an infection whose development is favoured by a hospital environment, such as one acquired by a patient during a hospital visit. OUH Microbiology supports screening programmes for methicillin-resistant Staphylococcus aureus (MRSA), Clostridium difficile (C. diff) and carbapenemase-producing Enterobacteriaceae (CPE).

Methicillin Resistant Staphylococcus aureus (MRSA)

Methicillin was the first widely used penicillinase resistant antibiotic and was therefore used in susceptibility testing in the laboratory as a marker of B-lactam producing Staphylococcus aureus.

Despite the fact that methicillin has long been superseded by oxacillin and cefoxitin for testing S. aureus in the laboratory, organisms resistant to these are still referred to as MRSA.

Patients colonised with MRSA pose a risk to themselves and others. MRSA is carried on the skin of patients. It only becomes a problem when the skin is breached either by surgical wounds or by devices that penetrate the skin. In this situation bacteria can cause wound infections and lead to systemic infections such as septicaemia.

Clostridium difficile (C. diff, C. difficile)

Clostridium difficile lives harmlessly in the gut of many people with an incidence of three in 100 for healthy adults and as high as seven in 10 healthy babies. However, in 1978, C. difficile was identified as the primary cause of pseudomembranous colitis and shown to be a primary isolate from the faeces of patients undergoing clindamycin treatment. It is now the major identifiable etiologic agent of antibiotic-associated diarrhoea and colitis and is an important cause of nosocomial disease.

All strains of C. difficile produce the common antigen glutamate dehydrogenase (GDH). Some strains also make the toxins, TcdA and TcdB, which have been studied intensively since their initial recognition as major C. difficile virulence factors. In addition to their contribution to disease, TcdA and TcdB are the primary markers for diagnosis of C. difficile disease.

There are different strains of Clostridium difficile, and some can cause a more serious illness than others depending on the amount of toxin that they produce.

Carbapenemase-Producing Enterobacteriaceae (CPE)

Enterobacteriaceae and Acinetobacter spp are carried commensally on the skin and in the gut of at least 25 percent of healthy people and can be easily spread between individuals in the hospital setting. In vulnerable patients they can cause urine infections, wound infections, pneumonia and septicaemia. CPE and Meropenem resistant Acinetobacter spp. are resistant to many antibiotics and therefore it is of particular importance that carriers of these organisms are identified in areas such as intensive care wards, so as to prevent staff from spreading them to other vulnerable patients.

Specimen requirements

Unlabelled swabs for these requests will not be processed in the laboratory. Samples should be transported to the laboratory as soon as possible. If specimen transport will be delayed, e.g. from primary care, specimens should be stored in a refrigerator until transported to the laboratory.


The OUH Infection Control team recommends the following method for collection of samples for the investigation of MRSA.

Procedure for MRSA Specimen Collection using Sigma-Transwab® (pdf, 725 KB)

C. diff

Non-formed faeces from symptomatic patients are required.

Formed stools, and stools from patients that have tested positive for C. diff in the previous 21 days, are not tested.


Rectal swabs are the preferred specimens for Carbapenemase Producing Enterobacteriaceae screening.

Swabs should be sent in bacterial transport media, but dry swabs are suitable if they are unavailable.

Laboratory turnaround time

Please see Turnaround times

Laboratory method


Swabs are inoculated directly onto a selective chromogenic agar.

C. diff

All samples are screened using enzyme immunoassay for the detection Clostridium difficile GDH (common antigen). Samples positive by this method are then screened for the presence of Toxins A and B using a quantitative indirect immunoassay.

Only patients whose faeces have toxin detected are considered to be at risk of C. difficile disease.


Rectal swabs are broken off aseptically into an enrichment broth into which an ertapenem disc is added and overnight at 37 degrees C in air. This broth is then cultured onto selective chromogenic media.

This method is used in order to enrich low numbers of CPE present in the sample whilst inhibiting the overgrowth of gut flora.

Where to find results of these tests

  • All results are returned electronically where possible (EPR, SunquestICE).
  • Some results may be phoned to clinicians and GPs.
  • Results are never given directly to patients by the laboratory staff.

Further information and contact details

For further information please email:

Confidential patient information should only be sent from accounts.

Microbiology Laboratory Users Manual (pdf, 684 KB)