Introduction

Infections in cardiothoracic intensive care units are common, either as the primary presenting illness as in the case of infective endocarditis or severe respiratory failure, or as a secondary complication of cardiothoracic procedures. Moreover, infectious complications are known to impact on morbidity and mortality. The sites of infection encountered include surgical site infections (including organ space), device related infections (prosthetic valve endocarditis, ventricular assist device infections), bloodstream infections, line related infections, respiratory tract, gastrointestinal tract and urinary tract infections.

The time taken to identify microorganisms in clinical samples can have an impact in the management of patients with sepsis. Best practice in collection and timely processing of microbiological samples is essential, not only to ensure optimal antimicrobial management and thereby outcome, but also to ensure optimal infection control management of patients within cardiothoracic units. The ability to culture organisms from clinical samples is affected by type and quality of the specimen, prior antibiotic therapy, transportation, storage conditions of samples and time to sample processing. Emerging technologies are enabling faster identification and quantification of pathogens, resulting in more rapid diagnostics. This has the potential not only to affect patient outcome but also to ensure better antimicrobial stewardship by enabling targeted antimicrobial therapy and avoidance of unnecessary antimicrobial use which can lead to adverse effects for patients and encourage development of resistance in bacteria. It is necessary to perform a systematic physical examination before requesting diagnostic tests as this will enable test selection and avoid unnecessary sampling.

The importance of microbiological diagnostics to cardiothoracic units cannot be underestimated and units need to ensure that processes are in place to enable appropriate sampling of patients and as short a time as possible to sample processing whether the unit has an on-site or off-site laboratory. There should be 24 hour access to the laboratory for handling urgent samples and for viewing results. Furthermore, round-the-clock accessibility to infection specialists is crucial to ensuring correct test selection, timely reporting, interpretation of microbiology results, infection control and antimicrobial advice.

Ordering of Tests

Most hospitals use an electronic ordering system for pathology requests, including those for microbiology. Testing protocols can be set up to ensure that the appropriate range of tests is ordered for different clinical scenarios. For example, patients admitted with severe respiratory failure for ECMO will require extensive testing on admission to critical care (see Table 6.1 for guidance on test selection for this scenario) whereas patients admitted for elective cardiac surgery, who have no complications, will only require preoperative screening samples. Electronic ordering systems can be set up as specimen or sample type based. It is important to ensure from the outset that the way the system is configured not only allows ease of ordering for the clinical user but also includes a degree of demand management to reduce inappropriate testing. Electronic test ordering also allows the development of testing sets whereby a standard protocol for microbiology testing can be agreed according to the patient’s circumstances, and the same testing strategy can be followed each time. This can be beneficial in cases of severe respiratory failure on ECMO where an infective cause is suspected or for patients who develop postoperative sepsis.

Correct Sampling Procedures

General principles apply to collection of all microbiology samples. They should be collected at the correct time, using the correct technique, the correct volume and in the correct specimen containers. Lids must be tightened securely as leakage may mean specimen rejection, and clinicians and laboratories must ensure that the correct procedures are followed so that samples are transported safely and in a timely manner to the laboratory. Samples requiring immediate attention for processing should be notified to the laboratory in advance and identified as urgent. All samples should be transported with completed information identifying the patient, time and date collected, tests required and antibiotic history. This may be in bar code format or with a physical request form. Samples with risk of infection should be identified by the clinical user and visible to the laboratory handling the sample. Where possible, samples should be collected prior to antibiotic therapy but this should not lead to delays in managing the patient or administering antibiotics.

Hand hygiene should be performed before and after specimen collection. Personal protective equipment (gloves, waterproof apron) is required during specimen collection when contact with bodily fluids is anticipated. Masks may be required for collection of respiratory samples, for example with sputum induction.

Blood cultures are taken when bacteraemia is suspected and should be taken via a dedicated venepuncture, peripherally, rather than through an existing line. Where endocarditis or device related infection is suspected, up to three sets can be taken at separate times over a 24 hour period. However, it is the actual volume of blood that is important, therefore inoculating one bottle with the correct volume of blood is of greater value than sharing the blood volume between multiple bottles. Local procedures should be followed when taking blood cultures to minimise the risk of contamination with skin flora. When using vacuum blood taking systems, care should be taken that blood cultures are inoculated first before filling other blood tubes. This is to prevent the possibility of bacterial contamination from blood tubes entering the blood culture bottles, resulting in a ‘pseudobacteraemia’ assigned to the patient.

Stool samples should only be sent for microbiology testing when an infective cause is suspected for patients with diarrhoea. The Bristol stool scale can be used to identify diarrhoea stools where types 5–7 indicate diarrhoea. Clostridium difficile should be considered as a cause of hospital acquired infective diarrhoea in cardiothoracic centres and requested as a specific test. Laboratory testing should follow national testing guidelines to ensure optimal diagnosis. In the UK this amounts to a combination of tests looking for presence of the C. difficile organism and the presence of toxin.

Care should be taken when obtaining respiratory samples that sputum is collected rather than saliva. Physiotherapists can help with obtaining a good quality respiratory sample. Any respiratory sample obtained in a trap should be transported in a leak-proof CE marked specimen container. Lower respiratory tract samples can be obtained by directed or non-directed BAL. Respiratory samples in particular must reach the laboratory in a timely manner and should be processed within 2–3 hours to maximise the chance of culturing respiratory tract organisms.

Wound swabs are best obtained after first cleansing the wound. This reduces the risk of contamination of the sample with therapeutic agents that may be contained within the dressing material. Dry swabs should be moistened with sterile water (or saline) or transport media. Where possible the whole wound should be swabbed using a zigzag movement while rotating the swab.

Fluid from vesicular lesions can be aspirated or swabs used to collect the vesicular fluid and inoculated into viral transport media (VTM).

Urine samples are collected as a midstream sample after first cleaning the urethral meatus with soap and water or saline. Disinfectants should be avoided as they can irritate the urethral mucosa. However, the vast majority of patients in ICU will have a urinary catheter in situ. Catheter specimens of urine should only be taken where urosepsis is suspected. The correct local procedure should be followed and urine sampled through the catheter sampling port.

If urine samples cannot be examined within 2 hours then they should be refrigerated until they can be processed by the laboratory. Urine samples held at room temperature will allow overgrowth of bacteria, affecting the result. The addition of boric acid to urine containers will preserve the urine sample for longer where transport delays exist.

Antibiotic Susceptibility Testing

Performing antimicrobial sensitivity testing is another important function of the microbiology laboratory. The aim is to inform antimicrobial treatment decisions and detect antimicrobial resistance. Sensitivity testing requires live organisms and is performed using a variety of testing methods. Manual disc diffusion assays are the mainstay of antimicrobial testing for most organisms in UK laboratories, alongside gradient diffusion methods (including E-tests). Disc testing provides a qualitative measurement, recording the organism as sensitive, intermediate or resistant. More qualitative methods that provide a more accurate minimum inhibitory concentration (MIC) are required for organisms that give borderline results with disc diffusion methods or where a more accurate measure is required, for example in management of endocarditis. In addition to manual methods, there are automated methods commercially available.