Hospital-Acquired Infections Workup

Updated: Oct 21, 2021
  • Author: Haidee T Custodio, MD; Chief Editor: Russell W Steele, MD  more...
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Laboratory Studies

Laboratory investigations should be guided by the results of a detailed physical examination and review of systems.

Caution should be taken when interpreting laboratory results because not all bacterial or fungal growth on a culture are pathogenic. Growth on cultures may reflect simple microbial colonization. Consider the following:

  • Clinical presentation of the patient

  • Reason for obtaining the test

  • The process by which the specimen was obtained (eg, a urine culture obtained through a newly placed Foley catheter is less likely to be contaminated by microbial colonization)

  • The presence of other supporting evidence of infection (eg, the significance of bacterial growth on tracheal aspirate culture is strengthened by the presence of radiographic changes and clinical signs compatible with pneumonia)

By the same token, known "contaminant" skin organisms such as coagulase-negative staphylococcus, viridans streptococcus, Micrococcus, Corynebacterium, Propionibacterium, and Bacillus species should not easily be dismissed as contaminants if they grew on cultures of normally sterile body fluids (eg, blood, joint fluid, cerebrospinal fluid [CSF]), especially if the patient was at high risk for severe infections (eg, immunocompromised, neonates). Repeating cultures may help establish presence or absence of infection. Fungal growth on a blood culture should never be dismissed as "contamination."

Bloodstream infections

Among the different methods used to establish the catheter as the source of bloodstream infections (catheter-associated bloodstream infection), the differential time to positivity of paired blood cultures is the simplest. [8] The catheter is confirmed as the source of bloodstream infection if the blood culture from the catheter showed microbial growth 2 hours or more earlier than a peripheral blood culture obtained at the same time. The other methods include quantitative cultures of blood obtained from the catheter and peripheral vein and also, quantitative culture of catheter segment. Unfortunately, quantitative culture is not readily available in most laboratories and culture of the catheter requires pulling out the device.

Multiple blood cultures over 24 hours and appropriate volume of blood sample may increase the yield in cases of intermittent or low-inoculum bacteremia. Fungal cultures should be obtained if fungal infection is suspected. The laboratory should incubate cultures longer for fungus detection than for other pathogens.

Imaging studies such as echocardiography should be considered if thrombosis or vegetations is a concern. Candidate patients include those who have prolonged or persistent bacteremia or fungemia despite antimicrobial therapy or in patients with a new-onset murmur.

In immunocompromised patients, special studies are occasionally requested, such as cultures for nocardia and atypical mycobacteria, cytomegalovirus, and cytomegalovirus antigenemia detection.


Acute phase reactants (peripheral WBC count, erythrocyte sedimentation rate, C-reactive protein) may be elevated but are not specific in distinguishing bacterial from viral pneumonia.

Decreasing oxygen saturation and worsening hemodynamic status are clues to the presence of pneumonia.

The presence of a new infiltrate on chest radiograph is supporting evidence of pneumonia; however, it may sometimes be difficult to differentiate from atelectasis.

Sputum gram stain and cultures may be useful. However, especially in the case of young children unable to effectively cough up phlegm, sputum samples maybe contaminated by saliva and upper respiratory tract organisms. An acceptable sample should have less than 10 squamous epithelial cells, more than 25 neutrophils per low-power field and culture growing a predominant organism.

As in the case of sputum samples, materials obtained via suctioning of endotracheal, nasotracheal, and tracheostomy tubes may not be reliable because these may be contaminated by upper respiratory tract organisms. Other methods to obtain specimens for microbiologic evaluation include bronchoalveolar lavage and thoracentesis.

Efforts to distinguish tracheobronchial colonization, ventilator-associated tracheobronchitis, and ventilator-associated pneumonia may help avoid inappropriate antibiotic use. [32]

Rapid diagnostic tests may be valuable in specific cases. Examples include the direct fluorescent antibody test for Legionella organisms; polymerase chain reaction tests for Bordetella pertussis, Mycoplasma pneumoniae, Chlamydophila pneumoniae; immunofluorescence tests for influenza, respiratory syncytial virus, and Pneumocystis jiroveci; and modified acid-fast stains for mycobacteria.

Urinary tract infection

Urinalysis and urine culture along with clinical findings are essential in differentiating asymptomatic bacteriuria, cystitis and pyelonephritis. The presence of pyuria, bacteria, nitrites and leukocyte esterase on urinalysis makes urinary tract infection likely.

Urinary tract infection is highly likely when the urine culture (obtained by transurethral catheterization) is growing more than 100,000 colony-forming units/mL of a single organism. Urine culture interpretation should be taken with caution as this may lead to overdiagnosis and subsequent unnecessary evaluation and treatment. The following factors should be kept in mind when interpreting urine cultures:

  • Number of colonies and species isolated

  • Method of sample collection

  • Time from collection to laboratory processing

  • Sex of the patient

  • Previous antibiotic use

Although imaging studies are controversial, they are recommended by most experts in evaluating children with first-time urinary tract infection. Renal ultrasonography and voiding cystourethrography are the 2 most commonly used modalities to evaluate for anatomical abnormalities. Renal ultrasonography may also help detect abscesses or phlegmons in patients unresponsive to antibiotic therapy.

Other healthcare-associated infections

Cultures of specimen from the surgical site infection may reveal pathogens and help tailor antibiotic therapy.

Identification of etiologic agents of gastroenteritis was traditionally done with either stool culture or antigen testing. However, the advent of multiplex PCRs able to detect multiple pathogens (bacteria, virus, and even parasites) in a single specimen with short turnaround time are now commercially available and are increasingly used in practice.

Available tests to detect Clostridium difficile include stool culture, enzyme immunoassay for toxin detection, and polymerase chain reaction tests.


Imaging Studies

Special imaging techniques (eg, ultrasonography, CT scan, MRI) may be helpful in evaluating obscure-site infections.