Laboratory diagnosis of HAI

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Republic of Iraq
Ministry of higher
Education and
Scientific research
University of Baghdad
College of Medicine
2019-2020
Laboratory diagnosis of Hospital acquired infections
Written by: ‫عارف‬ ‫رأفت‬ ‫كرار‬
Supervisor: ‫البياتي‬ ‫باسم‬.‫د‬.‫أ‬
3rd
Grade, Group-C3-
Phone no. : +9647732096972
Email address: karrar.raafat1800c@comed.uobaghdad.edu.iq
2020© Infectious Diseases Module

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Introduction:
Hospital acquired infections or HAIs are Infections which are acquired from
hospitals are called nosocomial infections. If the organisms come from another
patient it is called cross infections and if the patient himself carries the infection
to some other site then it is autoinfection. Infection may become apparent
during the stay of the patient in the hospital or after his discharge from the
hospital.
Hospital-acquired infections (HAI) are a global problem and a major public
health concern in hospitals throughout the world. Mostly caused by multi drug
resistance (MDR) organisms, HAI significantly contributes to increased
morbidity, mortality, and hospital cost. HAI is also a major global safety
concern for both patients and health-care professionals.
In developed countries, HAI rates of 5% to 15%, sometimes up to 50%, have
been reported among hospitalized patients in the regular wards and intensive
care units (ICUs) respectively. In developing countries, the problem is likely
much higher, and yet, the magnitude of the problem remains underestimated or
even unknown largely because HAI diagnosis is complex and surveillance
activities which requires expertise and resources, are lacking in most of these
countries. Furthermore, infection control practices remain rudimentary as most
hospitals lack effective infection control programs and trained professionals.
Quantification of HAI is needed through an effective surveillance system in
developing countries to understand the burden and help to justify resources
dedicated to infection control.
Hospital mode of infection can be through Direct Contact, e.g. hands, clothing,
etc., or airborne aerosols, contaminated food and water or contaminated hospital
equipment and instruments. (1)

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Commonest types of hospital acquired infections and their main causative
agents (bacteria, fungi or virus) in relation to important Laboratory and
diagnostic methods will be discussed.
There are many types of nosocomial infections such as:
1- UTIs: urinary tract infections or catheter induced infection.
2- Nosocomial pneumonia or ventilators acquired pneumonia.
3- Catheter-related bloodstream infection (CRBSI).
4- Surgical site infections (SSIs).
5- Hospital epidemics of diarrhea and vomiting.
6- Clostridium difficle infection.
7- Sepsis.
8- Hemodialysis viral infection (HIV, HBV, HCV). (2)
Laboratory diagnosis for commonest hospital acquired infections:
In order to reach the diagnosis for these commonest four HAIs. Laboratory
diagnostic tests and methods should be done as follows:
1- UTIs: are very common in the clinical microbiology laboratory. UTIs are
more common in women and girls than men.
Laboratory diagnosis (Urinalysis):-
 The presence of WBC in urine sample under microscope absolutely
indicates the presence of infection.
 Urine dipstick tests (i.e. nitrate-reductase and leucocyte esterase
detection).
 Urine culturing a test to find germs (such as bacteria) in the urine that can
cause an infection. This method is done through prospective steps :
a- Specimen collection: In adults, most urine specimens for laboratory
examination are obtained by the clean catch-voided midstream
technique. This technique is widely accepted and applied because it is
simple, inexpensive and non-invasive and there is no risk of

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complications disadvantage of this technique is that the urine can be
contaminated with commensal bacteria during its passage through the
distal urethra.in young children Supra-pubic aspiration is the best
method to avoid urethral contamination, but it is infrequently used
nowadays because it invasive, uncomfortable and time-consuming.
Other way, straight catheter technique is the next-best technique to
obtain urine specimens with minimal contamination risk. But of course
have some disadvantages.
b- Specimen transportation and storage : inoculation of urine specimens
should be done within 2 h after collection however, it have to be stored
in tubes with preservatives up to 24 h at 2–8 °C to prevent
microorganism death.
c- Result interpretation: a positive result of urinary tract infection should
exclude the genus uropathogenes by sensitivity tests or under
microscope by gram staining.
 UTIs causative agents include: Escherichia coli (almost 80-85% of cases)
due to uncomplicated or upper UTIs. Other organisms: Proteus,
Klebsiella, and Enterococcus. (3)
2- Nosocomial pneumonia (ventilators & non ventilators acquired): the
second most common nosocomial infection and accounts for 15–20% of the
total. HAP refers to any pneumonia contracted by a patient in a hospital at
least 48–72 hours after being admitted.
 Main causative agents’ bacterial (90%): Staph.aureus and Pseudomonas
aeruginosa, Streptococcus pneumonia and H. influenza. (5)
Less likely to
be found: klebsiella. Viral (<10%): Respiratory Syncytial Virus and
Influenzae virus. (4)
 Laboratory and diagnostic methods are:
a- Chest X-Ray: we can observe respiratory insufficiency, purulent
secretions, newly developed infiltrates.

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b- Blood sample :( red and white blood cell count, differential cell count,
creatinine and urea nitrogen, aminotransferases, sodium, potassium).
c- Arterial blood gas or pulse oximetry determinations (PO2, PCO2).
d- Bronchoscopy (sensitive).
e- Trans-thoracic needle aspiration (TNA): uses a cutting needle to
aspirate a core of tissue with some mucus to develop an accurate
diagnosis but it is recognized as an invasive procedure.
f- Sputum cultures with gram stain: is a test to detect and identify
bacteria, a sample of sputum is collected in a sterile, wide-mouthed,
purulent, leak-proof and break-resistant plastic-specimen. Fresh
morning sample is preferred.
g- Direct immunofluorescence & PCR: for detection of RSV, Influenzae
virus and corona viruses. (5)
3- Surgical site infections(SSIs): an infection that occurs after surgery in the
part of the body where the surgery took place , Wound infections account for
up to 20–30% of nosocomial infections.
 The most common pathogens of SSIs are S.aureus, coagulase-negative
staphylococci, and enteric and anaerobic bacteria.
 Laboratory diagnosis : depends on the site of infection as follows:
a- Culturing for microbiological purposes summarized in aspiration of the
wound abscess and exudates and prepares it for gram staining in order to
identify the specific invading organism. This method used for superficial
or mild SSIs.
b- Diagnosis of deeper organ-space infections or sub phrenic abscesses
requires a high index of suspicion and the use of CT or MRI. (4)
c- Standard blood test: increase in WBCs rate due to infection and increased
ESR and C-reactive protein (CRP) due to cellulitis.

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4- Catheter-related bloodstream infection (CRBSI): is defined as the
presence of bacteremia originating from an intravenous catheter. It is one of
the most frequent, lethal, and costly complications of central venous
catheterization and nosocomial infections. Clinical manifestations of
infections (i.e., fever, chills, and/or hypotension).
 Causative agents: bacteria: S. aureus, Pseudomonas aeruginosa, E. coli,
Klebsiella pneumonia, fungi: Candida albicans spp.
 Laboratory diagnostic methods:
a- Standard blood culturing: blood sample obtained from a peripheral vein.
Hint: Simultaneous quantitative paired blood cultures. However, a non-
quantitative blood culture drawn from the CVC that becomes positive at
least 2 hr. earlier than the peripheral blood culture, is a new method for
the diagnosis of CRBSI without removing the catheter. And as shown
figure below.
After that, the culture media are stained by gram or H&E stain. Then
gathered in microscopic studies.
b- Polymerase chain reaction (PCR): is a sensitive test used to detect
pathogen’s DNA.
c- Other methods : CT scan, MRI, FISH, and etc. (6)

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Conclusion:
With increased burden of nosocomial infections and antimicrobial resistance, it
has become difficult for healthcare administrations and infection control
committees to reach the goal for elimination of intervals. However, an efficient
surveillance method guided by WHO can help healthcare institutes to improve
infection control programs. It has provided Proper training to hospital staffs for
biosafety. Sufficient laboratory instruments and devices should present, to reach
to an accurate diagnosis for these types of infections as soon as possible.
References :
(1)Satish Gupte, “The Short Textbook of Medical Microbiology (Including
Parasitology)”, 10th edition, New Delhi, India: Jaypee Brothers Medical
Publishers (P) Ltd, 2010.
(2)Connie R. Mahon, Donald C. Lehman, “Textbook of diagnostic
microbiology”, 6th
edition, St. Louis, Missouri: Elsevier Inc., 2019.
(3) Wilson M, Gaido L, “Laboratory Diagnosis of Urinary Tract Infections
in Adult Patients”. “Clinical Infectious Diseases”, 2004;38(8):
p.1150-1158.Available from:
https://academic.oup.com/cid/article/38/8/1150/441696#32176083
(4)Dennis L. Kasper, Anthony S. Fauci, “HARRISON’S Infectious
Diseases”, 17th
edition, United States: The McGraw-Hill Companies,
2010.
(5)Woodhead M., “Guidelines for the management of adult lower
respiratory tract infections”, “European Respiratory Journal”. 2011;
38(6):p.1250-1251.
(6)Rupam G., Chaitanya N., “Catheter-related bloodstream infections”,
“International Journal of Critical Illness and Injury Science”. 2014; 4(2):
p.162–167.