Chapter 6 : Infection Control Epidemiology and Clinical Microbiology

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This chapter discusses the impact of nosocomial infections, outlines the organization of the hospital infection control program, and describes the important role of the clinical microbiology laboratory in the prevention and control of health care-associated infections. The indicated that the presence of an active surveillance and infection control program was associated with a 32% decrease in nosocomial infection rates while the absence of such a program was associated with an 18% increase in nosocomial infection rate. The hospital infection control program should include surveillance and prevention of nosocomial infections. The chapter focuses on the most important specific roles played by a microbiology laboratory in the day-to-day practice of infection control. Commercial identification and susceptibility testing systems allow most laboratories to identify microorganisms to species level and perform antimicrobial susceptibility testing (AST). However, the expanding spectrum of organisms that colonize and infect seriously ill patients challenges the ability of a clinical microbiology laboratory to identify and characterize nosocomial pathogens accurately. When the infection control team detects a cluster or outbreak of nosocomial infection, they must act promptly to identify the etiologic agent if it is not known, define the extent of the outbreak, learn the mode of transmission for the pathogen, and institute appropriate control measures. Development and application of new technologies in the clinical laboratory can greatly enhance infection control efforts.

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6

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Lower Respiratory Tract Infections
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Sample chart format for reporting nosocomial infection rates in an ICU compared with CDC NHSN benchmarks. MICU, medical ICU; CVC, central venous catheter.

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6
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Generic image for table

Commonly used terms in health care epidemiology

Adapted from reference .

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6
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Distribution of the five most common nosocomial pathogens isolated from major infection sites, reported to the NHSN from January 2006 to October 2007

From reference .

CoNS, coagulase-negative staphylococci.

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6
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Attributable mortality of nosocomial bloodstream infection due to selected pathogens

Adapted from reference .

bCoNS, coagulase-negative staphylococci.

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6
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Steps in nosocomial outbreak investigation, and role of the laboratory at each step

Adapted from reference .

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6
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Screening patients and health care workers for asymptomatic carriage of organisms of epidemiologic significance

Such cultures should only be done for the following reasons: (i) as part of an outbreak investigation, to seek carriage of an organism among patients or health care workers who are epidemiologically linked to cases; (ii) to seek carriers of MDROs as part of enhanced MDRO control strategies; (iii) to identify carriers in order to proceed with a decolonization strategy to decrease risk for acquisition of infection during a period of vulnerability (e.g., perioperative).

The “gold standard” method includes overnight broth enrichment and confirmation of species identification and antimicrobial susceptibility, which can increase turnaraound time to 96 hours. Most conventional agar-based screens (e.g., mannitol salt agar with or without oxacillin), without broth enrichment, provide a turnaround time of approximately 48 hours.

The nares provides the best sensitivity and specificity of any single site for detection of (including MRSA) detection ( ). However, several studies have demonstrated that sampling of additional sites, including oropharynx and perirectal sites, may increase yield by 10 to 40% ( ).

Positive results for chromogenic agar medium can be reported at 18 to 24 hours, but negative results are reported at 48 hours.

Currently available real-time PCR assays are FDA approved only for nares samples but have been used in some studies for oropharyngeal, skin, and perirectal samples.

No real-time PCR assay for VRE detection is FDA approved at the time of this writing, but numerous “home brew” assays are in use, and commercially available assays are likely to become available soon.

Several modifications of culture methods may enhance recovery by increasing medium selectivity for MDROs (e.g., addition of ceftazidime for ESBL-producing , levofloxacin for fluoroquinolone-resistant , etc.).

Sample site choice should be guided by likely reservoirs, gastrointestinal (e.g., ) and respiratory (e.g., ) being most common.

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6
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Screening environmental sources (air, water, and surfaces) for organisms of epidemiologic significance

With the exception of water and dialysate cultures for monitoring of hemodialysis, and potable water cultures for spp., environmental cultures should be performed only when an epidemiologic investigation suggests the environment may be involved in pathogen transmission.

Large-volume air samplers are preferred for air sampling for mould spores: settle plates should not be used for this purpose.

There are no standards for acceptable levels of bacteria in air samples, nor is there any evidence correlating bacterial burden to infection risk. Air sampling for bacteria should be performed only rarely, either as part of an outbreak investigation or a research protocol.

spp. will not grow on routine aerobic culture media. Buffered charcoal yeast extract agar is the most common medium used for isolation.

The larger volume (1 liter) is preferred. If the water source is chlorinated, 0.5 ml of 0.1 N sodium thiosulfate should be added to each liter sample to neutralize the chlorine. Water samples are filter concentrated. Swabs should be immersed in 3 to 5 ml of water taken during sampling of the same site, to prevent drying.

The role of waterborne fungi in infection transmission in the hospital environment remains poorly described, but cultures may be indicated as part of a search for environmental sources during an outbreak of invasive fungal infections in an immunocompromised patient population.

AAMI, Association for the Advancement of Medical Instrumentation, whose standards govern microbiological monitoring of hemodialysis.

The sterile swab or sponge should be moistened (e.g., with nutrient broth, sterile saline, etc.) before sample collection.

For , the contact agar plate should be optimized for anaerobic recovery (selective, prereduced media, promptly placed in anaerobic environment).

Citation: Diekema D, Pfaller M. 2011. Infection Control Epidemiology and Clinical Microbiology, p 73-84. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch6

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