Infectious Disease Epidemiology Unit

Conducts surveillance for infectious diseases and investigates clusters and outbreaks

Contact Info:

1-877-996-9000

Infection Prevention Orientation Manual

Section 10: Laboratory

Leslie Teachout MT(ASCP), CIC
October 2014

Download a printable PDF Version of this section.

Objectives

At the completion of this section the Infection Preventionist (IP) will:

  • Describe basic elements of laboratory that are pertinent to Infection Prevention and Control
  • Identify and interpret laboratory tests which have an impact on infection prevention and control
  • Become familiar and meet with laboratory department personnel (i.e. chemistry-which usually includes serology, microbiology, and hematology) and the Manager/Director
  • Become familiar with the State of Wyoming Public Health Laboratory
  • Become familiar with laboratory methods such as how test are performed, how to interpret results and normal values
  • Become familiar with the Wyoming Department of Health Reportable Conditions and diseases, notifications times and phone numbers
  • Determine who and IF the lab reports State reportable diseases and become familiar with their process of reporting.

Number of hours

  • Key Concepts – 1 hours
  • Methods – 2 hours

Required Readings

  • Grota P, Allen V, Boston KM, et al, eds. APIC Text of Infection Control & Epidemiolo 4th Edition. Washington, D.C.: Association for Professionals in Infection Control and Epidemiology, Inc.; 2014.
    • Chapter 25, Laboratory Testing and Diagnostics, by J Smyer
    • Chapter 108, Laboratory Services, by P Prinz Luebbert
  • Information available in Appendices A, B and C
  • Wyoming Infection Prevention Orientation Manual (WY IPOM), Section #11 Microbiology

Overview

The IP should view the laboratory setting from two perspectives: an employee health and safety perspective, and as an essential partner of IPs in the detection and characterization of pathogens. The IP in many other healthcare facilities such as ambulatory surgery, outpatient dialysis, and long term care will find this information helpful in networking, assuring quality reports, and answering questions with the Laboratory. Refer to the WY IPOM Microbiology Section #11 for more details on the identification of specific organisms.

Key Concepts

Most microorganisms (bacteria and fungus) are singe cells and exhibit characteristics common to all biological systems: reproduction, metabolism growth, irritability, adaptability, mutation and organization. In contrast, viruses are considered a prokaryote because they lack the characteristics of living things, except the ability to replicate, which they accomplish only in living cells. Therefore, the most commonly used test methods for the detection of viral diseases are blood tests and/or titers for an immunologic response also known as serology.

Serology is the scientific study of plasma serum and other bodily fluids and refers to the detection of antibodies (immune response) in the serum or titers.  Such antibodies are typically formed in response to an infection, against other foreign proteins (i.e. mismatched blood), or to one’s own proteins (i.e. autoimmune disease).

In addition to the microbiology sections of a laboratory, the hematology area performs the Complete Blood Count (CBC), hemoglobin and hematocrit, and the differential (diff). The CBC includes the white blood count (WBC). The hemoglobin and hematocrit tests determine red blood cells. The differential provides a percentage concentration of various cellular components of the white blood cells (neutrophils, lymphocytes, monocytes, eosinophils, basophiles, and platelets).  The results of these tests (CBC, WBC, hemoglobin, and hematocrit) will give information regarding the potential for a bacterial vs. viral infection.

Methods

The IP should become familiar with the laboratory tests needed to diagnose diseases and the types of organism which cause the diseases. The IP should understand the specific requirements for specimen collection and transportation in order to insure that the correct sample is collected and can be tested. If a sample is not collected, handled, or stored properly, testing may be refused by the laboratory. The testing of specimens not collected, handled or stored properly will cause results to be misleading, inaccurate, or entirely incorrect due to the breakdown of enzymes, overgrowth of bacteria, or for other reasons. The IP should have a relationship with either the in-house laboratory, or the reference laboratory with whom the facility is contracting.

Clinical Microbiology Laboratory Experience

The IP should spend time with a mentor in the laboratory including the sections of microbiology, virology/serology and hematology.

Exercise #1

Discuss the following items with your laboratory and/or IP mentor. In addition, follow a specimen from the time it is received in the laboratory until the report is finalized and sent to the ordering professionals. Use the information gained in your discussion and following a specimen through the process to complete Table 1 (Please download the printable PDF version of this section, linked above, to view Table 1).

  • Get an understanding of how lab work is divided
  • How long different tests take and why
  • The differences in the type of media for different tests
  • How the media are selected
  • How contamination of the specimens is avoided
  • Tests for identifying organisms
  • Review antibiotic sensitivity testing
  • How is a gram stain performed
  • How are reports generated

Exercise #2

Observe the following procedures applicable to the lab and make notes: Gram Stain, sensitivity method, blood culture, specimen for AFB, Urine culture, wound culture.

The Hospital Laboratory

Not all healthcare facilities have a laboratory in-house and must use an outside hospital laboratory or even a commercial laboratory for routine diagnostic services. However, the exercises below should be applicable to all facility types.

Exercise #3

Find out what laboratory your facility uses for routine diagnostics and set up a tour with the manager or director. Then answer the following questions. Abbreviations include: PCR (polymerase chain reaction), MRSA (methicillin-resistant Staphylococcus aureus), VRSA (vancomycin-resistant Staphylococcus aureus), VRE (vancomycin-resistant Enterococcus), ESBL (extended spectrum beta lactamase), WPHL (Wyoming Public Health Laboratory).

  1. What tests are performed in the laboratory?
  2. Who is your reference lab?
  3. What is the turnaround time for results from the reference lab?
  4. Who performs viral and fungal tests?
  5. Does your facility or reference lab perform PCR test?  If so, which tests?
  6. What type of test is used to determine if a patient has Clostridium difficile?
  7. What tests are typically performed on patients with gastrointestinal diarrhea?
  8. What are the specimen requirements (i.e. blood, swab for culture or urine)?
  9. How long does it take to get a report (ex. cultures, flu PCR testing, etc.)?
  10. Are there age criteria for certain test procedures?
  11. What is the notification process for results like MRSA, VRSA, VRE, ESBLs, carbapenem resistance?
  12. Are any samples referred to the CDC / State microbiology laboratory?*Note: samples can only be referred to the CDC through the WPHL. Samples cannot be sent directly to the CDC.
  13. Who can help with the antibiotic summary data for the antibiogram?

Wyoming Public Health Laboratory

The state public health laboratory is a great resource for IPs, laboratorians, and healthcare providers. Certain infectious diseases must be confirmed through the submission of a specimen or isolate to the Wyoming Public Health Laboratory (WPHL). Refer to the list of Reportable Diseases and Conditions in Wyoming in Appendix C. The most current version of this list can be accessed at: www.health.wyo.gov/phsd/epiid/reporting.html.

Exercise #4

Through discussions with your laboratory mentor, IP/CNO/DON mentor, or by contacting the WPHL directly, answer the following questions. Abbreviations include: MRSA (methicillin-resistant Staphylococcus aureus), VRSA (vancomycin-resistant Staphylococcus aureus), VRE (vancomycin-resistant Enterococcus), ESBL (extended spectrum beta lactamase),CNO (chief nursing officer), DON (director of nursing).

  1. What tests are referred to WPHL?
  2. What is the protocol for sending samples to WPHL on week-days versus week-ends?  Who is the courier and when are samples picked up?
  3. What is the protocol for sending samples to WPHL during an outbreak?
  4. What is the collection requirement for samples which must be transported to WPHL?
  5. How long does it take to get a report from WPHL?
  6. Does WPHL do a viral panel on respiratory samples? Is there a criterion around this procedure? (e.g. is it done only on patients less than 5 years and over 75 years)?
  7. Are samples for MRSA, VRSA, VRE, ESBLs, carbapenem resistance sent to the WPHL routinely?
  8. Are any samples referred to the National Microbiology Laboratory?
  9. Discuss with your CNO/DON mentor about a tour of the WPHL.

Microbiology

Specimen collection and transportation

Specimen collection and transport to the lab is an essential part of the culture process. All specimens should be collected aseptically and placed in a sterile container; some specimens may be placed directly into culture media (e.g., blood cultures, genital cultures). Special handling techniques may be necessary for some specimens such as those for anaerobic culture. Prompt delivery to the laboratory is essential to prevent the death of pathogenic organisms or the overgrowth of commensal organisms. Some specimens may be refrigerated (e.g., urine, stool, sputum) while others should be maintained at room temperature (e.g., genital, eye, or spinal fluid) while awaiting transport.

Exercise #5

In Table 5, describe the appropriate method for the collection, storage and transportation of specimens to the bacteriology portion of the laboratory (Please download the PDF Version of this section, linked at the top of the page, to view Table 5).

Specimen collection and transport are institution dependent. Refer to your institution’s laboratory manual for procedures and protocols.

Testing for Bacteria

The IP should know the general and specialized methods used to detect and identify bacteria. Please refer to Appendix B for more detailed information.

Exercise #6

In Table 6, give explanations for the following questions. Use the required readings listed at the beginning of this chapter, the texts listed at the end of the chapter under helpful resources, and discussions with your laboratory and/or IP mentor (Please download the PDF Version of this section, linked at the top of the page, to view Table 6).

Exercise #7

With the assistance of the microbiology laboratory manager and/or your IP mentor, complete Table 7 (Please download the PDF Version of this section, linked at the top of the page, to view Table 7).

Interpretation of Microbiology laboratory results

The IP should know how to submit laboratory results and interpret results. Please refer to Appendix A for tips and suggestions.

Exercise #8

Review 2 or 3 microbiology requisitions and determine the laboratory significance of each piece of information listed: Demographics, date collected, time collected, diagnosis, gender, person ordering the test, date received in lab, time received in lab, date reported, Gram stain, mixed count, amount of growth, specimen number, cell count, organism, sensitivity, intermediate sensitivity, beta lactamase positive, resistance, Thymidine dependent strain (TFG), Source of the specimen (leg, vagina, etc.), Type of test required.

Common Microbiology Requisition Problems

Awareness of common problems in microbiology submissions will help the IP avoid them and determine areas for improvement. Common problems include the denial of testing, the in ability to accurately interpret results, or other issues.

Exercise #9

Discuss with your laboratory if there are requisition problems commonly experienced in the microbiology lab and how they affect the testing methods and possibly the results. For each problem identified, come up with a suggestion for improvement.

Virology/Serology

Specimen collection and transport

The IP should know the protocol for specimen collection and transportation, testing and interpretation of results when a viral etiology is suspected or when the only test method available is serology.

Exercise #10

In Table 10, describe appropriate methods for the collection, storage and transportation of specimens to the virology and/or serology laboratory. Use the required readings listed at the beginning of this chapter, as well as the texts listed at the end of the chapter under helpful resources (Please download the PDF Version of this section, linked at the top of the page, to view Table 10).

Testing for Viruses

Unlike most bacteria, viruses are not complete cells that can function on their own. They cannot convert carbohydrates to energy, like bacteria and other living cells do. Viruses depend on other organisms for energy, and cannot reproduce unless they get inside a living cell. There are three categories of diagnostic tests for viruses: 1) direct examination of the specimen, 2) virus isolation (a.k.a. cell culture) and 3) serology (a.k.a. testing for the antibodies against the virus). Because cell cultures take a long time they are not used often. Serology forms the mainstay of viral diagnosis. Following exposure, the first antibody to appear is immune globulin M (IgM), which is followed by a much higher titre of immune globulin G. Detection of rising titres of antibodies between acute and convalescent stages of infection, or the detection of IgM in primary infection are techniques often used for diagnosis of viral infections. The IP should know these test methods.

Exercise #11

Using your required readings, helpful resources, and discussions with your laboratory mentor describe the three methods for identifying viruses in the lab. Complete Table 11 (Please download the PDF Version of this section, linked at the top of the page, to view Table 11).

Interpretation of virology/serology laboratory results

In addition to many of the pieces of information required for microbiology testing, there are several specific pieces of information important for virus testing.

Exercise #12

Review 2 or 3 virology requisitions and determine the laboratory significance of each of the following pieces of information: Date reported, PCR Report, IgM, IgG.

Common Virology/Serology Requisition Problems

Awareness of common problems in virology submissions will help the IP avoid them and determine areas for improvement. Common problems include the denial of testing, the in ability to accurately interpret results, or other issues.

Exercise #13

Discuss with your laboratory if there are requisition problems commonly experienced in the virology lab and how they affect the testing methods and possibly the results. For each problem identified give a suggestion for improvement.

Hematology

The IP should become familiar with: the hematology area. The hematology laboratory performs the Complete Blood Count (CBC), hemoglobin and hematocrit, and the differential (diff). The CBC includes the white blood count (WBC). The hemoglobin and hematocrit tests determinate red blood cells. The differential provides a percentage concentration of various cellular components of the white blood cells (neutrophils, lymphocytes, monocytes, eosinophils, basophils, and platelets). The results of these tests will give information regarding the potential for a bacterial vs. viral infection.

Exercise #14

Meet with the section head of hematology to review the CBC for various patients in the hospital. Explain what is meant by each of the following terms: Left Shift, Atypical or reactive lymphocyte, band or stab, hyper-segmented neutrophil, Megakaryocyte, Eosinophilia, Nucleated Red Blood Cell.

Documentation and Reporting

Documentation and reporting is a large part of the IP’s and the laboratorian’s job. The laboratory must be able to provide documentation and report specific processes, and testing results to the IP. For example, the laboratory may be responsible for reporting quality assurance and quality control to the IP and the quality improvement team. The laboratory may be required to report certain microorganisms (e.g. drug-resistant organisms) or the results of specific tests (e.g. Hepatitis) to the IP as soon as available. It is essential for the IP to know the reporting mechanisms for the laboratory. The IP must know the WDH reportable conditions and diseases, notification times, and phone numbers.  Please see the list in Appendix C. Numerous institution-specific responsibilities exist for using, handling, and summarizing laboratory reports. Such responsibilities include those listed in Table 15.

Exercise #15

Through discussions with the laboratory director or manager, describe the following laboratory reporting mechanisms:

  1. Determine what lab reports are sent to IP on a daily basis.
  2. How are routine reports sent to IP?
  3. Is there a process for stat reports to be sent to the IP for organisms such as TB, GAS, MRSA, VRE, ESBL, carbapenem resistance?
  4. How long does the lab keep specific samples such as MRSA, VRSA, VRE, ESBLs?
  5. Who in the laboratory is responsible for reporting diseases and conditions listed on the Wyoming Department of Health Reportable Diseases and Conditions list?Or is this the responsibility of the IP?

Exercise #16

Through discussions with the laboratory director or manager, with your IP mentor/supervisor, and reviews of policies in your institution, answer the following questions:

  1. Is there a designated surveillance program for certain microorganisms such as drug-resistant organisms?
  2. How are laboratory reports stored? (i.e. in a database?)
  3. Who is responsible for entering the data?
  4. Who is responsible for analyzing the laboratory data collected?
  5. Are there reports generated from the data and to whom are these reports sent?

Other Issues

Clinical laboratories have guidelines and standards to assure the information or test results they provide are performed correctly and are accurate. Two methods for assuring testing results are by adhering to the Clinical and Laboratory Standards Institute guidelines and by performing quality control checks.

Clinical and Laboratory Standards Institute

Clinical and Laboratory Standards Institute (CLSI) develops standards for antimicrobial susceptibility testing of bacteria isolates from clinical specimens.  The IPs need to know the CLSI guidelines. The CLSI standards guide laboratories in the use of breakpoints for antibiotic susceptibility testing; the most common method is the use of MICs (Minimal Inhibitory Concentration).  The standards guide has information on the appropriate antibiotics to report for a specific organism. For example Klebsiella species are naturally resistant to ampicillin, thus ampicillin susceptibility patterns should not be reported.  The information from the CLSI guide should be reviewed annually to assure the most accurate organism sensitivities are being reported.  These Standards can be found on the CLSI website clsi.org/standards/, purchased by the laboratory from CLSI, or obtained from the Wyoming Public Health Laboratory.

Quality Assurance/Quality Control

Laboratories assess quality daily to assure the tests are accurate and performing correctly.  Laboratory Quality Assurance (QA) encompass activities that enable laboratories to achieve and maintain accuracy and proficiency despite changes in test methods and the volume of specimens tested. A good QA system does four things:

  • establishes standard operating procedures (SOPs) for each step of the testing process, ranging from specimen handling to instrument performance validation;
  • defines administrative requirements, such as mandatory recordkeeping, data evaluation, and internal audits to monitor adherence to SOPs;
  • specifies corrective actions, documentation, and the persons responsible for carrying out corrective actions when problems are identified; and
  • sustains high-quality employee performance.

Ethics

Discuss with your ICP mentor the steps which have been taken at your facility to ensure the confidentiality of reports.

Resources

Helpful/Related Readings
  • Bennett J and Brachman P, eds. Bennett & Brachman’s Hospital Infection 6th Edition. Philadelphia, PA: William R Jarvis; 2014.
    • Chapter 11, The Role of the Laboratory in Prevention of Healthcare-Associated Infections, by MA Pfaller and DJ Diekema
    • Chapter 15, Multidrug-Resistanct Organisms: Epidemiology and Control, by MY Lin, RA Weinstein and MK Hayden
    • Chapter 22, Clinical Laboratory-Acquired Infections, by ML Wilson and LB Reller
  • Bennett G, Morrell G, and Green L, ed. Infection Prevention Manual for Hospitals; revised edition. Rome, GA: ICP Associates, Inc.; 2010. Section 7: pages 11-13.
  • Bennett G. Infection Prevention Manual for Ambulatory Care. Rome, GA: ICP Associates Inc.; 2009. Section 7: pages 9-11.
  • Bennett G and Kassai M. Infection Prevention Manual for Ambulatory Surgery Centers. Rome, GA: ICP Associates, Inc.; 2011. Section 7: page 12
  • Heymann D. Control of Communicable Diseases Manual. 19th Washington, D.C.: American Public Health Association; 2008.
  • Pickering L., et al, eds. Red Book: 2012 Report of the Committee on Infectious Diseases. 29th Elk Grove Village, IL: American Academy of Pediatrics; 2012.
  • Mandell G, et al, eds. Mandell, Douglas and Bennett’s Principles and Practice of Infectious Diseases. 7th Edition. Philadelphia, PA: Churchill Livingstone Elsevier; 2010.
  • Lautenbach E, Woeltje KF, and Malani PN, eds. SHEA Practical Healthcare Epidemiology (3rd Edition). University of Chicago Press, Chicago, IL 2010
    • Chapter 8 Twenty-First Century Microbiology Laboratory Support for Healthcare-Associated Infection Control and Prevention, by LR Peterson and MO Wright
    • Chapter 9 Molecular Typing Systems, by JHafkin, L Chandler and J Maslow
Helpful Contacts (in WY or US)
  • Leslie Teachout MT(ASCP), CIC, Infection Prevention at Riverton (307) 857-3552 and Lander (307)335-6442 Hospitals, teachout@lpnt.net, cellphone (406)570-9321
  • Cody Loveland, MPH, Infectious Disease Surveillance Epidemiologist and HAI Prevention Coordinator, Wyoming Department of Health, 307-777-8634, cody.loveland@wyo.gov
Related Websites/Organizations

My Facility/City/County Contacts

Find out who fills each of the following roles and develop a list with each of their names, phone numbers, and emails:

  • Pathologist (Physician head of laboratory)
  • Laboratory Director
  • Chemistry Supervisor/Charge
  • Hematology Supervisor/Charge
  • Microbiology Supervisor/Charge
  • Blood Bank  Supervisor/Charge
  • Note who does the “send out” tests
  • Note who does the serology and virology tests
  • Also include key contacts at the Wyoming Public Health Laboratory

Appendices

Please see the downloadable PDF version of this section to view the following appendices:

Appendix A: Reviewing and Interpreting Culture Results
Appendix B: Important Notes for Wound, Blood, Urine and Sputum Cultures.
Appendix C: Wyoming Department of Health Reportable Diseases and Conditions

WIPAG Logo

WIPAG welcomes your comments and feedback on these sections.
For comments or inquiries, please contact:

Cody Loveland, MPH, Healthcare-Associated Infection (HAI) Prevention Coordinator
Infectious Disease Epidemiology Unit,
Public Health Sciences Section, Public Health Division
Wyoming Department of Health
6101 Yellowstone Road, Suite #510
Cheyenne, WY  82002
Tel: 307-777-8634    Fax: 307-777-5573
Email: cody.loveland@wyo.gov