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Microbiology for the Health Sciences Chapter 11' Epidemiology and Public Health


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Title: Microbiology for the Health Sciences Chapter 11' Epidemiology and Public Health

Microbiology for the Health SciencesChapter
11.Epidemiology and Public Health
Chapter 11 Outline
  • Epidemiology
  • Interactions Among Pathogens, Hosts and the
  • Chain of Infection
  • Reservoirs of Infection
  • Modes of Transmission
  • Public Health Agencies
  • Bioterrorism and Biological Warfare
  • Water Supplies and Sewage Disposal

  • Introduction
  • Epidemiology can be defined as the study of
  • Epidemiologists study the factors that determine
    the frequency, distribution and determinants of
    diseases in human populations.
  • Epidemiologists also develop ways to prevent,
    control or eradicate diseases in populations.

Epidemiologic Terminology
  • A communicable disease is an infectious disease
    that can be transmitted from one person to
  • A contagious disease is a communicable disease
    that is easily transmitted from person-to-person.
  • A zoonotic disease is one that humans acquire
    from animal sources.
  • The incidence of a particular disease is the
    number of new cases of that disease in a defined
    population during a specific time period.
  • The morbidity rate is the number of new cases of
    a particular disease that occurred during a
    specified time period per a specifically defined
    population (usually per 1,000, 10,000 or 100,000

Epidemiologic Terminology (cont.)
  • Prevalence
  • Period prevalence is the number of cases of the
    disease existing in a given population during a
    specific time period (e.g., during the year
  • Point Prevalence is the number of cases of the
    disease existing in a given population at a
    particular moment in time.
  • Mortality rate is the ratio of the number of
    people who died of a particular disease during a
    specified time period per a specified population

Epidemiologic Terminology (cont.)
  • A sporadic disease is one that occurs only
    occasionally within the population of a
    particular geographic area example, tetanus.
  • An endemic disease is one that is always present
    within the population of a particular geographic
    area example, gonorrhea.
  • An epidemic disease is defined as a greater than
    usual number of cases of a disease in a
    particular region, usually within a short period
    of time example, the Legionnaires disease
    epidemic of 1976.

Epidemiologic Terminology (cont.)
  • A pandemic is a disease that is occurring in
    epidemic proportions in many countries
    simultaneously. Examples include
  • Influenza
  • Example, the Spanish flu pandemic of 1918 more
    than 20 million people were killed worldwide
    (500,000 in the U.S.)
  • Tuberculosis
  • Malaria

Interactions Among Pathogens, Hosts, and the
  • Whether an infectious disease occurs depends on
  • Factors pertaining to the pathogen (e.g.,
    virulence of pathogen, mode of entry, number of
  • Factors pertaining to the host these include
    health status, nutritional status, hygiene, age,
    travel, lifestyle etc.
  • Factors pertaining to the environment such as
    physical factors (e.g., climate, season,
    geographic location), availability of appropriate
    reservoirs, sanitary and housing conditions, and
    availability of potable water.

Chain of Infection
  • There are 6 components in the infectious disease
  • ? a pathogen
  • ? a source of the pathogen (a reservoir)
  • ? a portal of exit
  • ? a mode of transmission
  • ? a portal of entry
  • ? a susceptible host

The Chain of Infection
Reservoirs of Infection
  • The sources of microorganisms that cause
    infectious diseases are many and varied they are
    known as reservoirs of infection or simply
  • Living reservoirs humans, pets, farm animals,
    insects, arachnids.
  • Human carriers
  • Passive carriers
  • Incubatory carriers
  • Convalescent carriers
  • Active carriers

Reservoirs of Infection (cont.)
  • Animals
  • Infectious diseases that humans acquire from
    animal sources are called zoonotic diseases or
  • Zoonoses may be acquired by direct contact with
    an animal, inhalation or ingestion of the
    pathogen, or injection of the pathogen by an
  • Examples
  • Rabies
  • Lyme disease
  • Others

Reservoirs of Infection (cont.)
  • Arthropods
  • Many different types of arthropods serve as
    reservoirs of infection, including insects (e.g.,
    fleas, mosquitoes, lice) and arachnids (e.g.,
    mites and ticks)
  • When arthropods are involved in the transmission
    of infectious diseases they are referred to as
  • Examples of arthropod-borne diseases
  • Lyme disease
  • Malaria

Reservoirs of Infection (cont.)
  • Nonliving Reservoirs
  • Air, soil, dust, contaminated water and foods,
    insects, and infected humans.
  • Fomites - inanimate objects capable of
    transmitting pathogens (e.g., bedding, towels,
    eating and drinking utensils, hospital equipment,

Inanimate Vectors of Infection (Fomites)
Modes of Transmission
  • Direct skin-to-skin contact
  • Direct mucous membrane-to-mucous membrane contact
    by kissing or sexual intercourse
  • Indirectly by airborne droplets of respiratory
    secretions, usually by sneezing or coughing
  • Indirectly by contamination of food and water by
    fecal matter
  • Indirectly by arthropod vectors
  • Indirectly by contaminated fomites
  • Indirectly by transfusion of contaminated blood
    or blood products or by parenteral injection
    using nonsterile syringes or needles

Modes of Disease Transmission
Public Health Agencies
  • World Health Organization (WHO)
  • A specialized agency of the United Nations
    founded in 1948 www.who.org
  • Mission to promote technical cooperation for
    health among nations, carry out programs to
    control and eradicate diseases and improve the
    quality of human life.
  • Investigates outbreaks of Ebola virus, etc.
  • Eradicated smallpox
  • Attempting to eradicate polio and dracunculiasis

Public Health Agencies (cont.)
  • Centers for Disease Control and Prevention (CDC)
  • A federal agency administered by the U.S.
    Department of Health and Human Services, Atlanta,
    GA. Established in 1946 www.cdc.gov
  • Mission to promote health and quality of life
    by preventing and controlling diseases, injury,
    and disability
  • Certain infectious diseases, known as nationally
    notifiable diseases must be reported to the CDC.
  • Publishes Morbidity and Mortality Weekly Report

Public Health Agencies (cont.)
  • Measures for prevention and control of epidemics
  • Increase host resistance through the development
    and administration of vaccines that induce active
    immunity and maintain it in susceptible persons.
  • Ensure that persons exposed to a pathogen are
    protected against the disease.
  • Segregate, isolate and treat those who have
    contracted a contagious infection to prevent the
    spread of the pathogen to others.
  • Identify and control potential reservoirs and
    vectors of infectious diseases.

Bioterrorism and BiologicalWarfare Agents
  • Microbes purposely used to harm others in wartime
    are called biological warfare (bw) agents.
  • Pathogens used to create fear, chaos, illness and
    death are called bioterrorism agents. Examples
  • Bacillus anthracis
  • Clostridium botulinum
  • Smallpox virus (Variola major)
  • Yersinia pestis

Water Supplies and Sewage Disposal
  • Water is the most essential resource for the
    survival of humanity!
  • Sources of water contamination
  • rainwater and groundwater (from wells) can become
    contaminated by soil microbes and raw fecal

Water Supplies and Sewage Disposal (cont.)
  • Water Treatment
  • The major steps in water treatment are
    sedimentation, coagulation, filtration and
  • Water is tested for contamination by checking for
    the presence of coliform bacteria (coliforms),
    such as E. coli and other members of the family
  • Sewage Treatment
  • Raw sewage consists mainly of water, fecal
    material, garbage and bacteria.
  • Includes primary, secondary and tertiary sewage

Steps in Water Treatment
Review of Key Points
  • Epidemiology is the study of the frequency and
    distribution of diseases and contributing
  • Epidemic, endemic, pandemic and sporadic diseases
    are epidemiologic terms used to describe the
    prevalence of a disease in an area at a
    particular time.
  • The sources of pathogens are known as reservoirs
    of infection they may be living reservoirs or
    nonliving reservoirs.
  • The principal modes of transmission of pathogens
    contact, airborne, droplet, vehicular and vector.

Review of Key Points (cont.)
  • To eradicate certain diseases and prevent
    epidemics, epidemiologists must consider the
    virulence of the pathogens, susceptibility of the
    population, sanitation practices, reservoirs of
    infection and ways in which pathogens are
  • The World Health Organization, the Centers for
    Disease Control and Prevention, and public health
    and community agencies, at all levels, must work
    together to coordinate preventive health programs
    and maintain constant surveillance of sources and
    causes of epidemics.

Review of Key Points (cont.)
  • Prevention and control of epidemics include
    measures to increase host resistance by
    immunizations protect people from exposure to
    pathogens segregate, isolate and treat those
    with contagious infections identify and control
    potential reservoirs and vectors of infectious
    diseases and institute effective sanitation
    measures to control diseases transmitted through
    water supplies, sewage, and food.
  • The 4 most likely potential biological warfare or
    bioterrorism agents are Bacillus anthracis,
    Clostridium botulinum, smallpox virus and
    Yersinia pestis.

Review of Key Points (cont.)
  • The major steps in water treatment are
    sedimentation, coagulation, filtration and

Microbiology for the Health SciencesChapter
12.Healthcare EpidemiologyNosocomial
Infections and Infection Control
Chapter 12 Outline
  • Introduction
  • Nosocomial Infections
  • Infection Control
  • Concluding Remarks

  • Healthcare epidemiology is, any activity
    designed to study and/or improve patient care
    outcomes in any type of healthcare institution or
    settings. Health care epidemiology includes a
    variety of disciplines and activities directed at
    enhancing the quality of health care and
    preventing and controlling adverse outcomes.
    Among these activities are epidemiologic and
    laboratory investigation, surveillance, risk
    reduction programs focused on device and
    procedure management, policy development and
    implementation, education and information
    dissemination, and cost-benefit assessment of
    prevention and control programs.

Nosocomial Infections
  • Infectious diseases can be divided into 2
  • Those acquired within hospital or healthcare
    facilities (nosocomial infections).
  • Those acquired outside of healthcare facilities
    (community-acquired infections).
  • Frequency of Nosocomial Infections
  • Of approximately 40 million hospitalizations per
    year in the U.S., an estimated 2 million patients
    (5 of the total) acquire nosocomial infections.

Pathogens Most Often Involved in Nosocomial
  • The most common bacterial causes of nosocomial
    infections in the U.S. (1990-1996)
  • Gram-positive cocci caused 34 of the
    nosocomial infections.
  • Staphylococcus aureus, coagulase-negative
    staphylococci and Enterococcus spp.
  • Gram-negative bacilli caused 32 of the
    nosocomial infections.
  • Escherichia coli, Pseudomonas aeruginosa,
    Enterobacter spp. and Klebsiella spp.

Most Common Types of Nosocomial Infections
  • The 4 most common types of nosocomial infections,
    in descending order of frequency are
  • Urinary tract infections (UTIs).
  • Surgical wound infections (also referred to as
    postsurgical wound infections).
  • Lower respiratory infections (primarily
  • Bloodstream infections (septicemia).
  • Other types gastrointestinal diseases caused by
    Clostridium difficile (referred to as Clostridium
    difficile-associated diseases).

Patients Most Likely to Develop Nosocomial
  • Elderly patients
  • Women in labor and delivery
  • Premature infants and newborns
  • Surgical and burn patients
  • Diabetic and cancer patients
  • Patients receiving treatment with steroids,
    anticancer drugs, antilymphocyte serum and
  • Immunosuppressed patients
  • Patients who are paralyzed or are undergoing
    renal dialysis or catheterization

Major Factors Contributing to Nosocomial
  • The 3 major factors that combine to cause
    nosocomial infections are
  • An ever-increasing number of drug-resistant
  • The failure of healthcare personnel to follow
    infection control guidelines.
  • An increased number of immunocompromised
  • Additional factors include shortages of
    healthcare staff, indiscriminate use of
    antimicrobial agents, etc.

Three major contributing factors in nosocomial
What Can be Done to Reduce the Number of
Nosocomial Infections?
  • Handwashing is the single most important measure
    to reduce the risks of transmitting pathogens
    from one patient to another or from one anatomic
    site to another on the same patient!
  • Other means of reducing the incidence of
    nosocomial infections include disinfection and
    sterilization techniques, air filtration, use of
    ultraviolet lights, isolating especially
    infectious patients, and wearing gloves, masks
    and gowns whenever appropriate.

Healthcare professional washing her hands.
Infection Control
  • Infection control - measures taken to prevent
    infections from occurring in healthcare settings.
  • Asepsis means without infection there are 2
  • Medical asepsis
  • Precautionary measures necessary to prevent
    direct transfer of pathogens from person to
    person and indirect transfer of pathogens through
    the air or on instruments, bedding, equipment and
    other inanimate objects (fomites).
  • Surgical asepsis or sterile technique
  • Practices to render and keep objects and areas

Infection Control (cont.)
  • Surgical aseptic techniques are practiced in
    operating rooms, labor and delivery areas,
    certain areas of the hospital laboratory and at
    patients bedsides.
  • Differences between medical and surgical asepsis
  • Medical asepsis is a clean technique whereas
    surgical asepsis is a sterile technique, and
  • The goal of medical asepsis is to exclude
    pathogens, whereas the goal of surgical asepsis
    is to exclude all microorganisms.

Infections Control (cont.)
  • Standard Precautions are used to prevent
    transmission of pathogens and are used for the
    care of all hospitalized patients, regardless of
    their diagnosis or presumed infectious status.
  • They provide guidelines regarding handwashing,
    wearing of gloves, masks, eye protection and
    gowns cleaning of patient-care equipment
    environmental control handling of soiled linens
    resuscitation devices patient placement and
    disposal of used needles and syringes (sharps).

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Healthcare professional donning sterile gown (A),
mask (B), and gloves (C)
Various pieces of personal protective equipment,
(PPE), including masks, goggles, hair protection,
and disposable gowns.
One-handed scoop technique for resheathing
Transmission-Based Precautions
  • Transmission-based precautions are designed for
    patients known or suspected of being infected
    with highly transmissible pathogens for which
    additional precautions (i.e., beyond Standard
    Precautions) are required.
  • 5 main routes of transmission of pathogens
  • Contact (direct or indirect)
  • Airborne
  • Droplet
  • Vehicular
  • Vectors

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A type N95 respirator used when airborne
precautions are indicated.
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Contact transmission is divided into 2 subgroups
(1) direct-contact (i.e., transfer of
microorganisms by body surface-to- body surface),
and (2) indirect contact (i.e., transfer of
microorganisms by a contaminated intermediate
Source Isolation
  • Source isolation is when patients with
    tuberculosis or other contagious diseases are
    placed into a room to protect other people from
    becoming infected.
  • Isolation rooms are usually under negative
    pressure to prevent room air from entering the
  • Air evacuated from the room passes through a HEPA

Protective Isolation
  • Protective isolation or reverse isolation is for
    patients who are especially vulnerable to
    infection, such as those with burns, transplant
    patients, leukopenic patients and those receiving
    radiation treatment.
  • The room is under positive pressure and air
    entering the room passes through HEPA filters.

Handling Food and Eating Utensils
  • Some of the regulations for safe handling of food
    and eating utensils include
  • Using high-quality, fresh food.
  • Properly refrigerating and storing food.
  • Properly washing, preparing and cooking food.
  • Properly disposing of uneaten food.
  • Covering hair and wearing clean clothes and
  • Thoroughly washing hands after handling foods.
  • Keeping all cutting boards and other surfaces
    scrupulously clean.
  • Washing cooking and eating utensils in a
    dishwasher with a water temperature of gt 80oC.

Handling Fomites
  • Fomites are inanimate objects, other than food,
    that may harbor and transmit microbes. Examples
    patients gowns, bedding, towels, hospital
    equipment, telephone, computer keyboard, etc.
  • Transmission of pathogens by fomites can be
    prevented by observing certain rules
  • Use disposable equipment and supplies whenever
  • Disinfect or sterilize equipment
  • Use individual equipment for each patient.
  • Others

Medical Waste Disposal
  • General Regulations
  • Follow OSHA standards for disposal of medical
  • Disposal of Sharps
  • Sharps should be handled and disposed of
  • Dispose of sharps in specifically designed
    puncture-resistant containers.

Infection Control Committees and Infection
Control Professionals
  • All healthcare facilities should have some type
    of infection control program in place.
  • The Infection Control Committee (ICC) is composed
    of representatives from most of the hospitals
    departments, including medical and surgical
    services, pathology, nursing, hospital
    administration, risk management, pharmacy,
    housekeeping, food services and central supply.
  • The chairperson is usually an infection control
    professional such as an epidemiologist or
    infectious disease specialist, infection control
    nurse or microbiologist.

Role of the Microbiology Laboratory in Hospital
Epidemiology and Infection Control
  • CML personnel participate in infection control
  • Monitoring the types and numbers of pathogens
    isolated from hospitalized patients.
  • Notifying the appropriate infection control
    person should an unusual pathogen or an unusually
    high number of isolates of a common pathogen be
  • Processing environmental samples, including
    samples from hospital employees, that have been
    collected from within the affected ward(s).

Concluding Remarks
  • Nosocomial infections can add several weeks to a
    patients hospital stay and may lead to serious
    complications and even death.
  • Insurance companies rarely reimburse healthcare
    facilities for costs associated with nosocomial
  • Nosocomial infections can be avoided through
    proper education and disciplined compliance with
    infection control practices!
  • Healthcare workers must be completely
    knowledgeable about infection control practices
    and must personally do everything in their power
    to prevent nosocomial infections from occurring!

Review of Key Points
  • Infections acquired in a hospital or other
    healthcare setting are called nosocomial
    infections those acquired elsewhere are called
    community-acquired infections iatrogenic
    infections or diseases are the result of medical
    or surgical treatment by surgeons, other
    physicians and other healthcare personnel.
  • Nosocomial infections occur all too frequently
    and may be caused by a number of factors.
  • The 7 most common causes of nosocomial infections
    in the U.S. are S. aureus, coagulase-negative
    staphylococci, Enterococcus spp., E. coli, P.
    aeruginosa, Enterobacter spp., and Klebsiella spp.

Review of Key Points (cont.)
  • The 4 most common types of nosocomial infections
    are urinary tract infections, surgical wound
    infections, lower respiratory tract infections
    and bloodstream infections.
  • The patients most susceptible to nosocomial
    infections are women in delivery, newborn
    infants, and immunosuppressed, surgical, cancer,
    diabetic, paralyzed and burn patients.
  • Medical asepsis is a clean technique with the
    goal of excluding pathogens surgical asepsis is
    a sterile technique, the goal of which is to
    exclude all microorganisms.

Review of Key Points (cont.)
  • All healthcare personnel must follow the same
    procedures to prevent the spread of communicable
  • Standard precautions must be used for the care of
    all patients.
  • Transmission-based precautions are used in
    addition to standard precautions to protect
    healthcare personnel and hospital patients from
    airborne, droplet and contact modes of pathogen

Review of Key Points (cont.)
  • Patients with highly infectious diseases are
    placed in source isolation to protect other
    persons from becoming infected protective
    (reverse) isolation is used to protect highly
    susceptible patients from becoming infected.
  • Every hospital should have an Infection Control
    Committee that is responsible for ensuring that
    the hospital is in compliance with all applicable
    infection control regulations.
  • Clinical Microbiology Laboratory personnel
    participate in infection control by monitoring
    the types and numbers of pathogens, notifying the
    appropriate ICP should an unusual pathogen be
    detected and processing environmental samples
    from an affected ward.

Microbiology for the Health SciencesChapter
13.Diagnosing Infectious Diseases
Chapter 13 Outline
  • Introduction
  • Clinical Specimens
  • Role of Healthcare Professionals in the
    Submission of Clinical Specimens
  • Importance of High-Quality Clinical Specimens
  • Proper Selection, Collection, and Transport of
    Clinical Specimens
  • Types of Clinical Specimens Usually Required to
    Diagnose Infectious Diseases
  • The Pathology Department (The Lab)
  • Anatomical Pathology
  • Clinical Pathology
  • The Clinical Microbiology Laboratory
  • Organization
  • Responsibilities

  • The proper diagnosis of an infectious disease
  • Taking a complete patient history.
  • Conducting a thorough physical examination of the
  • Carefully evaluating the patients signs and
  • Implementing the proper selection, collection,
    transport and processing of appropriate clinical

Clinical Specimens
  • Specimens collected from patients such as blood,
    urine, feces, and cerebrospinal fluid (CSF), are
    known as clinical specimens.
  • Specimens commonly submitted to the hospitals
    Clinical Microbiology Laboratory (CML) include
    blood, bone marrow, bronchial washings, sputum,
    CSF, cervical and vaginal swabs, feces, hair and
    nail clippings, pus, skin scrapings, sputum,
    synovial fluid, throat swabs, tissue, urethral
    discharge material, urine and urogentital
  • All specimens should be of the highest possible

Clinical Specimens (cont.)
  • Role of Healthcare Professionals in the
    Submission of Clinical Specimens
  • There should be a close working relationship
    among the members of the healthcare team to
    ensure a proper diagnosis of infectious diseases.
  • Healthcare professionals who collect and
    transport specimens should exercise extreme
    caution during the collection and transport of
  • In the laboratory, all specimens are handled
    carefully, exercising standard precautions.

Importance of High-Quality Clinical Specimens
  • High-quality clinical specimens are required to
    achieve accurate, clinically relevant laboratory
  • 3 components of specimen quality are
  • Proper specimen selection
  • Proper specimen collection
  • Proper transport of the specimen to the
  • The laboratory must provide written guidelines
    (Laboratory Policies and Procedures Manual).
  • The person who collects the specimen is
    ultimately responsible for its quality.

Proper Selection, Collection, and Transport of
Clinical Specimens
  • Specimen must be properly selected.
  • Specimen must be collected properly.
  • Material (i.e., specimen) should be collected
    from a site where the suspected pathogen is most
    likely to be found.
  • Specimens should be obtained before antimicrobial
    therapy, if possible.
  • The acute stage of the disease is the most
    appropriate time to collect a specimen.
  • Specimen collection should be performed with care
    and tact to avoid harming the patient.
  • A sufficient quantity of the specimen must be
    obtained for all diagnostic tests.

Proper Selection, Collection, and Transport of
Clinical Specimens (cont.)
  • All specimens should be placed or collected into
    a sterile container to prevent contamination.
  • Specimens should be protected from heat and cold
    and promptly delivered to the laboratory.
  • Hazardous specimens must be handled with even
    greater care to avoid contamination of couriers,
    patients, and healthcare professionals.
  • Whenever possible, a sterile, disposable specimen
    container should be used.
  • The specimen container must be properly labeled
    and accompanied by an appropriate request slip
    with adequate instructions.
  • Specimens should be collected and delivered to
    the lab as early in the day as possible to allow
    sufficient processing time.

Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • Blood
  • Usually sterile
  • The presence of bacteria in the bloodstream is
    known as bacteremia.
  • Septicemia is a serious disease involving chills,
    fever, prostration, and the presence of bacteria
    or their toxins in the bloodstream.
  • To prevent contamination of a blood specimen with
    indigenous skin flora, extreme care must be taken
    to use sterile technique.

Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • Urine
  • Normally sterile in the bladder becomes
    contaminated by indigenous microflora of the
    distal urethra during voiding.
  • Contamination is reduced by collecting a
    clean-catch, midstream urine.
  • Urine culture involves 3 parts
  • A colony count (using a calibrated loop)
  • Isolation and identification of the pathogen
  • Antimicrobial susceptibility testing

Obtaining a Urine Colony Count
Urine Colony Count
  • The colony count is a way of estimating the
    number of viable bacteria that are present in a
    urine specimen.
  • A calibrated loop, either 0.01 mL or 0.001 mL, is
    used to inoculate the entire surface of a blood
    agar plate.
  • After incubation at 37oC overnight, the colonies
    are counted and the number is multiplied by the
    dilution factor, either 100 for the 0.01 mL loop,
    or 1000 for the 0.001 mL loop, to determine the
    number of CFUs.
  • Colonies x dilution factor CFUs/mL

Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • Cerebrospinal Fluid (CSF)
  • Meningitis is inflammation or infection of the
    membranes (meninges) that surround the brain and
    spinal column.
  • Encephalitis is inflammation or infection of the
  • Meningoencephalitis is inflammation or infection
    of both the brain and meninges.
  • Collected by a lumbar puncture into a sterile
    tube a surgically aseptic procedure performed by
    a physician.
  • CSF a STAT (emergency) specimen in the lab!

Technique of Lumbar Puncture
Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • Sputum
  • Sputum is pus that accumulates deep within the
    lungs of a patient with pneumonia, tuberculosis
    or other lower respiratory infection.
  • Often, specimens labeled sputum are actually
    just saliva saliva specimens dont provide
    clinically relevant information.
  • If TB is suspected, extreme care should be taken!
  • Better specimens can be obtain by bronchial
    aspiration or transtracheal aspiration.

Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • Throat Swabs
  • Routine throat swabs are used to determine
    whether a patient has strep throat.
  • Specific cultures may be necessary when Neisseria
    gonorrhoeae or Corynebacterium diphtheriae are
  • Wound Specimens
  • Whenever possible, a wound specimen should be an
    aspirate (i.e., pus collected by needle and
    syringe), rather than a swab.
  • Specimens collected by swab are frequently
    contaminated with indigenous microflora.

Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • GC Cultures (for Neisseria gonorrhoeae)
  • N. gonorrhoeae is a fastidious, microaerophilic
    and capnophilic bacterium.
  • Only Dacron, calcium alginate, or nontoxic cotton
    swabs should be used to collect GC specimens.
  • Specimens (e.g., vaginal, cervical, urethral,
    throat and rectal swabs) are cultured on special
    medium (e.g., Thayer-Martin) and incubated in
  • Special transport media is available and GC swabs
    should never be refrigerated.

Types of Clinical Specimens Usually Required to
Diagnose Infectious Diseases
  • Fecal Specimens
  • Ideally, fecal (stool) specimens should be
    collected at the laboratory and processed
    immediately to prevent a decrease in temperature,
    which would allow the pH to drop and cause the
    death of many Shigella and Salmonella species.
  • Fecal bacteria are obligate-, aerotolerant-, and
    facultative anaerobes.
  • A combination of direct microscopic examination,
    culture, biochemical tests, and immunologic tests
    may be performed to identify Gram-negative and
    Gram-positive bacteria, fungi, intestinal
    protozoa and intestinal helminths.

The Pathology Department (The Lab)
  • Clinical specimens are submitted to the Clinical
    Microbiology Laboratory (CML), which is a part of
    the Pathology Department.
  • The Pathology Department (often referred to as
    the Lab) is under the direction of a
    pathologist (a physician who has specialized
    training in pathology).
  • The pathology department is divided into 2 major
  • Anatomical pathology
  • Clinical pathology

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The Pathology Department (cont.)
  • Anatomical Pathology
  • Diseased organs, stained tissue sections, and
    cytology specimens are examined here.
  • Cytogenetic technologists, cytotechnologists,
    histologic technicians, histotechnologists, and
    pathologists assistants are employed in this
  • In addition, autopsies are performed in the
    morgue and some Pathology Departments may have an
    Electron Microscopy Laboratory.

The Pathology Department (cont.)
  • Clinical Pathology
  • Consists of several laboratories in addition to
    the Clinical Microbiology Laboratory Clinical
    Chemistry, Urinalysis, Hematology/Coagulation,
    Blood Bank, and Immunology.
  • Personnel include pathologists, chemists and
    microbiologists, clinical laboratory scientists
    (also known as medical technologists) and
    clinical laboratory technicians (also known as
    medical laboratory technicians).

The Clinical Microbiology Laboratory
The CML may be under the direction of a
pathologist, a microbiologist or a clinical
laboratory scientist.
The Clinical Microbiology Laboratory (cont.)
  • Responsibilities
  • Primary mission of the CML is to assist
    clinicians in the diagnosis and treatment of
    infectious diseases.
  • The 4 major day-to-day responsibilities are to
  • Process various clinical specimens that are
    submitted to the CML.
  • Isolate pathogens from those specimens.
  • Identify (speciate) the pathogens.
  • Perform antimicrobial susceptibility testing,
    when appropriate to do so.

Isolation and Identification (Speciation) of
  • Bacteriology Section
  • Bacterial pathogens are isolated from specimens,
    tests are performed to identify the bacterial
    pathogens, and antimicrobial susceptibility
    testing is performed whenever appropriate to do
  • CML professionals are very much like detectives
    and crime scene investigators, in that they
    gather clues about a pathogen until they are able
    to identify it.
  • Numerous phenotypic characteristics are used to
    identify the bacteria (e.g., Gram reaction, cell
    shape, motility, presence and location of spores,
    presence or absence of various enzymes, etc.)

CML professionals are much like detectives and
crime scene investigators -- gathering clues
about a pathogen until they can identify it. Who
can identify this famous literary detective?
Minisystems used to identify bacteria
API-20E for identification of Enterobacteriaceae
Enterotube II for identification of
Diagram illustrating the 3 types of hemolysis
that can be observed on a blood agar plate.
Isolation and Identification (Speciation) of
Pathogens (cont.)
  • Mycology Section
  • Responsibility is to assist clinicians in the
    diagnosis of fungal infections (mycoses).
  • The specimens processed here are the same as
    those that are processed in the Bacteriology
    Section, with the addition of hair and nail
    clippings and skin scrapings.
  • A variety of procedures are used to identify
    fungal pathogens including special media, the KOH
    prep, the tease mount, biochemical tests (for
    yeasts), and a combination of microscopic and
    macroscopic observations (for molds).

A colony (mycelium) of the mold Aspergillus
fumigatus, a common cause of pulmonary infections
in immunosuppressed patients.
Colonies (mycelia) of a Penicillium species
Isolation and Identification (Speciation) of
Pathogens (cont.)
  • Parasitology Section
  • Assists clinicians in the diagnosis of parasitic
  • Parasites are identified by observing and
    recognizing various parasite life cycle stages
    (e.g., cysts or trophozoites) in specimens, as
    well as their specific characteristics (e.g.,
    size, shape, internal details).
  • Virology Section
  • Assists clinicians in the diagnosis of viral
  • Techniques used in identification of viruses
    include immuno-diagnostic tests, cytologic or
    histologic examination, electron microscopy,
    molecular techniques, virus isolation by cell
    cultures, and cytopathic effect (CPE).

Isolation and Identification (Speciation) of
Pathogens (cont.)
  • Mycobacteriology Section (also called the TB Lab)
  • Assists clinicians in the diagnosis of
    tuberculosis (TB).
  • Various specimens are submitted, but sputum is
    the most common.
  • Mycobacterium spp. are identified by the
    acid-fast staining procedure and by using a
    combination of growth characteristics (e.g.,
    growth rate, colony pigmentation, photoreactivity
    and morphology) and a variety of biochemical

Review of Key Points
  • To avoid becoming infected, extreme care must be
    taken by those involved in collecting, handling
    and processing clinical specimens standard
    precautions should always be followed!
  • The quality of work performed by the CML
    laboratory can only be as good as the quality of
    the clinical specimens that are submitted to the
  • The 3 components of specimen quality are proper
    selection, proper collection, and proper
    transport of the specimen.

Review of Key Points (cont.)
  • The person collecting the specimen is ultimately
    responsible for its quality.
  • The laboratory is responsible for publishing a
    laboratory procedures manual that contains
    instructions for the proper selection, collection
    and transport of clinical specimens.
  • When collecting blood specimens for culture, the
    venipuncture site must be thoroughly cleansed and
    disinfected to prevent contamination of the
    specimen with indigenous skin flora.

Review of Key Points (cont.)
  • Aspirates are the preferred type of wound
  • All clinical specimens must be labeled properly
    and laboratory request slips must contain all
    necessary information.
  • The proper specimen to diagnose urinary tract
    infections (UTIs) is a clean-catch, midstream
  • CSF specimens are processed immediately upon
    their receipt in the CML because of the
    seriousness of meningitis, including possible
    death of the patients.
  • Routine throat swabs are collected to determine
    whether a patient has strep throat.

Review of Key Points (cont.)
  • Neisseria gonorrhoeae is a fastidious bacterium
    that is both microaerophilic and capnophilic
    special media are used and cultures are incubated
    in a CO2 environment.
  • The primary mission of the CML is to assist
    physicians in the diagnosis of infectious
  • The major responsibilities of those employed in
    the CML are (1) processing specimens, (2)
    isolating pathogens, (3) identifying pathogens,
    and (4) performing antimicrobial susceptibility
  • Environmental samples, collected from various
    sites within the hospital, are processed by the
    CML whenever an outbreak is suspected.
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