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

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Microbiology for the Health SciencesChapter
11.Epidemiology and Public Health
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Chapter 11 Outline

• Epidemiology
• Interactions Among Pathogens, Hosts and the
  Environment
• Chain of Infection
• Reservoirs of Infection
• Modes of Transmission
• Public Health Agencies
• Bioterrorism and Biological Warfare
• Water Supplies and Sewage Disposal

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Epidemiology

• Introduction
• Epidemiology can be defined as the study of
  disease.
• 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.

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Epidemiologic Terminology

• A communicable disease is an infectious disease
  that can be transmitted from one person to
  another
• 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
  population).

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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
  2006).
• 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

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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.

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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.)
• HIV/AIDS
• Tuberculosis
• Malaria

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Interactions Among Pathogens, Hosts, and the
Environment

• Whether an infectious disease occurs depends on
• Factors pertaining to the pathogen (e.g.,
  virulence of pathogen, mode of entry, number of
  organisms).
• 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.

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Chain of Infection

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

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The Chain of Infection
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Reservoirs of Infection

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

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Reservoirs of Infection (cont.)

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

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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
  vectors.
• Examples of arthropod-borne diseases
• Lyme disease
• Malaria

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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,
  etc.)

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Inanimate Vectors of Infection (Fomites)
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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

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Modes of Disease Transmission
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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

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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
  (MMWR).

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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.

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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

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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
  material.

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Water Supplies and Sewage Disposal (cont.)

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

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Steps in Water Treatment
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Review of Key Points

• Epidemiology is the study of the frequency and
  distribution of diseases and contributing
  factors.
• 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.

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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
  transmitted.
• 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.

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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.

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Review of Key Points (cont.)

• The major steps in water treatment are
  sedimentation, coagulation, filtration and
  chlorination.

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Microbiology for the Health SciencesChapter
12.Healthcare EpidemiologyNosocomial
Infections and Infection Control
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Chapter 12 Outline

• Introduction
• Nosocomial Infections
• Infection Control
• Concluding Remarks

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Introduction

• 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.

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Nosocomial Infections

• Infectious diseases can be divided into 2
  categories
• 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.

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Pathogens Most Often Involved in Nosocomial
Infections

• 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.

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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
  pneumonia).
• Bloodstream infections (septicemia).
• Other types gastrointestinal diseases caused by
  Clostridium difficile (referred to as Clostridium
  difficile-associated diseases).

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Patients Most Likely to Develop Nosocomial
Infections

• 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
  radiation.
• Immunosuppressed patients
• Patients who are paralyzed or are undergoing
  renal dialysis or catheterization

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Major Factors Contributing to Nosocomial
Infections

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

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Three major contributing factors in nosocomial
infections.
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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.

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Healthcare professional washing her hands.
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Infection Control

• Infection control - measures taken to prevent
  infections from occurring in healthcare settings.
• Asepsis means without infection there are 2
  types
• 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
  sterile.

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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.

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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)
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Various pieces of personal protective equipment,
(PPE), including masks, goggles, hair protection,
and disposable gowns.
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One-handed scoop technique for resheathing
needles.
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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
object).
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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
  hallway
• Air evacuated from the room passes through a HEPA
  filter.

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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.

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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
  aprons.
• 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.

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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
  possible.
• Disinfect or sterilize equipment
• Use individual equipment for each patient.
• Others

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Medical Waste Disposal

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

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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.

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Role of the Microbiology Laboratory in Hospital
Epidemiology and Infection Control

• CML personnel participate in infection control
  by
• 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
  detected.
• Processing environmental samples, including
  samples from hospital employees, that have been
  collected from within the affected ward(s).

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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
  infections.
• 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!

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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.

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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.

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Review of Key Points (cont.)

• All healthcare personnel must follow the same
  procedures to prevent the spread of communicable
  diseases.
• 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
  transmission.

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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.

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Microbiology for the Health SciencesChapter
13.Diagnosing Infectious Diseases
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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

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Introduction

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

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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
  secretions.
• All specimens should be of the highest possible
  quality!

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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
  specimens.
• In the laboratory, all specimens are handled
  carefully, exercising standard precautions.

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Importance of High-Quality Clinical Specimens

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

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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.

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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.

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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.

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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

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Obtaining a Urine Colony Count
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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

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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
  brain.
• 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!

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Technique of Lumbar Puncture
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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.

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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
  suspected.

• 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.

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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
  CO2.
• Special transport media is available and GC swabs
  should never be refrigerated.

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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.

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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
  divisions
• 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
  division.
• In addition, autopsies are performed in the
  morgue and some Pathology Departments may have an
  Electron Microscopy Laboratory.

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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).

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The Clinical Microbiology Laboratory
The CML may be under the direction of a
pathologist, a microbiologist or a clinical
laboratory scientist.
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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.

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Isolation and Identification (Speciation) of
Pathogens

• 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
  so.
• 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.)

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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?
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Minisystems used to identify bacteria
API-20E for identification of Enterobacteriaceae
Enterotube II for identification of
Enterobacteriaceae
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Diagram illustrating the 3 types of hemolysis
that can be observed on a blood agar plate.
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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).

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A colony (mycelium) of the mold Aspergillus
fumigatus, a common cause of pulmonary infections
in immunosuppressed patients.
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Colonies (mycelia) of a Penicillium species
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Isolation and Identification (Speciation) of
Pathogens (cont.)

• Parasitology Section
• Assists clinicians in the diagnosis of parasitic
  diseases.
• 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
  diseases.
• 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).

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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
  tests.

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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
  CML.
• The 3 components of specimen quality are proper
  selection, proper collection, and proper
  transport of the specimen.

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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.

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Review of Key Points (cont.)

• Aspirates are the preferred type of wound
  specimen.
• 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
  urine.
• 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.

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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
  diseases.
• The major responsibilities of those employed in
  the CML are (1) processing specimens, (2)
  isolating pathogens, (3) identifying pathogens,
  and (4) performing antimicrobial susceptibility
  testing.
• Environmental samples, collected from various
  sites within the hospital, are processed by the
  CML whenever an outbreak is suspected.