BASIC MICROBIOLOGY

FOR THE INFECTION

PREVENTIONIST
CARMENCHU ECHIVERRI –VILLAVICENCIO, MD,DPCP, FPSMID
ST. LUKE’S GLOBAL CITY
MAKATI MEDICAL CENTER
Microbiological Classification of
Infectious Diseases
 Disease is a disturbance in the state of health
 Microbes cause disease in the course of stealing
space, nutrients, and/or living tissue from their
symbiotic hosts (e.g., us)
HOW MICROBES CAUSE OF INFECTION

1. Gain access to the host (contamination)

2. Adhere to the host (adherence)
3. Replicate on the host (colonization)
4. Invade tissues (invasion)
5. Produce toxins or other agents that cause host harm
(damage)
BIOLOGIC CHARACTERISTICS OF
INFECTIOUS AGENTS
 Infectivity: The ability of the agent to enter a host and multiply to an infectious dose, thereby
producing the infection or disease.

Pathogenicity: The ability of the agent to cause disease in an infected host.

 Virulence: This term refers to the severity of the infection. A highly virulent strain of a disease
agent will most always produce severe cases or death.

Toxigenicity: This term refers to the ability of the agent to produce a toxin. The resulting illness or
disease is from the toxin produced by the organism/agent and not the microorganism itself.

Resistance: This term refers to the ability of the agent to survive under adverse environmental
conditions. It is also a measure of the agent's fragility.

Antigenicity: This term refers to the ability of the agent to induce antibody production in the host.
Agents that have a high antigenicity have a very low reinfection rate, whereas, agents with a low
antigenicity rate have a higher reinfection rate
CLASSIFICATION OF INFECTIOUS AGENTS

 Bacteria – survive on appropriate media, stain gram-positive or

-negative
 Viruses – obbligate intracellular parasites which only replicate
intracellularly (DNA, RNA)
 Fungi – non-motile filamentous, branching strands of
connected cells
 Metazoa – multicellular animals (e.g.parasites) with
complicated life cycles often involving several hosts
CLASSIFICATION OF INFECTIOUS AGENTS

 Protozoa – single cell organisms with a well-defined

nucleus
 Rickettsia – very small bacteria spread by ticks
 Prions – unique proteins lacking genetic molecules
 Chlamydia – bacteria lacking cell walls
MODES OF TRANSMISSION

 Direct
 Droplet
 Aerosol
 Skin to skin
 Indirect
 Fomites (clothes, blankets, door handles etc)
 Vectors (e.g. mosquitoes)
 Food and water
 Intermediate hosts (e.g. snails)
 CLINICAL RESPONSES TO INFECTION BY AN
AGENT
 Inapparent infection – no clinical symptoms generated
 Carrier state – usually no clinical symptoms but host can
transmit infection for long periods
 Clinical symptoms
 Mild disease
 Severe disease
 Residual impairment
 death
 Terms Used in Microbiology
• Infectious dose –number of organisms needed to successfully infect
• Latent period -exposure to infectiousness interval
• Incubation period – interval from exposure to clinical symptoms
• Infectious period – interval during which host can transmit infection
• Reproductive rate – ability of an agent to spread in populations
• Outbreak – limited spread
• Endemic – usually present; steady prevalence
• Epidemic – rapid spread
• Pandemic – occurring across countries and in multiple populations
Other Important Terms
Pathogenesis of infection
 When microbes find a new host and start to
multiply – called colonisation
 A balance can develop between colonised
microbes and humans – will lead to ‘so called’
normal flora
 If microbe causes disease – called an infection
 If source of microbe is patient’s own flora –
called an endogenous infection
 If source of microbe is flora from outside the
patient’s body – called exogenous infection
15
Basic microbiology
 Microorganisms are agents of infectious
diseases
 They are ubiquitous in nature and in/on human
body
 Most microorganisms harmless for humans
 Some can cause disease
 Microorganisms are divided into
 Bacteria
 Fungi
 Viruses
 Prions
 Parasites
16
Microorganism Transmission
 Spread to a new host from another human,
animal or environment
 Transmission direct or indirect
 Pathways of transmission could be
 Contact
 hands
 surgical instruments

 Contaminated surfaces or items (indirect contact)

 Air
 Water
 Food
 Live vectors, e.g., mosquitos
August 23,
17
2013
Bacteria

 Smallest microorganisms with all functions of life

 Multiply by simple division
 Form visible „colonies” on a solid surface
 Genetic material transferred vertically and
horizontally between different bacteria
 Some can form spores
 The most resistant form of life
August 23, 18
2013
Microbiological Classification of
Infectious Diseases
 Bacteria are classified by their Gram stain characteristics.
 Gram staining is the application of a crystal violet dye to a culture of bacteria. Bacteria
that retain the color of the dye are called Gram positive; bacteria that don't are Gram
negative.
 The Gram stain attaches to peptidoglycan in the bacterial cell wall.
 In Gram-negative bacteria, the peptidoglycan layer is protected by an outer membrane.
 The Gram Stain
In the late 1800’s, Christian Gram observed that some
genera of bacteria retained a dye-Iodine complex when
rinsed with alcohol, while other genera were easily
decolorized with alcohol and could be then visualized by
a contrasting counterstain.

This staining procedure defines two bacterial groups: those

which retain the primary dyes (“Positive by Gram’s
Method” or “Gram-Positive”) and those which are easily
decolorized (“Negative by Gram’s Method” or “Gram-
Negative”). This is the starting point for bacterial
identification procedures.
 The Gram Stain
The difference in dye retention is dependent on such physical
properties as thickness, density, porosity, and integrity of
the bacterial cell wall, as well as, to some extent, the
chemical composition.
Gram-Positive bacteria have thick, dense, relatively non-
porous walls, while Gram-Negative bacteria have thin
walls surrounded by lipid-rich membranes.
Some non-bacterial organisms with thick cell walls (e.g.,
some yeasts) also stain Gram-Positive.
Gram-Positive bacteria which have lost wall integrity
through aging or physical or chemical damage may stain
Gram-Negative.
Microbiological Classification of
Infectious Diseases
 The Gram Stain Procedure
•Step 1 - Prepare a Smear
Suspend some of the material to be stained in a
drop of water on a microscope slide, spread the drop
to about the size of a nickel.
Allow to air dry. Heat fix by gently warming
above a flame or other heat source.

Watch what happens to the “Bacteria” at each step

“Bacteria”
 The Gram Stain Procedure
•Step 2 - Apply the Primary Stain
Flood the Smear with Crystal Violet
Allow to stand 30 sec to 1 min
Rinse with water to remove excess stain
 The Gram Stain Procedure
•Step 3 - Apply the Fixing Agent

Flood the Smear with Iodine solution

Allow to stand 30 sec to 1 min
 The Gram Stain Procedure
•Step 4 - Rinse
Rinse with water to remove excess Iodine
 The Gram Stain Procedure
•Step 5 - Decolorize
Drip 95% Alcohol across the slide about 5 sec
The effluent should appear pale or clear
 The Gram Stain Procedure
•Step 6 - Rinse
Rinse with water to remove excess alcohol
 The Gram Stain Procedure
•Step 7 - Counterstain

Flood the slide with Safranin solution

Let stand 30 sec
 The Gram Stain
•Step 8 - Rinse, Dry and Observe
Rinse with water to remove excess stain
Blot dry
Observe under Oil Immersion

Gram-Positive Gram-Negative
 Examples of Gram Stains
Gram Positive Rods Gram Negative Rods
and Cocci and Cocci
Microbiological Classification of
Infectious Diseases
Bacteria Acinetobact Bordetella Campylobact Clostridium
er pertussis er jejuni, C. difficile
baumannii coli
Habitat Moist skin, NP mucosa GI tract GI tract
GI tract
Survival on 3 days – 5 3-5 days Up to 6 days Spores – 5
dry surfaces months months
Spread in HC Contact Droplets Faecal-oral, Faecal-oral;
water, food contact
HAIs UTI, sepsis, Pertussis Diarrhoea CDI
meningitis,
pneumonia
Specimens Urine, NP swab Stool Stool
blood, CSF,
sputum,
aspirates
Prevention Clean Isolation Safe food and Clean
environment water, clean environment,
, hands August 23, , hands, 35use
instruments, 2013
of antibiotics
hands
Bacteria Clostridium Coagulase C. Enterococcus
tetani negative diphtheriae species
staphylococ
ci (CNS)
Habitat Environment Skin, mucous NP GI tract, GU
membranes tract
Survival on 7 days – 6 5 days – 4
dry surfaces months months
Spread in HC Entering Contact Droplet, Contact,
umbilical contact endogenous
cord
HAIs Tetanus Various Diphtheria UTI, sepsis
Specimens Various NP swab Urine, blood
Prevention Sterilisation Clean Isolation, Clean
of environment vaccination environment,
instruments , hands, use of
instruments, cephalosporin
hands s
August 23,
36
2013
Bacteria Enterobacte Escherichia Helicobacte Klebsiella
r species coli r pylori pneumoniae
Habitat Environment GI, GU tract Gastric Environment,
, GI tract mucosa GI tract
Survival on 5-49 days 1.5 hours – 16 Less than 90 2 hours –
dry surfaces months minutes more than 30
months
Spread in HC Contact, Faecal-oral, GI Contact,
food contact, endoscopes endogenous
endogenous
HAIs UTI, sepsis, UTI, sepsis, Gastritis UTI, sepsis,
wound neonatal pneumonia
infection meningitis
Specimens Various Various Various Various
Prevention Clean Clean hands, Properly Clean hands,
environment use of disinfected use of
, equipment, cephalosporin GI cephalosporin
hands s endoscopes s
August 23,
37
2013
Bacteria Legionella Listeria M. Neisseria
pneumophila monocytogenes tuberculosis meningitid
is
Habitat Water GI tract, soil Respiratory NP
tract
Survival on 1 day - months 1 day – 4
dry months
surfaces
Spread in Aerosols Contaminated Airborne Droplets
HC food/equipmen
t ; perinatal
HAIs Legionnaire’s Meningitis, Tuberculosis Meningitis
disease bacteremia
Specimens Sputum, blood Blood, CSF Sputum CSF
for serology
Prevention Hyperchlorina Safe food, Isolation Isolation,
tion of water clean vaccination
or heating to equipment in
at least 55°C nurseries August 23,
38
2013
Bacteria Proteus Pseudomonas Salmonella Salmonella
species aeruginosa species typhi
Habitat GI tract GI tract, humid GI tract GI tract
areas
Survival on 1-2 days 6 hours to 16 1 day 10 months
dry months – 4.2 years
surfaces
Spread in Contact, Contact Faecal-oral Faecal-oral
HC endogenous
HAIs UTI, sepsis Various Diarrhoea, Typhoid
sepsis fever
Specimens Urine, blood Various Stool, blood Stool,
blood

Prevention Clean Clean, dry Safe food, Safe food,

environment, environment, water, clean water,
equipment, disinfected/ster hands clean
hands ilised hands
equipment; August 23,
39
clean hands, 2013

use of
Bacteria Salmonella Serratia Shigella S. aureus
typhimurium marcescens species
Habitat GI tract GI tract, humid GI tract Skin,
areas mucous
membranes
Survival on 10 months – 3 days – 2 2 days – 5 7 days - 7
dry 4.2 years months months months
surfaces
Spread in Faecal-oral Contact, IV Faecal-oral Contact,
HC fluids droplets,
equipment,
endogenous
HAIs Diarrhoea, Sepsis, wound Diarrhoea Various
sepsis infection
Specimens Stool, blood Blood, wound Stool Various
exudate
Prevention Safe food, Clean Safe food, Clean hands,
water, clean environment, water, clean environment
hands equipment, hands August 23, ; use of
40
hands 2013
antibiotics
Bacteria S. agalactiae S. pyogenes Vibrio Yersinia
(Group B (Group A cholerae enterocoliti
streptococcus streptococcus) ca
)
Habitat Birth canal Oropharyngeal GI tract GI tract
mucosa
Survival on 3 days-6.5 1 – 7 days
dry months
surfaces
Spread in Contact, Droplet, Faecal-oral Blood
HC Intrapartum contact, transfusion
endogenous
HAIs Sepsis and Pharyngitis, Cholera Bacteremia
meningitis of surgical wound
newborn infection
Specimens Blood, CSF Oropharyngeal Stool Blood, stool
swab, wound
exudate
Prevention Antibiotic Clean hands, Safe water
August 23, Safe blood
41
prophylaxis masks in and food 2013 products
during operating room
Non-susceptible >2 classes of
to drugs
XDR and PDR

Non-susceptible to at least 1
drug in all but two or fewer
classes

Non-susceptible to all
agents in all classes
What is a “class” of drugs?

Beta-lactams
What is a “class” of drugs?

Penicillins

Cephalosporins

Monobactams

Carbapenems
What is a “class” of drugs?

Aminopenicillins 1st gen. Cephalosporins

Ureidopenicillins 2nd gen. Cephalosporins

Carboxypenicillins 3rd gen. Cephalosporins

ß-lactamase resistant 4th gen. Cephalosporins

penicillins
5th gen. Cephalosporins
ß-lactamase inhibitor
combinations Cefamycins

Monobactams Carbapenems
What is resistance to a class?

Bug A Bug B Bug C Bug D

Gentamicin R R R I
Tobramycin R R S S
Amikacin R S S S
Resistant to
this class?
MDRO Definitions

Resistant to oxacillin, methicillin, or

cefoxitin, or positive by an FDA-
approved test for mecA on isolated
colonies or in specimens

Not a MRSA

http://www.cdc.gov/nhsn/PDFs/psc
Manual/12pscMDRO_CDADcurrent.pd
f, January 2013
MDRO Definitions

Any Enterococcus resistant to

vancomycin or positive by an FDA-
approved test for VRE

Any Klebsiella non-susceptible to

ceftriaxone, cefotaxime,
ceftazidime, or cefepime***

***Based on new breakpoints

http://www.cdc.gov/nhsn/PDFs/psc
Manual/12pscMDRO_CDADcurrent.pd
f, January 2013
MDRO Definitions

Non-susceptible to imipenem,
meropenem, or doripenem***, or
positive by a test for carbapenemase

***Based on new breakpoints

http://www.cdc.gov/nhsn/PDFs/psc
Manual/12pscMDRO_CDADcurrent.pd
f, January 2013
MDRO Definitions

http://www.cdc.gov/nhsn/PDFs/psc
Manual/12pscMDRO_CDADcurrent.pd
f, January 2013
 Call this Based on new
one the breakpoints
Back to CRE
“CRE
Toolkit”

http://www.cdc.gov/hai/organisms/cre/cre-
Is this an MDRO?

Amox/Clav S Linezolid S
Ceftriaxone S Oxacillin S
Clindamycin R Rifampin S
Cefazolin S Trim/Sulfa S
Daptomycin S Tetracycline R
Erythromycin R Vancomycin S
Gentamicin S
Levofloxacin R
Is this a CRE?

Amp/Sulbactam R Cefazolin R
Ampicillin R Cefepime S
Amox/Clav R Cefuroxime R
Aztreonam R Ertapenem R
Ceftriaxone R Imipenem I
Ceftazidime R Meropenem S
Cefotaxime R Piperacillin R
Cefoxitin R Pip/Tazo I
Fungi

 Unicellular (yeasts) or multicellular (moulds)

 Reproduce asexually (conidia) and sexually
(spores*)
 Ubiquitous in nature
 some are parts of human normal flora
 Most opportunistic pathogens
 Cause severe infections in immunocompromised host
* Fungal spores are not resistant to environmental factors like
bacterial spores! August 23,
55
2013
Fungi Candida Candida Candida
albicans glabrata parapsilosis
(yeast) (yeast) (yeast)
Habitat Environment, Environment, Environment,
mucosa mucosa mucosa
Survival on 1-120 days 120-150 days 14 days
dry
surfaces
Spread in Contact, Contact, Contact,
HC endogenous endogenous endogenous
HAIs Various Various Various
Specimens Various Various Various
Prevention Clean hands, Clean hands, Clean hands,
equipment equipment equipment

August 23,
56
2013
Fungi Aspergillus Mucor (mould) Rhizopus
species (mould) (mould)
Habitat Environment, air Environment Environment

Survival Conidia and Conidia and Conidia and

on dry spores are spores are spores are
surfaces resistant resistant resistant
Spread in Inhalation, Inhalation Inhalation
HC (contact)
HAIs Various Various Various
Specimen Various Various Various
s
Preventio Safe water, air, Safe food, Safe food,
n reverse/protectiv reverse/protectiv reverse/protecti
e isolation e isolation ve isolation

August 23,
57
2013
Viruses - 1
 Smallest infectious agents
 Require living cell for reproduction
 bacterial, plant or animal
 Consist of either DNA or RNA and a protein
coat
 Some have also an outside lipid envelope

August 23,
58
2013
Viruses - 2
 Entering the
cell, virus makes
the cell
synthesise its
nucleic acid and
proteins
 The cell is severely
damaged or destroyed
and infectious disease
develops

August 23,
59
2013
Virus Adenovirus Coronavirus, Coxackie B Cytomegalovirus
including virus
SARS
Habitat Water, Humans Humans Humans
fomites,
environment
Survival 7 days – 3 3 hours >2 weeks 8 hours
on dry months SARS virus:
surfaces 72-96 hours
Spread in Contact Droplet Faecal-oral; Blood products,
HC contact tissue and organs
HAIs Eye, Respiratory Generalised Various
respiratory infections disease of
infections newborn
Specimens Serum Serum Serum Serum sample
sample sample sample
Preventio Individual Isolation, Clean hands, Safe blood
n eye drops clean hands, environment products,
environment Augusttissues/
23,
2013
organs
60

for
transplantation
Virus Human Influenza Norovirus Respiratory
immunodeficien virus syncytial virus
cy virus
Habitat Humans Humans Humans Humans
Survival >7 days 1-2 days 8 hours – 7 Up to 6 hours
on dry days
surfaces
Spread in Blood, body Droplets, Faecal-oral, Droplets,
HC fluids, tissue, contact contact contact
organs for
transplant
HAIs Acquired immune Influenza Diarrhoea Acute
deficiency respiratory
syndrome infections
Specimens Serum sample Serum Serum NP exudate
sample sample
Preventio Safe blood Isolation, Clean hands, Isolation, clean
n products and vaccinatio environment, hands,
tissues/organs n safe food August2013
23,environment
61

for transplant
Virus Rotavirus Rubula virus Rubivirus
(mumps) (rubella)
Habitat Humans Humans Humans
Survival on 6-60 days
dry surfaces
Spread in HC Faecal-oral, Droplets Droplets
contact
HAIs Diarrhoea Mumps Rubella
(parotitis) (German
measles)
Specimens Stool Serum sample Serum sample
Prevention Clean hands, Isolation, Isolation,
environment vaccination vaccination

August 23,
62
2013
Virus Morbillivirus Varicella-zoster
(measles) virus
Habitat Humans Humans
Survival on
dry surfaces
Spread in HC Droplets Droplets, close
contact
HAIs Measles Varicella
Specimens Serum sample Serum sample
Prevention Isolation, vaccination Isolation,
vaccination

August 23,
63
2013
Prions
 Prions are proteinaceous particles
 Do not contain any nucleic acid
 Connected to several severe neurologic
diseases
 Highly resistant to usual disinfection and
sterilisation methods
 Possibility of iatrogenic transmission
 Through transplantation
 Through instruments contaminated with brain
tissue, dura or cerebrospinal fluid of infected
person
August 23,
64
2013
Parasites
 Include protozoa
 Unicellular microorganisms
 Live in nature or in human or animal host
 Some of them cause infections

 Multicellular parasites
 Worms, that can also cause infections (often
called infestations)
 Cause frequent diseases in humans,
especially in warm climates (e.g., malaria,
shistosomiasis)
 Not often the cause of HAI August 23,
65
2013
Parasite Cryptosporidiu Plasmodiu Trichomonas Enterobius
m (protozoa) m species vaginalis vermicularis
(protozoa) (protozoa) (helminth)
Habitat Liver, Vaginal mucosa Intestinal
erythrocyt tract
es
Survival 2 hours on dry Several hours Eggs: at least
on dry surface in humid 1 year
surfaces environment
Spread in Mosquito- Contaminated Faecal-oral
HC borne; equipment in
infected gynaecology
blood
HAIs Malaria Vaginal Enterobiasis
infection
Specimens Blood Vaginal Perianal tape
discharge
Preventio Safe blood Disinfected/ Clean
n products sterilised August2013
23, environment,
66

equipment in clean hands

gynaecology