Role of microbiology
laboratory in IP&C
1. Describe the basic properties of
microorganisms, including their natural habitat
and mode of transmission.
2. List the most important "alert" microorganisms
causing HAIs.
3. Explain the role of microbiology laboratory in
managing patients with infections.
4. Explain the four roles of the microbiology
laboratory in the prevention and control of
HAIs.
August 23, 2013
Objectives
2
• 60 minutes
August 23, 2013
Time involved
3
• Microorganisms are agents of infectious diseases
• They are ubiquitous in nature and in/on human
body
• Most microorganisms harmless for humans
August 23, 2013
Basic microbiology
• Some can cause disease
• Microorganisms are divided into
•
•
•
•
•
Bacteria
Fungi
Viruses
Prions
Parasites
4
• 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
August 23, 2013
Pathogenesis of infection
• 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
5
• Spread to a new host from another human,
animal or environment
• Transmission direct or indirect
• Pathways of transmission could be
August 23, 2013
Microorganism Transmission
• Contact
• hands
• surgical instruments
•
•
•
•
•
Contaminated surfaces or items (indirect contact)
Air
Water
Food
Live vectors, e.g., mosquitos
6
• Smallest microorganisms with all functions of life
• Multiply by simple division
• Form visible „colonies” on a solid surface
August 23, 2013
Bacteria
• Genetic material transferred vertically and
horizontally between different bacteria
• Some can form spores
• The most resistant form of life
7
Acinetobacter Bordetella
baumannii
pertussis
Campylobacter Clostridium
jejuni, C. coli
difficile
Habitat
Moist skin, GI
tract
NP mucosa
GI tract
GI tract
Survival on
dry surfaces
3 days – 5
months
3-5 days
Up to 6 days
Spores – 5
months
Spread in HC
Contact
Droplets
Faecal-oral,
water, food
Faecal-oral;
contact
HAIs
UTI, sepsis,
meningitis,
pneumonia
Pertussis
Diarrhoea
CDI
Specimens
Urine, blood,
CSF, sputum,
aspirates
NP swab
Stool
Stool
Prevention
Clean
environment,
instruments,
hands
Isolation
Safe food and
water, clean
hands
Clean
environment,,
hands, use of
antibiotics
August 23, 2013
Bacteria
8
Clostridium
tetani
Coagulase
negative
staphylococci
(CNS)
C. diphtheriae
Enterococcus
species
Habitat
Environment
Skin, mucous
membranes
NP
GI tract, GU
tract
7 days – 6
months
5 days – 4
months
Survival on
dry surfaces
Spread in HC
Entering
Contact
umbilical cord
Droplet,
contact
Contact,
endogenous
HAIs
Tetanus
Various
Diphtheria
UTI, sepsis
Various
NP swab
Urine, blood
Isolation,
vaccination
Clean
environment,
hands, use of
cephalosporins
Specimens
Prevention
Sterilisation of Clean
instruments
environment,
instruments,
hands
August 23, 2013
Bacteria
9
Enterobacter
species
Escherichia coli Helicobacter
pylori
Klebsiella
pneumoniae
Habitat
Environment,
GI tract
GI, GU tract
Gastric
mucosa
Environment,
GI tract
Survival on
dry surfaces
5-49 days
1.5 hours – 16
months
Less than 90
minutes
2 hours – more
than 30 months
Spread in HC
Contact, food
Faecal-oral,
contact,
endogenous
GI
endoscopes
Contact,
endogenous
HAIs
UTI, sepsis,
wound
infection
UTI, sepsis,
neonatal
meningitis
Gastritis
UTI, sepsis,
pneumonia
Specimens
Various
Various
Various
Various
Prevention
Clean
environment,
equipment,
hands
Clean hands,
Properly
use of
disinfected GI
cephalosporins endoscopes
August 23, 2013
Bacteria
Clean hands,
use of
cephalosporins
10
Legionella
pneumophila
Listeria
monocytogenes
M.
tuberculosis
Neisseria
meningitidis
Habitat
Water
GI tract, soil
Respiratory
tract
NP
1 day - months
1 day – 4
months
Survival on
dry surfaces
Spread in
HC
Aerosols
Contaminated
Airborne
food/equipment ;
perinatal
Droplets
HAIs
Legionnaire’s
disease
Meningitis,
bacteremia
Tuberculosis
Meningitis
Specimens
Sputum, blood
for serology
Blood, CSF
Sputum
CSF
Prevention
Hyperchlorinati
on of water or
heating to at
least 55°C
Safe food, clean
equipment in
nurseries
Isolation
Isolation,
vaccination
August 23, 2013
Bacteria
11
Proteus species Pseudomonas
aeruginosa
Salmonella
species
Salmonella
typhi
Habitat
GI tract
GI tract, humid
areas
GI tract
GI tract
Survival on
dry surfaces
1-2 days
6 hours to 16
months
1 day
10 months –
4.2 years
Spread in
HC
Contact,
endogenous
Contact
Faecal-oral
Faecal-oral
HAIs
UTI, sepsis
Various
Diarrhoea,
sepsis
Typhoid
fever
Specimens
Urine, blood
Various
Stool, blood
Stool, blood
Prevention
Clean
environment,
equipment,
hands
Clean, dry
environment,
disinfected/sterili
sed equipment;
clean hands, use
of antibiotics
Safe food,
water, clean
hands
Safe food,
water, clean
hands
August 23, 2013
Bacteria
12
Salmonella
typhimurium
Serratia
marcescens
Shigella
species
S. aureus
Habitat
GI tract
GI tract, humid
areas
GI tract
Skin, mucous
membranes
Survival on
dry surfaces
10 months –
4.2 years
3 days – 2
months
2 days – 5
months
7 days - 7
months
Spread in
HC
Faecal-oral
Contact, IV fluids
Faecal-oral
Contact,
droplets,
equipment,
endogenous
HAIs
Diarrhoea,
sepsis
Sepsis, wound
infection
Diarrhoea
Various
Specimens
Stool, blood
Blood, wound
exudate
Stool
Various
Prevention
Safe food,
water, clean
hands
Clean
environment,
equipment,
hands
Safe food,
water, clean
hands
Clean hands,
environment;
use of
antibiotics
August 23, 2013
Bacteria
13
S. agalactiae
(Group B
streptococcus)
S. pyogenes
(Group A
streptococcus)
Vibrio
cholerae
Yersinia
enterocolitica
Habitat
Birth canal
Oropharyngeal
mucosa
GI tract
GI tract
3 days-6.5
months
1 – 7 days
Survival on
dry surfaces
Spread in
HC
Contact,
Intrapartum
Droplet, contact,
endogenous
Faecal-oral
Blood
transfusion
HAIs
Sepsis and
meningitis of
newborn
Pharyngitis,
surgical wound
infection
Cholera
Bacteremia
Specimens
Blood, CSF
Oropharyngeal
swab, wound
exudate
Stool
Blood, stool
Prevention
Antibiotic
Clean hands,
prophylaxis
masks in
during delivery; operating room
clean hands
August 23, 2013
Bacteria
Safe water and Safe blood
food
products
14
• Unicellular (yeasts) or multicellular (moulds)
• Reproduce asexually (conidia) and sexually
(spores*)
• Ubiquitous in nature
August 23, 2013
Fungi
• 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!
15
Candida
Candida
albicans (yeast) glabrata (yeast)
Candida
parapsilosis
(yeast)
Habitat
Environment,
mucosa
Environment,
mucosa
Environment,
mucosa
Survival on
dry surfaces
1-120 days
120-150 days
14 days
Spread in
HC
Contact,
endogenous
Contact,
endogenous
Contact,
endogenous
HAIs
Various
Various
Various
Specimens
Various
Various
Various
Prevention
Clean hands,
equipment
Clean hands,
equipment
Clean hands,
equipment
August 23, 2013
Fungi
16
Aspergillus species
(mould)
Mucor (mould)
Rhizopus (mould)
Habitat
Environment, air
Environment
Environment
Survival on Conidia and spores
dry
are resistant
surfaces
Conidia and spores
are resistant
Conidia and
spores are
resistant
Spread in
HC
Inhalation,
(contact)
Inhalation
Inhalation
HAIs
Various
Various
Various
Specimens
Various
Various
Various
Safe food,
reverse/protective
isolation
Safe food,
reverse/protective
isolation
Prevention Safe water, air,
reverse/protective
isolation
August 23, 2013
Fungi
17
• Smallest infectious agents
• Require living cell for reproduction
• bacterial, plant or animal
• Consist of either DNA or RNA and a protein coat
August 23, 2013
Viruses - 1
• Some have also an outside lipid envelope
18
• Entering the cell,
virus makes the
cell synthesise its
nucleic acid and
proteins
August 23, 2013
Viruses - 2
• The cell is severely
damaged or
destroyed and
infectious disease
develops
19
Adenovirus
Coronavirus,
including
SARS
Coxackie B
virus
Cytomegalovirus
Habitat
Water,
fomites,
environment
Humans
Humans
Humans
Survival on
dry
surfaces
7 days – 3
months
3 hours
>2 weeks
SARS virus: 7296 hours
8 hours
Spread in
HC
Contact
Droplet
Faecal-oral;
contact
Blood products,
tissue and organs
HAIs
Eye,
respiratory
infections
Respiratory
infections
Generalised
disease of
newborn
Various
Specimens
Serum sample
Serum sample
Serum sample Serum sample
Prevention
Individual eye
drops
Isolation, clean Clean hands,
hands,
environment
environment
Safe blood
products, tissues/
organs for
transplantation
August 23, 2013
Virus
20
Human
immunodeficiency
virus
Influenza
virus
Norovirus
Respiratory
syncytial virus
Habitat
Humans
Humans
Humans
Humans
Survival on
dry
surfaces
>7 days
1-2 days
8 hours – 7
days
Up to 6 hours
Spread in
HC
Blood, body fluids,
tissue, organs for
transplant
Droplets,
contact
Faecal-oral,
contact
Droplets, contact
HAIs
Acquired immune
deficiency
syndrome
Influenza
Diarrhoea
Acute respiratory
infections
Specimens
Serum sample
Serum
sample
Serum sample
NP exudate
Prevention
Safe blood
products and
tissues/organs for
transplant
Isolation,
vaccination
Clean hands,
environment,
safe food
Isolation, clean
hands,
environment
August 23, 2013
Virus
21
Rotavirus
Rubula virus
(mumps)
Rubivirus
(rubella)
Habitat
Humans
Humans
Humans
Survival on dry 6-60 days
surfaces
Spread in HC
Faecal-oral,
contact
Droplets
Droplets
HAIs
Diarrhoea
Mumps
(parotitis)
Rubella (German
measles)
Specimens
Stool
Serum sample
Serum sample
Prevention
Clean hands,
environment
Isolation,
vaccination
Isolation,
vaccination
August 23, 2013
Virus
22
Morbillivirus (measles)
Varicella-zoster virus
Habitat
Humans
Humans
Spread in HC
Droplets
Droplets, close contact
HAIs
Measles
Varicella
Specimens
Serum sample
Serum sample
Prevention
Isolation, vaccination
Isolation, vaccination
Survival on dry
surfaces
August 23, 2013
Virus
23
• 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
August 23, 2013
Prions
• Through transplantation
• Through instruments contaminated with brain tissue,
dura or cerebrospinal fluid of infected person
24
• Include protozoa
• Unicellular microorganisms
• Live in nature or in human or animal host
• Some of them cause infections
August 23, 2013
Parasites
• 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
25
Cryptosporidium
(protozoa)
Habitat
Survival on
dry
surfaces
Plasmodium Trichomonas
species
vaginalis
(protozoa)
(protozoa)
Enterobius
vermicularis
(helminth)
Liver,
Vaginal mucosa
erythrocytes
Intestinal tract
Several hours in
humid
environment
Eggs: at least 1
year
2 hours on dry
surface
Spread in
HC
Mosquitoborne;
infected
blood
Contaminated
equipment in
gynaecology
Faecal-oral
HAIs
Malaria
Vaginal infection
Enterobiasis
Specimens
Blood
Vaginal discharge Perianal tape
Prevention
Safe blood
products
Disinfected/
sterilised
equipment in
gynaecology
Clean
environment,
clean hands
August 23, 2013
Parasite
26
The diagnosis of infections performed by the
laboratory has two important functions
• Clinical
August 23, 2013
Role of microbiology
laboratory: Introduction
• Diagnosis of infection in an individual patient for everyday
management of infections
• Epidemiological
• Support for infection prevention and control in searching
for source and route of transmission of HAI
27
1. Set up inside the facility
•
If not possible, negotiate a contract for diagnostic
microbiology with the nearest laboratory
August 23, 2013
Minimal requirements for
microbiology services - 1
2. Available every day, including Sundays and
holidays
•
Ideally on a 24-hour basis
3. Able to examine blood, cerebrospinal fluid,
urine, stool, wound exudate or swab,
respiratory secretions, and perform basic
serological tests (HIV, HBV, HCV)
28
4. Identify common bacteria and fungi to species
level
5. Perform susceptibility testing using discdiffusion methodology
6. Perform basic phenotyping
•
Serotyping
•
•
August 23, 2013
Minimal Requirements for
microbiology services - 2
Salmonellae, Shigellae, P. aeruginosa, N. meningitidis
Biotyping
• S. typhi
29
Diagnosis should be rapid and accurate to the
species level wherever possible
• Classical bacteriological methods
August 23, 2013
Clinical role: Diagnosis of
infection
• Direct smear
• Culture
• Antigen detection
• Sensitivity testing
• Antibody detection
• Not very useful in the early stages of infection
• Molecular methods
• Rarely used in routine work for the diagnosis of bacterial HAI
30
• Outbreak investigation
• Surveillance of HAIs
• Alert microorganisms reports
• Designing antibiotic policy
August 23, 2013
Role in prevention and control
of healthcare associated
infections
31
• To determine the cause of a single-source
outbreak the causative agent must be defined
• Then microbiology laboratory determines if two
or more isolated strains are same or different
August 23, 2013
Outbreak Investigation
32
• Sometimes the IP&C Team requires additional
data to clarify endemic or epidemic situations
• Microbiological tests may be required
•
•
•
•
•
•
•
Blood products
Environmental surfaces
Disinfectants and antiseptics
Air
Water
Hands of personnel
Anterior nares of personnel
August 23, 2013
Additional tests during an
outbreak
33
• The microbiology laboratory should produce
routine reports of bacterial isolates
• Allows the IPC& Team to make graphs for specific
pathogens, wards, and groups of patients
August 23, 2013
HAI surveillance
• A ‘baseline incidence’ can be established
• Any new isolate can then be compared with this
incidence
• If the laboratory is computerised, these data can
be made readily available
34
• Identify possible agreed ‘alert’ microorganisms
•
•
•
•
•
•
•
•
Methicillin-resistant Staphylococcus aureus (MRSA)
Vancomycin-intermediate S.aureus (VISA)
Vancomycin-resistant enterococci (VRE)
MDR Pseudomonas aeruginosa
MDR Acinetobacter baumannii
MDR Mycobacterium tuberculosis
ESBL enterobacteria
Clostridium difficile
August 23, 2013
Alert organism reports
35
• Regular reporting of changing resistance
patterns
– Newsletters
– Specialty specific data
August 23, 2013
Antibiotic policy
• Restricted antibiotic reporting
• Routinely only first line antibiotics
• Reserve antibiotics only if pathogen is resistant to first
line antibiotics
36
Role of Clinical Microbiologist/ID specialist
• Provide leadership to antimicrobial team
• Antibiotic ward rounds
• Interpretation of patient specific data to optimise
treatment
August 23, 2013
Antibiotic stewardship
• culture & sensitivity
• Active surveillance/ awareness
• Screening for carriage of resistant bacteria
• Molecular detection and typing
37
• Microbiologists interpret microbiological data for
IP&C staff
• Results of isolation, identification, susceptibility tests,
typing
August 23, 2013
Interpretation of Microbiology
Data
• Ideally should be medical doctor specialistt
• If this is not possible, then a properly educated
scientist is required
38
• Infection prevention staff
• how to interpret microbiological reports/charts
• Other healthcare workers
August 23, 2013
Role in education
• specimen collection and transport, interpretation of
reports and sensitivity tests
• Students (medical and nursing)
• basic microbiology
39
• Microbes are infectious agents not visible to the
naked eye
• Widespread in nature and some cause human disease
• Diagnosis of infection by the microbiology
laboratory has two important functions
August 23, 2013
Key points - 1
• Clinical
• Epidemiological
• The laboratory should determine the most
frequent microbes causing infections, including
HAI pathogens
40
• The laboratory should perform basic typing of
microorganisms
• The laboratory should produce routine reports
for IP&C personnel
August 23, 2013
Key points - 2
• To make incidence graphs for specific pathogens,
wards, and groups of patients
• Medical microbiologists interpret microbiological
findings for IP&C personnel and act together
with clinical and nursing colleagues in prevention
of HAI
41
•
•
•
Diekema DJ, et al. Infection Control Epidemiology and
Microbiology Laboratory. In Manual of Clinical
Microbiology, 8th Ed., Murray PR, Editor in Chief, ASM
Press, Washington, DC, 2003:129-138
Peterson LR, et al. Role of clinical microbiology
laboratory in the management and control of infectious
diseases and the delivery of health care. Clin Infect Dis
2001; 32:605-611
Gill VJ, et al. The clinician and the Microbiology
Laboratory. In: Mandell, Douglas and Bennett’s
Principles and Practice of Infectious Diseases, 6th ed.,
Mandell GL, Bennett JE, Dolin R, Editors, Elsevier,
Philadelphia, 2005:203-241
August 23, 2013
References
42
•
Stratton CW IV, Greene JN. Role of the Microbiology
Laboratory in Hospital Epidemiology and Infection
Control. In: Hospital Epidemiology and Infection
Control, 3rd Ed., Mayhall CG, Editor, Lippincott,
Williams & Wilkins, Philadelphia, 2004:1809-1825
•
Poutanen SM, Tompkins LS. Molecular Methods in
Nosocomial Epidemiology. In: Prevention and Control
of Nosocomial Infections, 4th Ed., Wenzel RP, Editor,
Lippincott, Williams & Wilkins, Philadelphia, 2003: 481499
August 23, 2013
References
43
1. Microorganisms that can cause disease in humans
cannot live in the inanimate environment. T/F
2. Genetic material in bacteria can be transmitted not
only vertically, but also horizontally. T/F
3. For the role of microbiology laboratory in HAI
surveillance, which of the following laboratory
characteristics is not necessary:
a.
b.
c.
d.
August 23, 2013
Quiz
Produce routine periodic reports of isolated microbes
Make „baseline incidence” graphs
Have a physician as a microbiologist
Have a vigorous quality assurance program
44
• IFIC’s mission is to facilitate international networking in
order to improve the prevention and control of
healthcare associated infections worldwide. It is an
umbrella organisation of societies and associations of
healthcare professionals in infection control and related
fields across the globe .
• The goal of IFIC is to minimise the risk of infection within
healthcare settings through development of a network of
infection control organisations for communication,
consensus building, education and sharing expertise.
• For more information go to http://theific.org/
December 1, 2013
International Federation of
Infection Control
45