Role of microbiology

laboratory in IP&C
Objectives

August 23, 2013

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.
2
Time involved
• 60 minutes

August 23, 2013

3
Basic microbiology
• Microorganisms are agents of infectious diseases

August 23, 2013

• 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 4
Pathogenesis of infection
• When microbes find a new host and start to

August 23, 2013

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
5
patient’s body – called exogenous infection
Microorganism Transmission
• Spread to a new host from another human,

August 23, 2013

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 6
• Live vectors, e.g., mosquitos
Bacteria
• Smallest microorganisms with all functions of life

August 23, 2013

• 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

7
Bacteria Acinetobacter Bordetella Campylobacter Clostridium
baumannii pertussis jejuni, C. coli difficile
Habitat Moist skin, GI NP mucosa GI tract GI tract
tract

August 23, 2013

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, blood, NP swab Stool Stool
CSF, sputum,
aspirates
Prevention Clean Isolation Safe food and Clean
environment, water, clean environment,,
instruments, hands hands, use of
hands antibiotics 8
Bacteria Clostridium Coagulase C. diphtheriae Enterococcus
tetani negative species
staphylococci
(CNS)

August 23, 2013

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 cord contact endogenous
HAIs Tetanus Various Diphtheria UTI, sepsis
Specimens Various NP swab Urine, blood
Prevention Sterilisation of Clean Isolation, Clean
instruments environment, vaccination environment,
instruments, hands, use of
hands cephalosporins

9
Bacteria Enterobacter Escherichia coli Helicobacter Klebsiella
species pylori pneumoniae
Habitat Environment, GI, GU tract Gastric Environment,
GI tract mucosa GI tract

August 23, 2013

Survival on 5-49 days 1.5 hours – 16 Less than 90 2 hours – more
dry surfaces months minutes than 30 months
Spread in HC Contact, food Faecal-oral, GI Contact,
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 GI use of
equipment, cephalosporins endoscopes cephalosporins
hands
10
Bacteria Legionella Listeria M. Neisseria
pneumophila monocytogenes tuberculosis meningitidis
Habitat Water GI tract, soil Respiratory NP
tract

August 23, 2013

Survival on 1 day - months 1 day – 4
dry surfaces months
Spread in Aerosols Contaminated Airborne Droplets
HC food/equipment ;
perinatal
HAIs Legionnaire’s Meningitis, Tuberculosis Meningitis
disease bacteremia
Specimens Sputum, blood Blood, CSF Sputum CSF
for serology
Prevention Hyperchlorinati Safe food, clean Isolation Isolation,
on of water or equipment in vaccination
heating to at nurseries
least 55°C
11
Bacteria Proteus species Pseudomonas Salmonella Salmonella
aeruginosa species typhi
Habitat GI tract GI tract, humid GI tract GI tract
areas

August 23, 2013

Survival on 1-2 days 6 hours to 16 1 day 10 months –
dry surfaces months 4.2 years
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, clean
equipment, disinfected/sterili hands hands
hands sed equipment;
clean hands, use
of antibiotics 12
Bacteria Salmonella Serratia Shigella S. aureus
typhimurium marcescens species
Habitat GI tract GI tract, humid GI tract Skin, mucous
areas membranes

August 23, 2013

Survival on 10 months – 3 days – 2 2 days – 5 7 days - 7
dry surfaces 4.2 years months months months
Spread in Faecal-oral Contact, IV fluids Faecal-oral Contact,
HC 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 use of
hands antibiotics 13
Bacteria S. agalactiae S. pyogenes Vibrio Yersinia
(Group B (Group A cholerae enterocolitica
streptococcus) streptococcus)
Habitat Birth canal Oropharyngeal GI tract GI tract

August 23, 2013

mucosa
Survival on 3 days-6.5 1 – 7 days
dry surfaces months
Spread in Contact, Droplet, contact, Faecal-oral Blood
HC Intrapartum endogenous transfusion
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 and Safe blood
prophylaxis masks in food products
during delivery; operating room 14
clean hands
Fungi
• Unicellular (yeasts) or multicellular (moulds)

August 23, 2013

• 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 15

bacterial spores!
Fungi Candida Candida Candida
albicans (yeast) glabrata (yeast) parapsilosis
(yeast)
Habitat Environment, Environment, Environment,

August 23, 2013

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

16
Fungi Aspergillus species Mucor (mould) Rhizopus (mould)
(mould)
Habitat Environment, air Environment Environment

August 23, 2013

Survival on Conidia and spores Conidia and spores Conidia and
dry are resistant are resistant spores are
surfaces resistant
Spread in Inhalation, Inhalation Inhalation
HC (contact)
HAIs Various Various Various
Specimens Various Various Various
Prevention Safe water, air, Safe food, Safe food,
reverse/protective reverse/protective reverse/protective
isolation isolation isolation

17
Viruses - 1
• Smallest infectious agents

August 23, 2013

• 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

18
Viruses - 2
• Entering the cell,

August 23, 2013

virus makes the
cell synthesise its
nucleic acid and
proteins
• The cell is severely
damaged or
destroyed and
infectious disease
develops
19
Virus Adenovirus Coronavirus, Coxackie B Cytomegalovirus
including virus
SARS
Habitat Water, Humans Humans Humans

August 23, 2013

fomites,
environment
Survival on 7 days – 3 3 hours >2 weeks 8 hours
dry months SARS virus: 72-
surfaces 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 sample Serum sample Serum sample Serum sample

Prevention Individual eye Isolation, clean Clean hands, Safe blood

drops hands, environment products, tissues/ 20
environment organs for
transplantation
Virus Human Influenza Norovirus Respiratory
immunodeficiency virus syncytial virus
virus
Habitat Humans Humans Humans Humans

August 23, 2013

Survival on >7 days 1-2 days 8 hours – 7 Up to 6 hours
dry days
surfaces
Spread in Blood, body fluids, Droplets, Faecal-oral, Droplets, contact
HC tissue, organs for contact contact
transplant
HAIs Acquired immune Influenza Diarrhoea Acute respiratory
deficiency infections
syndrome
Specimens Serum sample Serum Serum sample NP exudate
sample
Prevention Safe blood Isolation, Clean hands, Isolation, clean
products and vaccination environment, hands,
tissues/organs for safe food environment 21
transplant
Virus Rotavirus Rubula virus Rubivirus
(mumps) (rubella)
Habitat Humans Humans Humans

August 23, 2013

Survival on dry 6-60 days
surfaces
Spread in HC Faecal-oral, Droplets Droplets
contact
HAIs Diarrhoea Mumps Rubella (German
(parotitis) measles)
Specimens Stool Serum sample Serum sample
Prevention Clean hands, Isolation, Isolation,
environment vaccination vaccination

22
Virus Morbillivirus (measles) Varicella-zoster virus

Habitat Humans Humans

August 23, 2013

Survival on dry
surfaces
Spread in HC Droplets Droplets, close contact
HAIs Measles Varicella
Specimens Serum sample Serum sample
Prevention Isolation, vaccination Isolation, vaccination

23
Prions
• Prions are proteinaceous particles

August 23, 2013

• 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
24
Parasites
• Include protozoa

August 23, 2013

• 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 25
Parasite Cryptosporidium Plasmodium Trichomonas Enterobius
(protozoa) species vaginalis vermicularis
(protozoa) (protozoa) (helminth)
Habitat Liver, Vaginal mucosa Intestinal tract

August 23, 2013

erythrocytes
Survival on 2 hours on dry Several hours in Eggs: at least 1
dry surface humid year
surfaces environment
Spread in Mosquito- Contaminated Faecal-oral
HC borne; equipment in
infected gynaecology
blood
HAIs Malaria Vaginal infection Enterobiasis
Specimens Blood Vaginal discharge Perianal tape
Prevention Safe blood Disinfected/ Clean
products sterilised environment,
equipment in clean hands
26
gynaecology
Role of microbiology
laboratory: Introduction

August 23, 2013

The diagnosis of infections performed by the
laboratory has two important functions
• Clinical
• 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
Minimal requirements for
microbiology services - 1

August 23, 2013

1. Set up inside the facility
• If not possible, negotiate a contract for diagnostic
microbiology with the nearest laboratory
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
Minimal Requirements for
microbiology services - 2

August 23, 2013

4. Identify common bacteria and fungi to species
level
5. Perform susceptibility testing using disc-
diffusion methodology
6. Perform basic phenotyping
• Serotyping
• Salmonellae, Shigellae, P. aeruginosa, N. meningitidis
• Biotyping
• S. typhi
29
Clinical role: Diagnosis of
infection

August 23, 2013

Diagnosis should be rapid and accurate to the
species level wherever possible
• Classical bacteriological methods
• Direct smear
• Culture
• Antigen detection
• Sensitivity testing
• Antibody detection
• Not very useful in the early stages of infection
• Molecular methods
30
• Rarely used in routine work for the diagnosis of bacterial HAI
Role in prevention and control
of healthcare associated
infections

August 23, 2013

• Outbreak investigation
• Surveillance of HAIs
• Alert microorganisms reports
• Designing antibiotic policy

31
Outbreak Investigation
• To determine the cause of a single-source

August 23, 2013

outbreak the causative agent must be defined
• Then microbiology laboratory determines if two
or more isolated strains are same or different

32
Additional tests during an
outbreak

August 23, 2013

• 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 33
• Anterior nares of personnel
HAI surveillance
• The microbiology laboratory should produce

August 23, 2013

routine reports of bacterial isolates
• Allows the IPC& Team to make graphs for specific
pathogens, wards, and groups of patients
• 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
Alert organism reports
• Identify possible agreed ‘alert’ microorganisms

August 23, 2013

• 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
35
Antibiotic policy
• Regular reporting of changing resistance

August 23, 2013

patterns
– Newsletters
– Specialty specific data
• Restricted antibiotic reporting
• Routinely only first line antibiotics
• Reserve antibiotics only if pathogen is resistant to first
line antibiotics

36
Antibiotic stewardship

August 23, 2013

Role of Clinical Microbiologist/ID specialist
• Provide leadership to antimicrobial team
• Antibiotic ward rounds
• Interpretation of patient specific data to optimise
treatment
• culture & sensitivity
• Active surveillance/ awareness
• Screening for carriage of resistant bacteria
• Molecular detection and typing

37
Interpretation of Microbiology
Data

August 23, 2013

• Microbiologists interpret microbiological data for
IP&C staff
• Results of isolation, identification, susceptibility tests,
typing
• Ideally should be medical doctor specialistt
• If this is not possible, then a properly educated
scientist is required

38
Role in education
• Infection prevention staff

August 23, 2013

• how to interpret microbiological reports/charts
• Other healthcare workers
• specimen collection and transport, interpretation of
reports and sensitivity tests
• Students (medical and nursing)
• basic microbiology

39
Key points - 1
• Microbes are infectious agents not visible to the

August 23, 2013

naked eye
• Widespread in nature and some cause human disease
• Diagnosis of infection by the microbiology
laboratory has two important functions
• Clinical
• Epidemiological
• The laboratory should determine the most
frequent microbes causing infections, including
HAI pathogens
40
Key points - 2
• The laboratory should perform basic typing of

August 23, 2013

microorganisms
• The laboratory should produce routine reports
for IP&C personnel
• 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
References
•

August 23, 2013

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,
42
Philadelphia, 2005:203-241
References
•

August 23, 2013

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: 481-
499

43
Quiz
1. Microorganisms that can cause disease in humans

August 23, 2013

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. Produce routine periodic reports of isolated microbes
b. Make „baseline incidence” graphs
c. Have a physician as a microbiologist
d. Have a vigorous quality assurance program
44
International Federation of
Infection Control

December 1, 2013
• 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/
45