MIKROBIOLOGI DASAR

DR CHERRY SIREGAR, MKES

(MEDICAL MICROBIOLOGIST )
 INTRODUCTION

• Microbes are ubiquitous.

• They live inside and outside of our bodies
and in the surrounding environment
(water, food, vegetables, animals, etc)

• Microbes :
- Fungi
- Bacteria
- Virus
• Normal flora

“microorganisms that are frequently found In

various body sites in normal, healthy
individuals”.

The constituents and numbers of the flora vary

in different areas and sometimes at different
ages and physiologic states
 NORMAL FLORA
resident flora
strains that have an established
niche at one of the many body sites,
which they occupy indefinitely
Transient Flora
Transients are acquired from
the environment and establish
themselves briefly but tend to
be excluded by competition
from residents or by the host’s
innate or immune defense
mechanisms.
NORMAL HUMAN FLORA
PATHOGENESIS OF INFECTIOUS DISEASES

• Number of Microbes:
infective dose ; low vs high
Shigella spp.: 103
Salmonella spp. dan Vibrio spp. : 105-108
• Virulence:
Capacity for microbial strain to produce
diseases
• PVL toxin-producing S.aureus

• Immune status of patients

immunosuppresed ; transplant, AIDS, cancer
chemotherapy
 CHAIN OF INFECTION
1. Causative agent
“any microorganism capable of producing
disease “
- Bacteria, fungi, viruses, jamur, virus,rickettsiae,
protozoa, helminthes
2. Reservoir of infection
• Infected person, animal, item/equipment,
and/or the environment on which
microorganism can survive, or multiply
• Pseudomonas spp  in wet environment,
survive & multiply
• Hepatitis B virus  survive
Healthcare
-Reservoir : patient, visitors,staff, furniture, medical equipment
food,water, blood.
-Human reservoir : infected /carrier
-Carrier :
 Incubatory carrier: infection, incubating the illness, no
symptom
 Convalescent carrier : recovery stage of illness but
continious to shed …. Salmonella infection
 Intermitten
 Chronic carrier :infectious organism in their system ( Hep
B, Hep C )
3. Portal of Exit

• GI, Respiratory ,Genitourinary Tract

• Skin , membran mucous
4. Mode of Transmission
- Contact transmission : the most frequent of
transmission of HCAI’s - Hand Hygiene !!!!
- Droplet transmission : cough, sneezes or talk
Droplet heavy , do not remain suspended in the
air for a long time, negative pressure ventilation
is not necessary
- Airborne transmission:
 inhalation small of small droplet nuclei of partical size ( <
5 um )
 Very light in nature, inhalation - reach alveoli ,
therefore HCW should wear a respirator when entering
the room.
 Negative pressure ventilation ( 6-12 ACH)
 M.tbc, varicella-zoster virus, rubeola virus
5. Portal of entry
6.Susceptible host
- immunocompromised
- very young, very old risk for infection
 SPECIAL PATHOGENS

1. Clostridium difficile-associated diarrhoea

• Anaerobic bacteria, gram positif
• Gut ( 5%)
• Fecal-oral route
• Prolonged use AB

2. Mycobacterium tuberculosis
• airborne droplet nuclei ( 1-5 μ )
• sputum smear positive 6-10 x more contangious than
smear negative
• prolonged, close contact, indoor
3. Blood borne viral infections
• Hepatitis B :
• Hepatitis C
• HIV
• The risk of infection following percutaneous exposure
to the blood from an infectious source :
Hepatitis B : 5-30%
Hepatitis C : 3-10%
HIV : needle stick injury  0,3% ;
mucous membrane exposure  0,09%
4. Multi drug resistance organism ( MDRO )
 Resistance to one or more commonly used
antibiotics
a. MRSA ( Methicillin Resistance Staphylococcus
aureus)
 S.aureus - 30 % in healthy people (nasal, groin,
axilla )
 MRSA : resistant to all betalactam
 High mortality & morbidity
 Screening MRSA

b. VRSA ( Vancomycin Resistance Staphylococcus

aureus )
c. VRE ( Vancomycin –resistant Enterococcus)

d. ESBL – E coli, Klebsiella pneumoniae

e. Carbapenem - resistant
WHY STOPPING THE SPREAD MDRO IS
IMPORTANT ?

• CDC ; 94.000 MRSA cases /year in USA—18.650 death

annually

• MDRO Infections are associated with:

Increased length of stay in hospitals

Increased morbidity and mortality

Decrease in quality of life

Loss of limb or life

How transmission occurs:

 Transfer from contaminated environment/ reusable

medical equipment (RME) to a compromised
patient
 By healthcare worker’s hands
 By direct contact with the organism (in an open
wound)
 Staphylococcus spp

•They are Gram-positive cocci that appear

microscopically like a bunch of grapes

• S.aureus is coagulase positive

• Coagulase negative staphylococci are

many in number eg. S. saprophyticus

EPIDEMIOLOGY OF STAPHYLOCOCCUS

• S.aureus is ubiquitous.
– Colonise ( nares, axillae, perineum,etc ) about 30% of
humans.
– Person-to-person spread by hands (common), nasal
discharges and aerosol ( rare )
• CNS are ubiquitous on skin and mucosal surfaces.
– Infection usually endogenous and is common cause of
nosocomial line infections
– Bacteria has low pathogenicity but cause infection in
patients with foreign bodies
 Pathogenesis of Nosocomial
Infection by Enterococci

• Generally enterococci are part of normal flora and

have little pathogenic potential in normal host

• Opportunistic pathogens in the elderly,

immunocompromised or when invasive procedures
are done

• Little known about virulence factors

• Cause UTI, bacteremia, endocarditis,

intraabdominal/pelvic infections, skin/soft tissue
 Modes of Transmission and
Outbreaks of Enterobacteriaceae

 Escherichia coli

 Klebsiella species (pneumoniae)

 Enterobacter species

 Proteus mirabilis

• Primarily spread from person to person via unwashed hands of

HCWs or from environmental reservoirs to patients.

• Extensive use of 3rd generation cephalosporins mostly as

monotherapy is a risk factor for ESBLs (extended spectrum β
lactamases) in ICUs and oncology wards.
EPIDEMIOLOGY OF P. AERUGINOSA INFECTIONS

• Conveyed into hospitals via food (vegetables) and

tap water. Reservoir in hospitals are moist areas, fluids
etc.

• Patients especially haematology-oncology patients

are colonised in the rectum and pharynx.

• Nosocomial transmission via contact with

environmental sources or from patient-to-patient
spread via personnel.
 ACINETOBACTER spp
• Widely distributed in nature.
• Part of normal flora of humans (one-fourth of normal
and one-third of hospitalised individuals) and many
animals.

• Usually infects immunocompromised or debilitated

hosts.

• Multiple modes of transmission involving environment

and hands of HCWs.

• Sometimes cause outbreaks in ICUs and Burns

• Pseudomonas spp. and Burkholderia cepacia
replicate in a wide range of moist environments
eg. tap & deionised water.

• Capable of prolonged survival in moist or dry

environments eg. A. calcoaceticus survived 9
days on dry Formica surface cf. 1 day for P.
aeruginosa.
Environment = Reservoir for infectious organisms

May survive (even thrive) on environmental surfaces for

months if surfaces not cleaned & disinfected

•E. coli & Pseudomonas aeruginosa – up to 16 months

•MRSA – up to 9 - 10 months

•TB & C. diff – up to 5 months

•VRE – up to 4 months

•Proper cleaning & disinfecting is essential to reduce

transmissions/ infections !!!
 MICROBIOLOGY DIAGNOSIS

• The microbiology laboratory plays a crucial role in

the diagnosis of infectious diseases. .

• There are therefore several ways of making a

microbiological diagnosis.

• 1 Microscopical methods.

• 2 Cultural methods.

• 3 Serological methods.

• 4 Molecular methods.
 SPECIMENS

- Specimens handling
 DIRECT MICROSCOPIC EXAMINATION

• Types of microscopy for the diagnosis of

infections
1.Unstained preparations.
2.Simple stains: Gram, Giemsa.
3.Special stains: Ziehl–Nielsen, Gomori–Grocott,
India ink.
4. Immunofl uorescence: direct and indirect.
5.Electron microscopy.
• Diagnostic

• Neisseria gonorhoe,Neisseria
meningitidis pada pewarnaan Gram:
diplococcus Gram negatif

• Mycobacterium tuberculosis dan

M.leprae pada pewarnaan Ziehl Neelsen:
BTA positif
• The main reason for performing culture is to identify
the infecting pathogen

• culture allows the susceptibility pattern of the

infecting organism to be determined

• Culture has an important epidemiological purpose,

not related to the treatment of individual patients

• Screening

screen patients andhealthcare workers for

colonization with pathogens such MRSA
MYCOBACTERIUM TUBERCULOSIS
DIPLOCOCCUS GRAM NEGATIF
 2. CULTURE
• Culture can aid diagnosis in bacterial, parasitic and
viral diseases.

• In bacteriology, culture permits amplification of the

number of bacteria.
• Limitations of culture :time required for incubation
Infected patients requiring immediate treatment,
decisions on initial therapy must be made based on the
clinical features of the case, plus rapid microscopical
examination and haematological or biochemical results.
STREAK PLATE METHOD OF
ISOLATION