Mikrobiologi Terkait HAIs

dr. Fera Ibrahim,MSc., Ph.D, SpMK(K)

Departemen Mikrobiologi Klinik FKUI-RSCM

PELATIHAN IPCD YCKS

Tgl. 20 – 23 Juni 2022
Pokok Bahasan

• Pendahuluan
• Mikroba
• Pertahanan Hidup Mikroba
• Mekanisme Resistensi
• Multi-drugs resistant organisms (MDRO)
• Mikroba dan HAIs
• Microbiology
is the study of
microorganisms or
microbes, such as
bacteria, viruses, archaea,
fungi and protozoa. This
discipline includes
fundamental research on
the biochemistry,
physiology, cell biology,
ecology, evolution and
clinical aspects of
microorganisms, including
the host response to these
agents.
MIKROBA/MIKROORGANISME
 What is the difference between a
cells and a virus ?

Foundations in Microbiology, 8th ED. 2008, McGraw-Hill,New York

 Most fungal pathogens do not
require a host to complete their life
cycles, and the infections they cause
are not communicable.

Most fungal pathogens are opportunists that preferentially invade hosts with immune defects.
 Pathogenesis of Fungal Infection
Localized disease (left) is caused by local trauma
or the superficial invasion of flora resident on the
oropharyngeal (thrush), gastrointestinal, or vaginal
mucosa.
Systemic disease (right) begins with inhalation of
conidia followed by dissemination to other sites.
Environmental conidia are inhaled or injected
Endogenous yeasts may invade

Immunity to fungal infections.

A. Pathogenic fungi are able to survive and multiply
slowly in nonactivated macrophages.
B. When macrophages are activated by cytokines from
T-cells the growth is restricted and the fungi digested.

Most fungi are readily killed by neutrophils

Citation: Chapter 43 Pathogenesis and Diagnosis of Fungal Infection, Ryan KJ, Ray C. Sherris Medical Microbiology, 6e; 2014. Available at:
https://accessmedicine.mhmedical.com/content.aspx?bookId=1020&sectionId=56968786 Accessed: May 22, 2022
Copyright © 2022 McGraw-Hill Education. All rights reserved
 VIRUS
Makhluk hidup:
1. Tubuhnya terstruktur
2. Komposisi kimia yang stabil
3. Membuat energi dan menggunakannya
4. Merespon rangsangan
5. Tumbuh dan berkembang
6. Dapat berkembang biak (seksual atau non-seksual)
7. Terdapat variasi genetik
8. Beradaptasi pada lingkungan

Apakah virus makhluk hidup?

VIRUSES ARE DISTINCT FROM LIVING ORGANISMS

• All living cells have RNA and DNA, can carry out chemical reactions,
and reproduce as self sufficient units, viruses have only RNA or
DNA and can reproduce only by using the cellular machinery of
other organisms
• Viruses are NOT A CELLS, non cellular infectious agent,
submicroscopic, obligate intracellular parasites.
• Virus definition : A virus is a very small, non-cellular parasite of
cells. Its genome, which is composed of either DNA or RNA, is
enclosed in a protein coat.
VIRUS
 SIZE OF MICROBES
Virus is an agent smaller
than bacterium, that most
cannot be seen by light
microscopy

The smallest viruses have a

diameter of 10 nm
whereas the largest are
approximately 300 nm in
diameter, which is about
the size of the smallest
bacterial cell

Comparison of the size of selected viruses to E. coli and a human red blood cell

Baumann, RW. Microbiology with Diseasesby taxonomy 3rd ed. Pearson International . 2011
VIRAL CLASSIFICATION
Structure : size, morphology,
and nucleic acid

Biochemical characteristics :
structure and mode of
replication

Diseases : encephalitis,
hepatitis viruses

Means of transmission :
arbovirus spread by insects

Host cell (host range) : animal,

plant, bacteria

Tissue or organ (tropism) :

enterovirus
Murray PR, et al, Medical Microbiology 5th eds, 2005
Bagaimana virus menginfeksi ?

Varian2 baru
BACTERIA

POSITIVE GRAM
AND NEGATIVEGRAM

REPRODUCTION :
BINARY FISSION
 Morfologi Sel Bakteri
• Bentuk Bacteria
• Batang
• Kokus
• Spiral
G+ G- Acid Wall Intra
• Filamen fast less cellular

Rod Cocci Rod Cocci Spiral

• Populasi sel bakteri
• Individual
• Diplo-
• Staphylo-
• Strepto-
• Filamen
Klasifikasi Berdasarkan Struktur
Dinding Bakteri
Pewarnaan Gram
(Hans Christian Gram)
 Pewarnaan Gram: Manfaat
• Pada spesimen
• Menilai kualitas spesimen, kecurigaan infeksi
(lekosit)
• Membantu menentukan pilihan antibiotik
empirik (bila morfologi sel khas, mis. diplokokus)
• Tidak digunakan untuk semua spesimen (feses,
usap tenggorok) karena interpretasi sulit

• Pada isolat
• Kemurnian isolat
• Identifikasi untuk menentukan uji lanjutan
Pertumbuhan Populasi Bakteri
Kecepatan tumbuh
 Strategi pertahanan hidup
 Extremophiles
• Extreme temperature
• Thermophiles: >450C
• Mesophiles: 200C – 400C (human pathogens)
• Exception: Legionella sp.
• Psychrophiles : <10C – 200C
• Chemical Extremes: Extreme Acidophiles; Alkaliphiles; Halophiles
 Sporulation
 Bacterial communication: Quorum Sensing
 Evolution of Microbes
 Mechanisms of Antibiotics
Resistance
Klasifikasi Berdasarkan Kebutuhan O2

• Aerob obligat: O2 - 21%

• Anaerob obligat: O2 - 0-3%
• Anaerob fakultatif: ada O2
atau tidak
• Mikroaerofilik: O2 – 5-10%
Siklus Sporulasi pada Bacillus
• Endospores dihasilkan:
Bacillus and Clostridium

• Lokasi dalam sel: sentral,

sub-terminal, terminal

• Resisten terhadap
• kering, panas, radiasi, dan
zat kimia yang mematikan
• Perlakuan yang dapat
menghambat pertumbuhan
mikroba lain
Biofilm
 Evolution of Microbe
• Bacteria are very adaptable. The short generation span of
bacteria helps them adapt to changing environments
• This is true in the evolutionary sense of adaptation via
natural selection and the physiological sense of adjustment
to changes in the environment by individual bacteria

Mutation and other genetic

changes include gene
duplication, horizontal gene
transfer, and gene loss.
In addition to mutations, genetic
recombination generates diversity
within bacterial populations.
Recombination is defined as the
combining of DNA from two
individuals into a single genome
PANDEMIC INFLUENZA VIRUS
 Cara Pemusnahan Mikroba
• Sterilisasi
proses yang memusnahkan (destroy) semua bentuk
mikroba termasuk spora
Sterilant ; Sterile

• Disinfeksi
proses menghilangkan (remove) mikroba, tidak
termasuk spora
disinfectant ; germicide ; antiseptic ; sanitizer
 Cara Pemusnahan Mikroba
• Fisik:
• Sinar Ultraviolet
• Pemanasan:
• Boiling: suhu tinggi
• Pasteurisasi: suhu rendah, beberapa kali

• Kimia:
• Desinfeksi
• antiseptik
• Sterilisasi
Ketahanan Mikroba
 INFECTION
1) The presence of microbes in the body
2) The symptoms of disease

The presence of microbes in the body does not always result in symptoms of disease
Faktor yang menentukan bakteri adalah
penyebab infeksi
• Lokasi pengambilan specimen (organ atau sistem)

• Terdapatnya pertumbuhan beberapa bakteri 

kontaminasi?

• Status imunologi pasien

• Infeksi, Kolonisasi atau kontaminasi ??

Flora Normal
 Bakteri adalah prokariotik:
• lebih sederhana daripada
eukariotik
• Berkembang biak sangat Penanganan spesimen:
cepat
• Pengambilan
• kemampuan adaptasi pada
pengaruh antibiotik atau • Transportasi
respon imun • Penyimpanan
sangat mempengaruhi
interpretasi hasil

“Pre-analytical specimen management

in microbiology is CRITICAL TO ACCURACY”

IDSA Guidelines. Clin. Inf. Diseases Advance Access published July 10, 2013
 Pre-analitik

IDSA Guidelines. Clin. Inf. Diseases Advance Access published July 10, 2013
Alur Prosedur Laboratorium
Mikrobiologi Klinik

Patient/Client Prep
Sample Collection

Reporting

Personnel Competency
•Data & Test Evaluations
Laboratory
Management
•Safety
•Customer Sample Receipt and
Service Accessioning

Record Keeping

Quality Control Sample Transport

Testing
KONSENSUS MIKROBIOLOGI KLINIK 2005
Microbiological Examination
Conventional Technology

biochemical tubes

Molecular testing
MALDI-TOF
Automation
 Hasil Pemeriksaan Mikrobiologi 
Tatalaksana Pasien dengan Infeksi
• Terapi antibiotik empirik berdasarkan antibiogram
local

• Terapi antibiotik definit berdasarkan hasil identifikasi

mikroba dan uji kepekaan antimikroba

• Keterlambatan hasil  meningkatkan kemungkinan

pasien mendapat pilihan terapi empirik yang kurang
tepat
The Action of Antimicrobial Drugs
 Bagaimana Bakteri menjadi Resisten?
• Intrinsik: sifat resisten didapat secara alami,
merupakan sifat biologi mikroba

• Didapat:
• Bacteria yang bersifat sensitif terhadap suatu antibiotik
kemudian menjadi resisten
• Terjadi akibat mutasi atau mendapatkan materi genetik
baru
• Mutasi kromosomal dan seleksi: vertical evolution
• Mendapatkan materi genetik baru dari bakteri lain yang
resisten: horizontal evolution
Tenover, FC. The American Journal of Medicine (2006) Vol 119 (6A), S3–S10
Hawkey, P. M BMJ 1998;317:657-660
 Mekanisme Resistensi
• Bakteri menghasilkan enzim
yang dapat menghancurkan
antibiotik sebelum terikat
• Pompa efluks: bakteri
mengeluarkan molekul
antibiotik yang masuk ke
sitoplasma sebelum terikat
pada target

• Mengubah protein target tempat

antibiotik terikat dan bekerja https://www.reactgroup.org/toolbox/understand/antibiotic-
resistance/resistance-mechanisms-in-bacteria/

• Mengubah “outer membrane protein channel” yang diperlukan

antibiotik untuk masuk ke sel
Tenover, FC. The American Journal of Medicine (2006) Vol 119 (6A), S3–S10
The Selection vs. Induction Paradigm

the preadaptation theory the post-adaptation theory

Araos, R., et al.. In: Antimicrobial Stewardship: Principles and Practice. CAB International. 2017.
How does antibiotic resistance
emerge?
 Bagaimana Sifat Resistensi Dipindahkan?
• Mendapatkan gen pengkode sifat resistensi dari sel
bakteri lain Horizontal Gene Transfer
Microorganism Resistance ….

• MDR (multidrug-resistant)
Resisten terhadap 3 kelas antimikroba
• XDR (extensively drug-resistant )
Resisten terhadap semua kecuali 1 - 2 (colistin /tigecycline)
• PDR (pandrug-resistant)
Resisten terhadap semua AB yang ada
• CR (carbapenems resistant)
Resisten to imipenem or meropenem

Falagas ME et al. Clin Infect Dis 2008;41:848-54.

45
 MDROs
 Gram positive organisms
• MRSA (Methicillin Resistant Staphylococcus aureus)
• VRE (Vancomycin Resistant Enterococcus)

 Gram negative organisms

• ESBLs (extended Spectrum Beta Lactamase)
• CRE (Carbapenem Resistant Enterobacteriaceae)
• Pan Resistant Pseudomonas
• Pan resistant Acinetobacter

CDC: Management of Multidrug-Resistant Organisms in Healthcare Settings, Healthcare Infection

Control Advisory Committee, Jane D. Siegel et. al. pg 7-12
 Kepentingan Klinis MDRO

• Manifestasi klinis sama dengan infeksi akibat bakteri yang

sensitif

• Pilihan antibiotik untuk terapi sangat terbatas

• Pasien dengan infeksi akibat MDRO dirawat di RS lebih

lama  biaya meningkat

• Mortalitas yang meningkat

 Faktor Risiko Infeksi MDRO

• Penggunaan antibiotik sebelumnya

• Perawatan RS yang lama
• Penggunaan alat invasif (infus, kateter)
Kemungkinan pembentukan biofilm
• Tinggal dalam waktu lama di tempat perawatan
diluar RS
• Praktik pengendalian infeksi yang tidak adekuat
 Penggunaan antibiotik dalam waktu yang
lama
Faktor Utama yang Berhubungan
dengan HAIs

HAIs
 THE TRANSMISSION OF INFECTION
IN HOSPITAL

The source of infection may be :

Human  from other patient or hospital staff and occasionally visitors
Environmental, from contaminated objects (fomites), food, water or air
 Surface Contamination (in hospitals) with
MRSA, VRE, and C. Difficile
Blood Pressure Windowsill:
Cuff:
C. Difficile 33%
VRE 14%

Commode:
Overbed Table:
C. Difficile 41%
MRSA 40%
VRE 20% Patient Gowns:
MRSA 51%
Bedrail:
MRSA 29% Floors:

VRE 28% MRSA 55%

C. Difficile 19% C. Difficile 48%

Bedsheets:
MRSA 53%
Did you know that every time you get a new roommate, there is an increase of
VRE 40%
3-10% that you will acquire an HAI.
Huang SS, Datta R, Platt R. Risk of acquiring antibiotic-resistant bacteria from prior room occupants. Arch Intern Med. 2006 Oct
9;166(18):1945-51
Boyce J.M. et al.: Environmental contamination due to methicillin-resistant Staphylococcus aureus: Possible infection control implications. Infect Control Hosp Epidemiol
18:622-627, Sep. 1997.
Slaughter S., et al.: A comparison of the effect of universal use of gloves and gowns with that of glove use alone on acquisition of vancomycin-resistant enterococci in a
medical intensive care unit. Ann Intern Med 125: 448-456, Sep 15, 1996.
Samore M.H., et al.: Clinical and molecular epidemiology of sporadic and clustered cases of nosocomial Clostridium difficile diarrhea. Am J Med 100:32-40, Jan. 1996.
Survival times of nosocomial pathogens on environmental surfaces

Current Infectious Disease Reports (2018) 20: 12

 Gram-negative bacteria associated with water and
moist environments

Bacteria Implicated contaminated environmental vehicle

Burkholderia cepacia Distilled water; Contaminated solutions and disinfectants; Dialysis machines; Nebulizers; Water
baths; Intrinsically-contaminated mouthwash (This report describes contamination occurring
during manufacture prior to use by the health-care facility staff. All other entries reflect extrinsic
sources of contamination.); Ventilator temperature probes
Stenotrophomonas Distilled water; Contaminated solutions and disinfectants; Dialysis machines; Nebulizers; Water;
maltophlia, Ventilator temperature probes
Sphingomonas spp.
Ralstonia pickettii Fentanyl solutions; Chlorhexidine; Distilled water; Contaminated respiratory therapy solution

Serratia marcescens Potable water; Contaminated antiseptics (i.e., benzalkonium chloride and chlorhexidine);
Contaminated disinfectants (i.e., quaternary ammonium compounds and glutaraldehyde)
Acinetobacter spp. Medical equipment that collects moisture (e.g., mechanical ventilators, cool mist humidifiers,
vaporizers, and mist tents);
Room humidifiers; Environmental surfaces
Enterobacter spp. Humidifier water; Intravenous fluids; Unsterilized cotton swabs; Ventilators; Rubber piping on a
suctioning machine;
Blood gas analyzers

CDC, Guidelines for Environmental Infection Control in Health-Care Facilities (2003)

Estimated route and role of the respiratory droplets
in terms of spreading COVID-19 after an infected
person coughs

Aydogdu MO. 2021. J. R. Soc. Interface 18: 20200798. https://doi.org/10.1098/rsif.2020.0798

 Persistence and viability of different coronavirus
strains with different viral titres on most commonly
used surface material types

Aydogdu MO. 2021. J. R. Soc. Interface 18: 20200798. https://doi.org/10.1098/rsif.2020.0798

Minimum reduction of viral infectivity values obtained in
suspension tests using various disinfectants in different
concentrations against different coronaviruses

Comparison of results of the carrier

tests in terms of selected threshold 3
log10 using different disinfectants
against human-COV on a stainless-steel
surface for 1 min of exposure at room
temperature (22–24°C).

Aydogdu MO. 2021. J. R. Soc. Interface 18: 20200798. https://doi.org/10.1098/rsif.2020.0798

Microbial
Extermination/
Decontamination

• Physical:
• Ultraviolet Light
• Heat:
• Boiling: high
temperature
• Pasteurization:
low temperature,
several times

• Chemical:
• Disinfection
• Antiseptic
• Sterilization
 Native
Organisms
Decontamination
Antibiotic Isolation/
Management Barrier
Precautions

Hand Hygiene

Health
Policy

Komite/Tim
PPRA Komite/Tim
PPI

Eradication Surveillance

Emergence Transmission
Perl TM. Gram Negative Bacterial Resistance in Healthcare: The Brave New World Healthcare
 Simpulan
• Mikroba meliputi bakteri, virus, jamur, parasit, amuba,
cacing dan protozoa
• Mikroba yang terkait HAIs umumnya bakteri dan virus
• Pertahanan hidup mikroba : Extremophiles, Sporulasi,
Pembentukan biofilm, Evolusi, Mekanisme resistensi
antimikroba
• Kualitas hasil pemeriksaan mikrobiologi tergantung fase
pre-analitik, analitik, pasca-analitik
• MDRO meningkat di Indonesia dan Dunia, memerlukan
pencegahan terjadi infeksi dan pemberian antimikroba
yang bijak serta pengendalian penyebaran infeksinya.
# Stay Healthy
# Stay Safe
# Vaccination