BACT211: CLINICAL BACTERIOLOGY

TOPIC: INTRODUCTION TO DIAGNOSTIC BACTERIOLOGY

2ND SEMESTER | S.Y 2023-2024
LECTURER: Ma’am Christy Gonzales
TOPIC colonial morphology (growth of
SUBTOPIC bacteria in the surface of a culture
SUB SUBTOPIC medium)]
o Bacteria, like human, have distinct/specific
characteristics as well.
GENERAL DEFINITIONS o In specialized laboratories, they also
• Microbiology – a branch of biology which deals with the examine genotypical characteristics
study of living organisms that are small to be seen by [molecular; PCR, DNA composition, nucleic
the naked eye. acid composition, etc.]
- We need to use microscope for us to be able to o After identifying the bacteria, the genus and
see/visualize them (microorganisms) the species, antibiotic testing is also
• Medical Microbiology – a branch of medical science performed to identify what antibiotics/anti-
which deals with the study of medically important microbial agents that could kill the
microorganisms specifically their role in human disease bacteria.
which includes diagnosis, treatment, and prevention of o Each bacterium or each family of bacterium
infectious diseases. has a unique set of antibiotics that could kill
- Focus of other medical courses: medicine, nursing, them.
physical therapy ▪ Iba iba ang reaction ng bacteria sa
particular antibiotic
• Diagnostic Bacteriology – a branch of medical
▪ There are certain bacteria that
microbiology that focuses on the laboratory
couldn’t be killed by a particular
identification of medically important bacteria by
antibiotic. Thus, the need to identify
phenotypical and genotypical characterization including
the antibiotic that could kill it.
antibiotic susceptibility testing.
- This is the focus of our program
- Diagnostic Microbiology includes bacteriology,
mycology, virology, and parasitology. MICROBIOLOGY
- To be more specific, diagnostic bacteriology, we are • Study of microorganisms
dealing with the laboratory identification of • Study of certain nonliving entities as well as certain
medically important bacteria by their molecular living organisms.
characteristics.
• We have two types of microorganisms:
- Routinely [commonly performed], in the laboratory
- Acellular infectious agents
in the hospital settings, we are identifying the
o They do not have the characteristics that
phenotypical [visible trait; seen by the naked eye;
are similar to the characteristics of a cell
morphology, colonial morphology] of the bacteria
o Instead, they do depend in other cells in
o We have two ways of visualizing bacteria:
terms of reproduction [use cellular
▪ Microscopic [with the aid of
organelles of their hosts]
microscope; can know its
o Prions and Viruses [contain nucleic acid and
morphology (coccus, spirochetes,
protein]
etc.), and many more]
- Cellular microorganisms
▪ Macroscopic [we can see this
o Contains cellular organelles (nucleus,
without the use of microscope;
ribosomes, ER, etc.)
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 o Has 2 types: MICROBES
▪ Prokaryotes
• Microbes are said to be ubiquitous. Meaning, they are
• Lack true nucleus [involves
seen everywhere; virtually everywhere.
not only the presence of
- Origin of Bacteria:
nucleus itself, but should be
o HUMAN
enclosed in a nuclear
▪ normal flora; non-pathogenic (not
membrane]
capable of causing diseases in
• Has nucleus and genetic
normal circumstances, but they
material (DNA,
have the possibility of transforming
chromosome), but lacking
from non-pathogenic to
nuclear membrane. Thus,
pathogenic)
we call it a nucleoid region.
▪ Human → Human
• Archaea, bacteria
o ANIMALS
▪ Eukaryotes
▪ They are medically important if
• Has true nucleus
their bacteria are transmitted to
• Nucleus is enclosed in a
humans
nuclear membrane
▪ Animal → Human
• Nucleus contains the o ENVIRONMENT
genetic material of the cell ▪ Includes soil, water, and air
(DNA, Chromosome) ▪ Reservoir of bacteria
• Algae, Fungi, Protozoa, ▪ Acquisition of bacteria from the
animal cell, plant cell environment
• Microbes are subdivided into one of four groups:

DEFINITION
• Very simple microbes; consisting of
nucleic acid, a few proteins, and (in
some), a lipid envelope
• Completely dependent on the cells they
VIRUS
infect for their survival and replication
• Specific to their host cell [lock-and-key;
specific receptor]
- HIV → CD4 cell
With both RNA and DNA; metabolic
machinery for self-replication, and a
BACTERIA complex cell wall structure (ASEXUAL)
• Prokaryotic – simple unicellular
organisms
Subdivided into single-celled organisms
(yeasts) or multi-celled organisms (molds),
with a few medically important members
existing in both forms (dimorphic fungi)
FUNGI - Monophormic (exists in uni or
multi: yeast or mold; iisa lang ang
form)
- Dimorphic (has 2 forms: yeasts and
molds)

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 Subdivided into single-celled organisms o Not all Staphylococcus Aureus has
PARASITES (protozoa) or multi-celled organisms Endotoxin B. Not all Staphylococcus Aureus
(worms and bugs) has Protein A. Same goes with
Streptococcus Pneumoniae in having
capsule.
DEFINITION OF TERMS RELATED TO INFECTIOUS
• Pathogenic Determinants/Virulence Factors – refers to
PROCESS AND DISEASE TRANSMISSION
any genetic, biochemical, or structural features that
• Pathogens – disease causing microorganisms such as enable a pathogen to cause disease in a host organism
bacteria, fungi, protozoans, and viruses, as long as they • Infection – refers to the entry, invasion, and
are capable of causing diseases then they are pathogens multiplication of pathogens in or on to the host body
system which results to subsequent tissue injury and
TYPES OF PATHOGENS
progress to overt disease.
TRUE Refers to an organism that will cause
- Bacteria will attach to the host surface.
PATHOGENS disease in a healthy host
Refers to organisms that will cause - Ex. The mode of transmission is inhalation for it to
OPPORTUNISTIC disease in an immunocompromised go to the lining of our respiratory tract [invade and
PATHOGENS host [the immune system is multiply]. The bacteria will multiply into that host’s
compromised; immunity is low] surface and will cause subsequent tissue injury. That
• Pathogenicity – refers to the ability of an organism to is when manifestation of signs and symptoms occur.
cause disease in a host organism When the bacteria successfully passed our immune
• Virulence – refers to the degree of pathogenicity; the system, then that’s the time na makakapaginvade
power by which a pathogen can cause severe disease siya and multiply.
- Bawat microorganism have several power in which
TYPES OF INFECTION BASED ON SOURCE OF PATHOGEN
pathogens can cause disease. Infection arising from colonizing
- Severity of diseases that a pathogen causes flora [also known as indigenous
depends on their power. microflora; also known as resident
- Ex. Staphylococcus aureus – in order for this to flora, microbiota]
cause disease, it has virulence factor [any feature - Normal flora – non-
(biochemical/enzymes, genetic, or even the pathogenic under normal
structure the bacteria) which will enable it to cause condition; have restricted
disease. number in the human
- Ex. Biochemical – Endotoxin is a biochemical system for it not to be
component of Staphylococcus aureus. When it have pathogenic
endotoxin B, this is capable of causing food - Normal flora can be
pathogenic once an
poisoning. However, when you have Protein A [this ENDOGENOUS
individual is
is enabling the Staphylococcus aureus to be anti- INFECTION
immunocompromised;
phagocytic]. Protein A blocks the pathway of increase in number [low
phagocytes. immunity; the bacteria will
- Ex. Staphylococcus aureus is in our blood stream. increase in terms of their
Then, one of the members of our immune system number and when that
will try to eliminate it, but if Staphylococcus aureus happens, they will be able to
has Protein A, then it will inhibit or block the cause disease].
antibodies for it to be protected. Thus, - It also can be pathogenic
Staphylococcus aureus can still cause infection. once they transfer site [Ex.
- Ex. Streptococcus pneumoniae’s structure has GIT → urinary tract]. Once it
capsule. Then, it has the same function as Protein A happens, that could cause
infection.
[anti-phagocytic]. Thus, causing infection.

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 Infection arising from invading • Colonization – refers to the establishment of substantial
pathogen from the external number of microorganisms usually in the skin or mucosa
EXOGENOUS
environment but there’s no penetration of tissues.
INFECTION
- Nakuha ang bacteria from - Number of normal flora in our body are restricted
animals or environment by our immune system. Once exceeded or increase
TYPES OF INFECTION BASED ON CLINICAL SIGNS AND in number, they can now cause disease/s.
SYMPTOMS
Rapid/sudden onset of signs and
ACUTE
symptoms which are usually severe
INFECTION
to fatal that may lead to death
Gradual onset of signs and
CHRONIC symptoms that are usually mild to
INFECTION moderate that may progress to long
standing infection
TYPES OF INFECTION BASED ON ETIOLOGIC/CAUSATIVE
AGENT
Infection acquired during
hospitalization
NOSOCOMIAL - Acquired from the hospital:
INFECTION another patient,
environment, equipment,
etc.
ZOONOTIC Is an animal disease which can
INFECTION spread to humans; animal acquired
(ZOONOSIS) infection
TYPES OF INFECTION BASED ON CLINICAL
MANIFESTATION
SUBCLINICAL/ No obvious appearance of signs and
ASYMPTOMATIC/ symptoms and the person is
NONAPPARENT unaware of the infection - Not all anatomic sites in our body have normal flora
CLINICAL/ Associated with presence of overt
1. Sterile Site – without normal flora
SYMPTOMATIC/ signs and symptoms of the disease.
2. Non-Sterile Site – with normal flora
APPARENT
- Specimens that are obtained in sterile areas [TSF,
• Disease – an altered health state in an infected host
Peripheral Blood, Body Fluids like synovial fluid] are
• Infectious disease – is an illness caused by pathogen
called Sterile Specimens.
which invades body tissues and causes damage
- Specimens that are obtained in non-sterile areas
• Communicable disease – is an infectious disease that is
[GIT: stool, rectal swab] are called Non-Sterile
capable of spreading from person to person
Specimens
• Symptoms – refers to any subjective evidence of
disease. These are usually perception of the patient
having the disease such as headache, dizziness, etc.
• Signs – refers to readily observable evidence of disease.
These are usually physical manifestation of the disease
such as rashes, bleeding, etc.
• Normal Flora – bacteria that are in or on different sites
of the body that usually do not harm the host unless the
host defense is compromised.
- SYNONYMS: Indigenous Flora, Resident Flora,
Normal Microbiota

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 EARLIEST KNOWN INFECTIOUS DISEASES • There are early accounts of rabies, anthrax, dysentery,
smallpox, ergotism, botulism, measles, typhoid fever,
• During the ancient times, before the birth of Christ,
typhus fever, diphtheria, and syphilis
some believed that diseases are acquired from
- The most common among this is syphilis [caused by
punishment of the gods, etc.
treponema pallidum; sexually transmitted infection]
- They believed that once they praise those gods,
• Treponema pallidum – causing syphilis [spirochete: its
they will be spared from diseases.
morphology is spiral]
• Nowadays, we now know that diseases are caused by
• Syphilis – First appearance in Europe in 1493
particular microorganisms.
- Was carried to Europe by Native Americans who
• Pestilence & Plague – Represent the first recorded
were brought to Portugal by Christopher Columbus
epidemic
- Neapolitan Disease
• Around 1900 BC, near the end of the Trojan War, the
- French or Spanish Disease
Greek army was decimated by an epidemic of what is
- French pox
thought to have been plague [bubonic plague; caused
- Spanish, German, Polish, and Turkish pocks
by the yersinia spp.]
- They believed that the epidemic was caused by evil
spirits; many have died during those times.
• 1500 BC – Ebers Papyrus [Egyptian Medical Papyrus]
- Papyrus – documents;
- The Egyptian Medical Papyrus contains list of
diseases and treatments [during their time]
• 1122 BC – Smallpox occurred in China
• Epidemics of plague occurred in Rome in 790, 710, and
640 BC and in Greece around 430 BC

PIONEERS IN THE SCIENCE OF MICROBIOLOGY

ANTON VAN LEEUWENHOEK (1632-1723)
• First person to see live bacteria and protozoa
• “Father of Microbiology”
- Plague is a zoonotic infection [rodents] • “Father of Bacteriology”
o Transmitted to human via rat flee • “Father of Protozoology”
o Yersinia pestis – mode of transmission: bite • He ground tiny glass lenses, which the mounted in small
of a rat flee metal frames, thus creating what today are known as
- Plague has 3 types: single-lens microscopes or simple microscopes.
o Bubonic Plague – swollen lymph glands - not the first one to build a microscope, but was the
[bubo]; Black Plague first one to see an organism under a microscope.
o Septicemic Plague – already progressing in - The first one to build a microscope is Descartes.
our systemic organs [Ex. The infection is o Quality of his lens of the microscope is not
scattered to out organs and blood] sufficient enough to see microorganisms
o Pulmonary Plague – respiratory tract - Magnification: x30-x260
infection; acquired via inhalation through • He observed various tiny living creatures, which he
respiratory tract. called “animalcules” [tiny animals]

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• First one to made a drawing of bacteria to document; - In this experiment, there are 2 set-ups:
the first drawing was drafted in 1684. o Inside the swan neck flask, it contains a
culture medium, wherein there is a growth
in bacteria.
LOUIS PASTEUR (1822-1895) o The first set-up is vigorously heated, so that
the bacteria could die [sterile medium]
• Demonstrated that different types of microbes produce o The second set-up has a culture medium,
different fermentation products. growth of bacteria, and is also heated.
- Can use carbohydrate → acid or alcohol However, the first set-up remained intact
• Disapproves the Theory of spontaneous generation while the second set-up, the swan neck
- Life arises from non-living matter [based on flask was broken.
Aristotle theory] o For the first set-up, the microorganisms did
- John Baptista Van Helmon – 17th century Flemish not go to the culture media; remained
scientist; had a proposition that “life could arise sterile
from rags and wheat kernels which is left in an open o For the second set-up, the microorganisms
container for 3 weeks” → could form a mice [not from the environment were directly went to
possible] the culture media
• He introduced the terms “aerobes” and “anaerobes” o If spontaneous generation is true then,
- Aerobes require oxygen for growth microorganisms should be able to grow in
- Anaerobes do not require oxygen for growth the first set-up
• Introduced the terminology – Pasteurization
- Anti-microbial technique where you heat a liquid in
a certain temperature [63-65 degree Celsius for 30 ROBERT KOCH (1843-1910)
mins or 70-73 degree Celsius for 15 seconds]
- Has 2 types: Batch & Flash • Made many significant contributions to the germ theory
• Germ theory of disease of disease
- Specific microbes cause infectious diseases • Discovered that Bacillus anthracis [spore-producing
• Developed vaccines to prevent chicken cholera, anthrax, bacteria] produces spores, capable of resisting adverse
and swine erysipelas conditions
- Only 2 is capable of producing bacteria:
o Bacillus spp.
o Clostridium spp.
- Spores is a virulence factor
o It can cause disease when bacillus or
clostridium were exposed in extreme
conditions [high temp, low pH, high pH, loss
of oxygen, high CO2,], it will form a spore as
a form of their survival. They are still
capable of causing infection
• Developed methods of fixing, staining [methylene blue:
the one used in M. tuberculosis (heat is applied)], and
photographing bacteria, methods of cultivating bacteria
on solid media
- Methylene blue [1877]
- Acid-fast staining
o Used methylene blue then employed heat

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 o M. Tuberculosis is not an ordinary FERDINAND COHN
bacterium [cell wall is hard to penetrate
• Clarified the reason that heat would sometimes fail to
using ordinary stain]
completely eliminate all microorganisms
▪ Methylene blue alone cannot
penetrate the cell wall of M. • “STERILE” was established
Tuberculosis • Sterile – completely free of all life forms (including
o In 1822, Robert Koch found a way to spores) and virus particles.
penetrate the waxy cell wall of M. • Staining of histological specimen
Tuberculosis by applying heat. [methylene - Histologic specimens: tissue specimens [carmine
blue + heat = fast stain] and hematoxylin (vegetable dyes)]
• Discovered the bacterium Mycobacterium tuberculosis • Basal medium
that causes tuberculosis and the bacterium Vibrio - Culture media have basal medium in to which
cholerae that causes cholera. factors can be added to non-fastidious bacteria
- Two types of bacteria in terms of requirement:
fastidious [require additional or special nutrient] vs.
non-fastidious [standard requirement for growth]

THE DEVELOPMENT OF ASEPTIC TECHNIQUES

DR. OLIVER WENDELL HOLMES
• Observed that mothers who gave birth at home
experienced fewer infections than did mothers who
gave birth in the hospital.
- Mas maraming makukuhang infection sa hospital
kaysa sa bahay

DR. IGNAZ SEMMELWEIS

• Showed quite clearly that women became infected in
THE DISCOVERY OF SPORES AND STERILIZATION the maternity ward after examinations by physicians
coming directly from the autopsy rooms
JOHN TYNDALL
- Infection of newly mothers after giving birth:
• Provided the initial evidence that some of the microbes childbed fever
in dust and air have very high heat resistance and that • Father of Handwashing
particularly vigorous treatment is required to destroy
them JOSEPH LISTER
- Hindi lahat ng microorganism could not be killed by • First to introduce aseptic techniques aimed at reducing
very high temperature. Instead, they can be killed microbes in a medical setting and preventing wound
by vigorous treatment [tyndallization] infections.
o You use repeated heating and resting
method [consecutive heating then resting
then heat then rest, and repeat the process
until the microorganism dies]
- Most bacteria requires 100 degree Celsius to be
killed, some requires higher than that.

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 PROTOZOOLOGIST
• Explore the area of protozoology — the study of
protozoa and their activities

MYCOLOGIST
• Those who specialize in the study of fungi, or mycology

VIROLOGISTS AND CELL BIOLOGISTS

• May become genetic engineers who transfer genetic
material (deoxyribonucleic acid or DNA) from one cell
type to another
• Virologists also study prions and viroids, acellular
infectious agents that are even smaller than viruses

- When identifying the bacteria or microorganism

present, we need to check the clinical diagnosis of
• ADDITIONAL: the patient [suspected clinical diagnosis]
- Friedrich Loeffler in 1890 – He discovered or - Then, we need to correlate it to the bacteria we’ve
demonstrated the presence of bacterial flagella seen and then, release the form.
[motile, non-motile] - Once we’ve identified the bacteria, we need to
- Baijerinck in 1898 – enrichment medium identify what specific antibiotic needed to kill the
- Chamberland in 1884 – discovered the autoclave bacteria.
- Mcintosh & Fildes – anaerobic jar

CAREERS IN MICROBIOLOGY
BACTERIOLOGIST
• scientist who specializes in bacteriology — the study of
the structure, functions, and activities of bacteria

PHYCOLOGISTS (OR ALGOLOGISTS)

• Scientists specializing in the field of phycology (or
algology) study the various types of algae

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 BACT211: CLINICAL BACTERIOLOGY
TOPIC: TAXONOMY AND CLASSIFICATION
2ND SEMESTER | S.Y 2023-2024
LECTURER: Ma’am Christy Gonzales

TOPIC
SUBTOPIC
SUB SUBTOPIC

NAMING, CLASSIFYING, AND IDENTIFYING

MICROORGANISMS
• Taxonomy – the science of classifying living things
- In Greek, taxonomy came from “taxes” and
“nomos”
- “taxes” – arrangement
- “nomos” – law - specie can still be subdivided by:
- Involves 3 structured and interrelated category that o sub-specie [based on differences of
include: phenotypic characteristics]
o Nomenclature – is the assignment of o serovarieties [serologic differences; antigen,
scientific names to the various taxonomic antibody composition]
categories and individual organisms. [based o biovarieties [biochemical test result]
on international rulings]
ROBERT WHITTAKER
▪ 1 label for a specific microorganism
[universal] • Whittaker’s tree
o Classification – attempts the orderly • based on structural similarities and differences, such as
arrangement of organisms into a hierarchy prokaryotic and eukaryotic cellular organization, and
of taxa (categories). the way these organisms obtained their nutrition
▪ Taxa – plural; Taxon – singular • Monera → Protists → Plants → Fungi → Animals
▪ Classified based on their similarities
or relationships; closely related
o Identification – is the process of discovering
and recording the traits or organisms so
that they may be recognized or named and
placed in an overall taxonomic scheme.

CLASSIFICATION
CARL VON LINNÉ
(ALSO KNOWN AS LINNAEUS; 1701-1778)
• a Swedish botanist
• laid down the basic rules for classification and
established taxonomic categories, or taxa

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 - Bacteria is under the monera kingdom • Commonly, the genus is abbreviated with the first letter
(capitalized) of the genus followed by a period and the
CARL R. WOESE species. To avoid confusion, the first two letters of the
• devised a Three-Domain System of Classification first syllable are used when two or more genera begin
• There are two domains of procaryotes (Archaea and with the same first letter.
Bacteria) and one domain (Eucarya or Eukarya), which - S. aureus
includes all eucaryotic organisms o Maraming genus na nagsisimula sa S, so we
avoid abbreviation to avoid confusion as
well
o WE WILL NOT USE ABBREVIATION [IN
EXAMINATIONS OR QUIZZES]
• The genus followed by the word species may be used to
denote the entire genus as a whole. The species are
abbreviated as “sp.” (singular) or “spp.” (plural) when
the species is not specified.
• Lastly, when bacteria are referred to as a group, their
names are neither capitalized nor underlined
- Kapag ang tinutukoy ay yung buong genera [as a
group; as is]

NOMENCLATURE
IDENTIFICATION
• International Code of Nomenclature of Bacteria (ICNB)
GENOTYPIC CHARACTERISTICS
or the Bacteriological Code (BC)
- Provides the accepted labels by which organisms • relate to an organism’s genetic makeup, including the
are universally recognized. nature of the organism’s genes and constituent nucleic
• Binomial system of nomenclature acids.
- every organism is assigned a genus and a species of
Latin or Greek derivation. PHENOTYPIC CHARACTERISTICS
o Sometimes, it includes the subdivision of • are based on features beyond the genetic level and
specie, but normally, 2 lang: genus and include both readily observable characteristics and
specie characteristics that may require extensive analytic
- Each organism has a scientific “label” consisting of procedures to be detected.
two parts:
o GENUS - the first letter is always capitalized
o SPECIES – first letter is always lower case
- Printed in italics or underlined in script.

GUIDELINES
• The first letter of the family name (similar to a human
“clan”) is capitalized and has a suffix – aceae
- Hindi na need na italicized/underlined
• The first letter of the genus is capitalized followed by
the species in lowercase; both the genus and species
should be italicized in print or should be underlined
when written in script.

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 - to locate the nucleoid region, it is usually attached
to the mesosomes that can be found at the plasma
membrane of the cell
- in terms of the cellular organelle, ribosomes are the
only cellular organelle present in both prokaryotes
and eukaryotes
- in reproduction, bacteria: binary fission [asexual]
- Peptidoglycan [can be seen in the cell wall of
prokaryote]

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