Download Commensal and Pathogenic Microbial Flora in Humans

General Principles of Medical Bacteriology
Dongwoo Shin
Laboratory of Molecular Bacteriology
Department of Molecular Cell Biology
Sungkyunkwan University School of Medicine
Features of Bacteria
-Unicellular organism
-Small size: 1~2 µm in length
-Haploid: number of a gene (or
allele) is one
-Short generation time: in the
case of E. coli, ~20 min
-Asexual replication
Structure of a Bacterial Cell
Classification of Bacteria
Introduction
Never Underestimate the Power of Bacteria!
 Why
bacteria are once again in the public health spotlight
• Antibiotics
-first introduced into widespread clinical use in the 1950s
-miracle drugs
-appeared to give humans the final victory over bacteria
• However....
-during the late 1980s, an increase in bacterial infections
-by 1995, bacterial infectious diseases became one of the top
five causes of death in the US (e.g. pneumonia, sepsis)
Introduction
 Why
bacteria are once again in the public health spotlight
• Emerging infectious diseases
-power of rapid evolution
-acquire genes that confer new virulence traits or resistance
to antibiotics
• Unfortunately....
-human victory over bacteria had not occurred and is not
going to occur anytime in the future
Introduction
 Current
public health issues caused by bacterial infections
• Emerging infectious diseases
-new diseases caused by newly discovered bacteria:
Legionella pneumophila
-long-known pathogens acquiring traits that make them more
dangerous: antibiotic-resistant bacteria (Streptococcus
pneumoniae, Staphylococcus aureus)
• Food-borne infections
-Outbreaks of Escherichia coli O157:H7 infections: in
Japanese schoolchildren, 1996
Introduction
 Current
public health issues caused by bacterial infections
• Modern medicine as a source of new diseases
-transplantation, cancer chemotherapy
-suppressed immune systems of patients
-increase in the chance of opportunistic infection:
Pseudomonas aeruginosa
• Microbiota shift diseases
-Outgrowth of pathogens in the large intestine by antibiotics
treatment
Human Microbiota
Commensal and Pathogenic Microbial Flora in Humans
The adult human intestine is...
- Home to an inconceivable number of microorganisms
: The size of population is up to 100 trillion, ~10 times
greater than the total number of our somatic and germ cells
“Thus, it is appropriate to view ourselves as a composite of
many species and our genetic landscape as an amalgam of genes
embedded in our Homo sapiens genome and in the genomes of
our affiliated microbial partners (the microbiome)”
- Jeffrey I. Gordon, Science (2005)
Commensal and Pathogenic Microbial Flora in Humans
 In
a healthy human,
- The internal tissues (e.g. brain, blood, muscles): normally
free of microorganisms
- Conversely, the surface tissues (e.g. skin and mucous
membrane): constantly in contact with environmental
microorganisms and become colonized by certain microbial
species
- Normal microbiota (= microflora, normal flora): mixture of
microorganisms regularly found at any anatomical site
- Bacteria make up most of the normal microbiota over the
fungi and protozoa
Commensal and Pathogenic Microbial Flora in Humans

Exposure of an individual to an organism
1. Transient (hours or days) colonization
2. Permanent colonization
3. Disease production (Infection)
Note: colonization vs. infection
Commensal and Pathogenic Microbial Flora in Humans
The Relationship between Normal Microbiota and the Host
 Normal
microbiota
- participates in the metabolism of food products → provides
essential growth factors
- protects against infections with virulent microorganisms
- stimulates immune response
“Without these organisms life would be impossible”
Commensal and Pathogenic Microbial Flora in Humans
The Relationship between Normal Microbiota and the Host
 Normal
microbiota for causing disease
- opportunistic pathogens: members of the patient’s normal
microbiota; no disease in normal setting but disease when
introduced into unprotected sites (e.g. blood, tissues);
immunocompromised patients are more susceptible
Staphylococcus aureus
Escherichia coli
- cf. strict pathogens: a few infections
Mycobacterim tuberculosis (tuberculosis)
Neisseria gonorrhoeae (gonorrhea)
Commensal and Pathogenic Microbial Flora in Humans
 Microbiota
IN and ON the human body
- A continual state of flux: determined by age, diet, hormones,
health, and hygiene
- Human fetus: in sterile environment
- Newborn human: exposed to microbes from the mother and
the environment; skin → oropharynx → gastrointestinal (GI)
tract → other mucosal surfaces
- Microbial population continues to change throughout the life
Commensal and Pathogenic Microbial Flora in Humans
 Current
knowledge of composition of human microbiota
- Based on culture methods: only a small proportion of the
microbes can be cultivated
- Human Microbiome Project (HMP): initiated 2008; a largescale project for characterization of comprehensive human
microbiota and analysis of its role in human health and
disease; genomic techniques
Commensal and Pathogenic Microbial Flora in Humans
Respiratory Tract and Head
 Upper Respiratory Tract: Mouth, Oropharynx, and Nasopharynx
- The most common anaerobic bacteria: Peptostreptococcus, Veillonella,
Actinomyces, Fusobacterium
- The most common aerobic bacteria: Streptococcus, Haemophilus,
Neisseria
- Rarely associated with disease unless introduced into sterile sites (e.g.
sinuses, middle ear, brain)
- Potential pathogens: Streptococcus pyogenes, Streptococcus
pneumoniae, Staphylococcus aureus, Neisseria meningitidis,
Heamophilus influenzae, and Enterobacteriaceae
Commensal and Pathogenic Microbial Flora in Humans
 Ear
- The most common bacteria colonizing out ear: coagulase (-)
Staphylococcus
- Potential pathogens: Streptococcus pneumoniae, Pseudomonas
aeruginosa, and Enterobacteriaceae
Commensal and Pathogenic Microbial Flora in Humans
 Eye
- The surface of the eye: colonized with coagulase (-) Staphylococcus
- S. pneumoniae, S. aureus, H. influenzae, N. gonorrhoeae, P. aeruginosa,
Chlamydia trachomatis, and Bacillus cereus: associated with disease
 Lower Respiratory Tract
- Larynx, trachea, bronchioles, and lower airways: generally sterile
- Acute disease of lower airways: virulent bacteria in mouth; S.
pneumoniae, S. aureus, Klebsiella
- Polymicrobial disease by chronic aspiration: Peptostreptococcus,
anaerobic cocci, and anaerobic gram-negative rods
Commensal and Pathogenic Microbial Flora in Humans
Gastrointestinal Tract
 Colonized with microbes at birth
 Home for diverse population of organisms throughout the life of the host
 The populations remains relatively constant: But, antibiotic treatment
disrupting the balanced flora
 Esophagus
- Most organisms isolated from the esophagus: transient colonizers
- Bacteria rarely cause disease of esophagus
 Stomach
- Only small numbers of acid-tolerant bacteria: HCl, and pepsinogen
- Helicobacter pylori: gastritis and ulcerative disease
Commensal and Pathogenic Microbial Flora in Humans
 Small intestine
- Colonized with many different anaerobic bacteria: Peptostreptococcus,
Porphyromonas, and Prevotella
- Gastroenteritis-causing bacteria: Salmonella and Campylobacter;
present in small numbers as asymptomatic residents
- Obstruction of small intestine (e.g. after surgery) → blind loop syndrome
(막힌 고리 증후군): colonization and proliferation of the microbes in the
large intestine → malabsorption syndrome (음식물 흡수 저해)
Commensal and Pathogenic Microbial Flora in Humans
 Large intestine
- The biggest populations of microbes in the human body: ~1011 bacteria /
g of feces
- The most common bacteria: Bifidobacterium, Eubacterium, Bacteroides,
Enterococcus, and Enterobacteriaceae (e.g. Escherichia coli)
- E. coli: present from birth to death, ~1% of the intestinal population but
the most common aerobe responsible for intraabdominal disease
- Bacteroides flagilis: a minor member of the intestinal flora but the most
common anaerobe responsible for intraabdominal disease
- Bifidobacterium and Eubacterium: the most common bacteria in large
intestine but harmless
Commensal and Pathogenic Microbial Flora in Humans
 Large intestine
- Antibiotic treatment:
 Rapidly alters the population
 Causes proliferation of antibiotic-resistant bacteria (e.g.
Enterococcus, Pseudomonas)
 Rapid growth of Clostridium difficile → psedomembranous
colitis (거짓막염)
- Infection by enteric pathogens:
 Shigella, and enterohemorrhagic E. coli
 Disruption of the colonic flora → intestinal disease
Commensal and Pathogenic Microbial Flora in Humans
Genitourinary Tract
 Only anterior urethra and vagina: permanent colonization by microbes
 Urinary bladder: transient colonization cleared by bactericidal activity of the
uroepithelial cells and flushing action of voided urine
 Anterior urethra
- Lactobacillus, Streptococcus, coagulase (-) Staphylococcus
- Transient colonization with fecal organisms: Enterococcus and
Enterobacteiaceae urinary tract infection (UTI)
- N. gonorrhoeae and C. trachomatis: common causes of urethritis
Commensal and Pathogenic Microbial Flora in Humans
 Vagina
- Diverse populations influenced by hormones
- Newborn girls: Lactobacillus at birth → declined maternal estrogen →
Staphylococcus, Streptococcus, and Enterobacteriaceae → estrogen
production at puberty → Lactobacillus (predominant), Staphylococcus,
Streptococcus, Enterococcus, Enterobacteiaceae
- N. gonorrhoeae: common cause of vaginitis
Commensal and Pathogenic Microbial Flora in Humans
Skin
-Coagulase (-) Staphylococcus
- Clostridium perfringens
- Acinetobacter
Power of Rapid Evolution of Bacteria
Bacterial Gene Transfer
 Inter-strain transfer of DNA provides ‘genetic
diversity’ of bacteria: Horizontal Gene Transfer
- e.g. Evolutionary process of pathogenic bacteria from
nonpathogenic bacteria
- e.g. Spread antibiotics resistance among bacteria
 Three ways of bacterial gene transfer
- Conjugation: by physical interaction
- Transformation: transfer of a naked DNA
- Transduction: by bacteriophages
Bacterial Plasmids
 Plasmid
-Small and circular dsDNA molecules that can exist independently
of host chromosome
-Contains own replication origin
-e.g. F plasmid
Bacterial Plasmids
 Major types of plasmids
Type
Names
Size (kb) Copy No.
Hosts
Phenotypes
Fertility Factor
F Factor 95-100
1-3
E. coli, Salmonella Conjugation
R plasmids
R1
80
1-3
G(-) bacteria
ApR, KmR, CmR
Col plasmids
ColE1
9
10-30
E. coli
Colicin production
83
E. coli
Enterotoxin
56
S. aureus
Enterotoxin B
75
Pseudomonas
Virulence plasmids Ent
pZA10
Metabolic plasmids TOL
Toluene degradation
Bacterial Conjugation
 Conjugation
- Transfer of genetic information by direct
cell to cell contact
 An electron micrograph of two E. coli cells
in an early stage of conjugation
Bacterial Conjugation
e.g. F+×F- mating
- Donor strain (F+) contains F factor
carrying the genes for pilus formation
and plasmid transfer
DNA Transformation
 Transformation
- Uptake of naked DNA by a cell
 ‘Competent’ cell
- One able to take up DNA and be
transformed
DNA Transformation
1. Natural transformation
- Streptococcus, Bacillus,
Thermoactinomyces, Haemophilus,
Neisseria, Moraxella, Acinetobacter,
Helicobacter, Pseudomonas
- Mechanism in S. pneumoniae
- DNA uptake machinery
2. Artificial transformation
- Treatment of E. coli with CaCl2
- Electric shock (electroporation)
Transduction
e.g. Generalized transduction
-Occurs during the lytic cycle
of phages and can transfer any
part of the bacterial genome
-Formation of transducing
particle
-E. coli P1 and Salmonella P22
phages
 Genetic mechanism of evolution of pathogenic E. coli
Biological Mechanisms of Drug Resistance
 Genetic mechanism of evolution of methicillin
and vancomycin resistant Staphylococcus aureus