Bactriology Lecture 3 Wk7 Flashcards

1
Q

Evolutionary timetable

A

Rise of oxygen stimulates rise of diverse range of living organisms

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2
Q

rRNA sequence - phylogenetic analysis

A

Bacteria -
Archaea
Eukarya

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3
Q

Bacterial evolutionary marker - ribosomal RNA

A
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4
Q

E. Coli 16s rRNA

A
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5
Q

16s rRNA gene amplification, sequencing

A

Cell culture -> DNA extract and PCR -> electrophoresis (check 16s DNA) -> sequencing -> align sequences, create phylogenetic tree.

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6
Q

Internal nodes - ancestor species
External nodes - extant known species

A

Branch - lengths represent evolutionary distance between species

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7
Q

Systematics, phylogeny and taxonomy

A

Systematics or phylogeny= study of evolutionary history of organisms
Taxonomy = science of classification to show similarities among organisms

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8
Q

Traditional taxonomy = practical aspects, visible properties
Modern taxonomy = DNA sequences + practical aspects

A

Modern bacterial taxonomy by polyphasic approach
1. Phenotypic 2. Genotypes 3. Phylogenetic
Petri dish. DNA. Tree

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9
Q

Biochemical test to separate bacterial species

A

Gram staining
Lactose fermentation
Oxidase
Catalase
Slide agglutination

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10
Q

Fatty acid analysis
Bacterial culture
Extract fatty acids
Derivatize to form methyl esters
Gas chromatography
Peaks from various fatty acid methyl esters
Compare pattern with database
Identify organism

A

Classes in bacteria
I. Saturated
II. Unsaturated
III. Cyclopropane
IV. Branched
V. Hydroxy

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11
Q

Genotype

A

GC content (%) = G+C/A+T+G+C X 100

GC-ratio= A+T/ G+C

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12
Q

Bacterial taxonomy y- genotype

A
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13
Q

Taxonomic Classification + nomenclature
- bacterial taxonomic hierarchy

A

Escherichia coli Staphylococcus aureus Streptomyces coelicolor

Domain Bacteria Bacteria Bacteria
Phylum Proteobacteria Firmicutes Actinobacteria
Class Gammaproteobacteria Bacilli Actinobacteria
Order Enterobacteriales Bacillales Actinomycetales
Family Enterobacteriaceae Staphylococcaceae Streptomycetaceae
Genus Escherichia Staphylococcus Streptomyces
Species coli aureus coelicolor

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14
Q

Genus epithet (=species)
Escherichia coli

A

Italicise the name
Escherichia coli
Genus name starts with upper case
A space between genus and species name
Species name starts with lower case

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15
Q

Gram-negatives - proteobacteria

A
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16
Q

Alphaproteobacteria

A
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17
Q

Proteobacteria

A

Alphaproteobacteria : caulobacter

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18
Q

Alphaproteobacteria : Hyphomicrobium

A

Hyphomicrobium cell cycle

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19
Q

Bacterial life cycle - binary fission vs budding

A

Alphaproteobacteria : diverse positioning of stalks in budding bacteria
Polar - small tail
Sub-polar - long tail
Bi-lateral - two tails either side

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20
Q

Bacterial diversity proteobacteria

A
  • Alphaproteobacteria : Rizobiales (Agrobacterium, Rizobium)
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21
Q

Proteobacteria - gammaproteobacteria

A
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22
Q

Gammaproteobacteria : Pseudomonadales

A

Pseudomonas aeruginosa
Pyoverdine production by Pseudomonas aeruginosa
Biofilm formation of Pseudomonas aeruginosa

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23
Q

Enterobacteriales

A

Eschericia coli

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24
Q

Proteobacteria - Epsilonproteobacteria

A

Stomach
H.pylori

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25
Q

Actinobacteria/Firmicutes

A
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26
Q

Gram-positive bacteria

A

Firmicutes : lactic acid bacteria
Lactobacillus delbruekii

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27
Q

Lactate fermentation

A

Glucose —> 2pyruvate —> 2lactate
Glycolysis Lactate fermentation

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28
Q

Gram-positive bacteria

A

Firmicutes : endoscope forming bacteria (clostridium, Bacillus)

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29
Q

Gram-positive bacteria
Firmicutes : endoscope forming bacteria (Clostridium, Bacillus)

A

Exosporium nap (BcIA)
Exosporium basal layer

30
Q

Firmicutes : staphylococcus

A

|| aureus = purple circles in clumps
Staphyloxanthin = beige rounds blobs

31
Q

Hemolysis (=haemolysis)

A
  1. Alpha hemolysis
  2. Bete hemolysis
  3. Gamma hemolysis
32
Q

Alpha hemolysis (α-hemolysis)

A

Incomplete / partial hemolysis, green hemolysis
Caused by hydrogen peroxide produced by bacteria
Oxidising hemoglobin to green methemoglobin

33
Q

Beta hemolysis (β-hemolysis)

A

Complete hemolysis
Caused by enzyme (streptomycin or exotoxin)
Produced by bacteria

34
Q

Gamma hemolysis γ-hemolysis

A

Non-haemolytic

35
Q

Firmicutes : Enterococcus

A

6 VRE phenotype

36
Q

Actinobacteria

37
Q

Actinobacteria
Comparison of microbial genome sizes

A

Mycoplasma : ~0.6 Mb
Bifidobacteria : ~2 Mb
staphylococci : 2.8-3 Mb
Escherichia : 4.5 - 5 Mb
Actinomycetes : 8-9 Mb
Yesterday : ~14 Mb

38
Q

Actinobacteria : Corynebacterium

39
Q

Actinobacteria : Mycobacterium

A

Mycobacterium tuberculosis
Complex cell envelope of Mycobacterium

40
Q

Actinomyces

A

-bovis
-israelii

41
Q

Streptomyces

A

Free spore - germination + growth of substrate mycelium - development of aerial mycelium - growth of an apical aerial hypha - coiling of apical hyphal cell - sporulation-specific septum formation - completion of septation- maturation of spores - dispersal of spores

42
Q

Streptomyces

A

Spore germination
Vegetative growth
Substrate mycelium
Antibiotic production
Formation of reproductive aerial hyphae
Aerial hypha
Chromosome segregation and separation
Spore mutation
Spore dispersal

43
Q
  • Actinobacteria : Streptomyces (Streptomyces coelicolor)
A

8,667,507bp

44
Q

Respiratory infections

A

Streptococcus pneumoniae, Mycobacterium tuberculosis

45
Q

Gastrointestinal infection

A

Camphylobacter jejuni, salmonella species, Shigella species, Escherichia coli 0157:H7, Helicobacter pylori

46
Q

Skin infection

A

Enterobacter species, Pseudomonas aeruginosa, Enterococcus species, Staphylococcus species.

47
Q

Upper respiratory trace
Nasal cavity
Pharynx
Larynx

A

Lower respiratory tract
Trachea
Primary bronchi
Lungs

Pneumonia
Tuberculosis

48
Q

Pneumonia
Fluid filling air space in alveolus
Pleurisy
Infection irritating pleura (thin outer layer of lung)

A

Lung inflammation
Streptococcus pneumoniae
Symp- cough, chest pain, fever, diff breathing
Vaccination, various antibiotics

49
Q

Streptococcus pneumoniae

A

Normal inhabitant of human respiratory tract, causes pneumonia
Common cause of bacterial meningitis, ear infections
Gram-positive 0.5-1.25 µm in diameter
doesn’t form spores, non-motile, alpha hemolytic when cultured on blood agar
Encapsulated coccoid bacteria
Polysaccharide capsule (virulence factor)
1 cirlcular chromosome = 2 base pairs, GC content of ~40%

50
Q

Streptococcus pneumoniae : antibiotic resistance

A
  1. Commonly used antibiotics
    : β-lactams (penicillin, amoxicillin, ampicillin)
    : Cephalosporins (cefotaxime, ceftriaxone)
    : Macrolides (erythromycin, azithromycin)
    : Fluroquinolones
    : Glycopeptides (vancomycin)
  2. Antibiotic resistance
    : Penicillin and Cephalosporins – resistance is common, mediated by altered PBP,
    transmissible to other pneumococcal strains
    : Macrolides – efflux pump or ribosomal mutations
    : Quinolones – efflux pump or DNA gyrase mutations
    : Vancomycin – no resistance yet
51
Q

Pneumonia vaccine

A
  1. Pneumococcal polysaccharide vaccine (PPV or PPSV) : contains long chains of polysaccharide (sugar) molecules that make up the surface capsule of the bacteria
    : a pure polysaccharide vaccine induces only short-term immunity and doesn’t work as well
    in children younger than 2 years
    : PPSV (Pnuemovax 23 = PPV-23 is known as the latest version) is the first vaccine
    derived from a capsular polysaccharide
    : widely used in high-risk adults
  2. Pneumococcal conjugate vaccine (PCV)purified capsular polysaccharides from the bacteria that are “conjugated” (or joined) to a
    harmless variety of diphtheria toxin
    : produces an immune response in infants and antibody booster response to multiple
    doses of vaccine
    : the British immunisation schedule for infants, with the first dose given at two months old, and is now licensed to protect against invasive disease caused by Streptococcus
    pneumoniae in adults aged 50 years and older
    : PCV7, PCV13
52
Q

Tuberculosis (TB)

A

Attacks lungs
Lethal infectious disease caused by mycobacteria
Spread through air
1/3 infected
1.3 M deaths 2022
Treatment long course of multiple antibiotics
Chronic cough, blood-tinged sputum, fever, night sweats, weight loss

53
Q

Mycobacterium tuberculosis (MTB)
Causative agent

A

-rod-shaped, non-motile, related to actinomycetes
-Acid-fast gram-positive or gram-resistant bacteria - waxy coating on cell surface (mycolic acid) = impervious to gram staining
-slow growth: divides 15-20 hours
-strain variation: significant phenotypic differences between clinical isolates
-circular chromosome, GC content 65%: H37Rv strain (4 mega base with 3959 genes)
-multi drug-resistant TB (MDR-TB) extensively drug-resistant TB (XDR-TB) major problem

54
Q

Chemotherapy protocol for treatment

A

Isoniazid
Rifampin
Pyrazinamide
Ethambutol

Isoniazid
Rifampin

55
Q

Salmonella

A

Food borne illness: gastroenteritis, typhoid fever, paratyphoid fever
-two species, salmonella enterica + salmonella bongori
-zoonotic
-gram-negative, rod-shaped, non-spore-forming, anaerobic, motile with flagella
-0.7-1.5 µm in diameter, 2 - 5µm in length- chemoorganotrophes : obtaining energy from oxidation and reduction reactions using organic
sources
- produce hydrogen sulfide

56
Q

Salmonella typhi

A

Salmonella enterica, serotype Typhi
-infects humans only, causes enteric bacterial infection, typhoid fever
-symptoms
High fever, sweating, diarrhoea, inflammation of stomach /+ intestines.
Enlargement of liver + spleen “rose spotted” skin rash on chest + abdomen
- 2 million cases, 500,000 deaths
-treatment
Drug resistance (MDR)
-prevention
Hygienic life style
Vaccines- the live, oral vaccine (Ty21a) + injectable tyhpoid polysaccharide vaccine
- 1st genome sequence S. typhi CT18 (MDR) strain
4.8 Mb circular chromosome, 2 plasmids pHCM1 (MRC) + pHCM2

57
Q

Escherichia coli 0157:H7

A
  • Gram-negative, rod shaped bacteria
  • “O” refers to the cell envelope (LPS) antigen number, “H” refers to the flagella antigen
  • Enterohemorrhagic E. coli (EHEC)
  • Shiga-like toxin producing E. coli (STEC)
  • symptoms of E. coli 0157:H7 infection : a low fever, nausea, vomiting, stomach cramps, and
    bloody diarrhoea
  • fatal condition : hemolytic uremic syndrome (HUS)
  • treatment
    : non-specific supportive therapy, including hydration, is important
    : no evidence that treatment with antibiotics is helpful, and taking antibiotics may increase
    the risk of HUS
    : antidiarrheal agents such as Imodium should be avoided
    as it may prolong the duration of the infection
58
Q

Helicobacter pylori

A

Causes gastritis, gastric ulcers + stomach cancer
Helix-shaped, motile, gram-negative, 3 3 µm long with 0.5 µm diameter
- genome : 1.6 Mb with 1590 coding genes, 29% of genome is involved in the pathogenesis
- virulence of Helicobacter pylori
: measured by the ability to produce cotoxin-associated protein (CagA) and active
vacuolating cytotoxin (VacA)
: Cag pathogenicity island : about 40 Kb long, responsible for pathogenesis, usually
absent from H. pylori strains isolated from humans
: other important virulent factors
- surface-exposed lipopolysaccharide
- iron-scavenging system
- urease
- motility for colonization
- type IV secretion system

59
Q

Helicobacter pylori- treatment, prevention + vaccination

A
  • therapy one week ‘triple therapy’
    1 proton pump inhibitor
    2 antibiotics - clarithromycin + amoxicillin, || + metronidazole
  • additional rounds of antibiotic therapy after failure ^
    “Quadruple therapy” + bismuth colloid drug
    Treatment of clarithromycin-resistant H.pylori vaccine levofloxacin
    -prevention
    Vaccination
    Probiotic diet
60
Q

Skin infection
Pseudomonas aeruginosa

A

50% mortality, 4th commonly-isolated nosocomial pathogen
-gram-negative, rod-shaped, motile + long monoflagellum
-Single cell size 1-5 µm long and 0.5-1.0 µm wide
- P. aeruginosa often identified by the production of pyocyanin and fluorescein and ability to grow at 42°C.
- pollution control - break down aromatic hydrocarbons
- intrinsic resistance to antibiotics

P. aeruginosa genome (PA01 strain)
: circular form, 6.2 Mb size with
~65% GC content

61
Q

Pseudomonas aeruginosa – biofilm formation

A

reversible attachment
irreversible attachment
microcolony formation
development of 3-dimensional structure
Dispersal

62
Q

Biofilm formation + motility

A

Swarming
Swimming
Twitching

63
Q

Pseudomonas aeruginosa – biofilm formation and quorum sensing

A

N-acyl homoserine lactone

64
Q

Pseudomonas aeruginosa – treatment

A

-low permeability to antibiotics = resistant
- biofilm
-s ome antibiotics have shown to be active against P. aeruginosa
: aminoglycosides (gentamicin, amikacin, tobramycin)
: quinolones (ciprofloxacin, levofloxacin, moxifloxacin)
: carbapenems (meropenem, imipenem, doripenem)
: polymyxins (polymyxinB, colistin)
: monobactams (aztreonam)
: cephalosporines (ceftazidime, cefepime, cefoperazone, cefpirome)
: antipseudomonal penicillins (ureidopenicillins, carboxypenicillins)
- phage therapy combined with antibiotics

65
Q

Enterococcus species

A
  • nosocomial infections - UTI
    -genus of lactic acid bacteria
    -tolerant of wide range of environmental conditions 10-45 °C), pH (4.5-10) and high sodium chloride concentrations
    -common in intestines : Enterococcus faecalis (90-95%), Enterococcus faecium (5-10%)
  • pathogenicity : cytolysin, a toxin causes rupture of a variety of target membranes, including
    bacterial cells, erythrocytes, and other mammalian cells
  • vancomycin resistant enterococcus (VRE)
66
Q

Vancomycin Resistant Enterococcus (VRE)

A

-1st VRE genome sequence from VanB-type Enterococcus faecalis V583 strain
: 1 circular chromosome with 3.2 Mb long (3337 genes), 3 plasmids
: more than 25% of total genes are exogenously acquired
- 7 integrated phage regions
- 38 insertion elements
- conjugative and composite transposons
- pathogenicity island
- vancomycin resistance genes encoded within a previously unknown mobile element
in genomic DNA (similar to Tn1549 in other VanB-type E. faecalis)

  • some other VanA-type VRE carry van resistance allele in plasmid
    : pIP816 in E. faecium BM4147
    - 11 kb long, 9 encoding vancomycin resistance cluster
    - orf1, orf2, vanR, vanS, vanHAX, vanY, vanZ
67
Q

Staphylococccus species

A

Greek = bunch of grapes + granule
-gram-positive (thicker peptidoglycan cell wall)+ immotile
- 40 species
-yellow colonies - S. aureus
White colonies - S. epidermidis
-first genome sequence

S. aureus strain NCTC8325
: circular genomic DNA with 2.8 Mb long with
2900 genes.
: 33% GC content

68
Q

Staphylococcus aureus

A

Most common
-nosocomial infections, post surgical wound infections
-successsful pathogen - immunodeficiency-evasive strategies
-emergence of MRSA (Methicillin-Resistant S. aureus)
: resistant to almost all clinically available β-lactam antibiotics including penicilins and
cephalosporins
: vancomycin became the primary antibiotic used to combat MRSA
: due to mecA encodes a modified PBP

69
Q

MRSA
1.27 million (direct) 4.95 million (associated)

A

Drug resistance in six pathogens 929,000 (direct) + 3.57 million (associated)
Escherichia coli
Staphylococcus aureus
Klebsiella pneumoniae
Streptococcus pneumoniae
Acinetobacter baumannii
Pseudomonas aeruginosa

MRSA itself > 100,000

70
Q

Pharmageddon?!

71
Q

Staphylococcus aureus :VRSE

A

Resistant to vancomycin + teicoplanin
-acquired VanA type vancomycin resistance genes from VanA-type VRE via horizontal gene - transfer mediated by transposon
-antibiotics
Trimethoprim/sulfamethoxazole, quinuprisitin/dalfopristin, tigecycline, linezolid and daptomycin
- novel antibiotics against VRSA is urgently required

72
Q

Vancomycin resistant MRSA = VRSA (carrying mecA and vanA genes)