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I
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C
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ESGMYC EGDC course
Gaining expertise in mycobacterial infections
Paris, May 27-29, 2013
Emerging Bacterial Pathogens Unit
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Field of science that
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Carl N. Linnaeus Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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c (1959):
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•  Photochromogenic
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•  Rapid growers
C
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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Phylogenesis
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Phylogenetic taxonomy
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M
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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0.02
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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0.02
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
y
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i
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Starting with x sequences of yenucleotides
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multiple threes can tbe
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C
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Bootstrap
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
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Unit Unit
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
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Unit Unit
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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Emerging
Emerging
Bacterial
Bacterial
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Unit Unit
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Emerging
Emerging
Bacterial
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Unit Unit
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Emerging
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Bacterial
Bacterial
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Unit Unit
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M. terrae complex
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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SLOW GROWERS
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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M. simiae complex
r
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I
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RAPID GROWERS
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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c
•  Clear phylogenetic
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I
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•  M. terrae
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intermediate
S
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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eprotein
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•  hsp65
65kD heat shock
u
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rRNA polymerase
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c
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70kD heatth
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n
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smallaprotein
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PHYLOGENY: the concatenation of
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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•  Old definition: group ofc species sharing
e
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S
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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b
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e
r
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•  M. avium
t
c
•  M. intracellulare
e
r
L
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D
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•  M. marseillense
M
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C
S
•  M. timonense
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•  a number of still unclassified mycobacteria
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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• 
• 
• 
• 
• 
• 
• 
r
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I
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M. simiae
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M. genavense
M. lentiflavum
M. sherrisii
M. stomatepiae
M. triplex
• 
• 
• 
• 
• 
• 
• 
• 
• 
• 
M. europaeum
M. intermedium
M. interjectum
M. heidelbergense
M. kubicae
M. montefiorense
M. palustre
M. parascrofulaceum
M. parmense
M. saskatchewanense
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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• 
• 
• 
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M. terrae
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C
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• 
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• 
• 
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• 
• 
M. algericum
M. arupense
M. engbaekii
M. heraklionense
M. hiberniae
M. kumamotonense
M. longobardum
M. minnesotense
M. senuense
E
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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c
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L
o
•  M. fortuitum complex
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•  M. chelonae-abscessus
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y
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D © complex
I
M
C
S
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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KINGDOM
TYPE
CLASS
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FAMILY
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SPECIES
Bacteria
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Mycobacteriaceae
Mycobacterium
152 + 9
E
Gao and Gupta. Microbiol.Mol.Biol.Rev. 2012
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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KINGDOM
TYPE
CLASS
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FAMILY
GENUS
SPECIES
Bacteria
Actinobacteria
Actinobacteria
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Mycobacteriaceae
Mycobacterium
152
E
Gao and Gupta. Microbiol.Mol.Biol.Rev. 2012
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
M
C
S
KINGDOM
TYPE
CLASS
ORDER
FAMILY
GENUS
SPECIES
Bacteria
Actinobacteria
Actinobacteria
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Mycobacteriaceae
Mycobacterium
152
E
Gao and Gupta. Microbiol.Mol.Biol.Rev. 2012
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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Merhej et al. Biology Direct 2009
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
y
r
a
r
b
i
L
e
r
u
t
When the their relatedness,
measured by
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DNA-DNA hybridization,
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I
M
C
S
E
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
y
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e
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When the their relatedness,
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u
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I
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Int.J.Syst.Evol.Microbiol. (2006), 56:2049-54
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
y
r
a
r
b
i
L
e
r
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t
When the their relatedness,
measured by
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D © investigating DNA-DNA
I
hybridization
M
C
S
E
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
y
r
a
r
b
i
L
e
r
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t
When the their relatedness,
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r
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M
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•  The
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S
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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Great is the expectation forcthe contribution that
e
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WGS will bring to the definition
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phylogeny
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D
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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C
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SPECIES
ORFs
M. smegmatis
6,940
M. rhodesiae
6,340
M. fortuitum
6,300
M. chubuense
6,070
M. vanbaalenii
6,050
M. kansasii
5,960
M. marinum
5,500
M. avium
5,400
M. intracellulare
5,280
M. abscessus
4,990
M. ulcerans
4,310
M. tuberculosis
4,060
M. leprae
2,750
http://www.genomesonline.org
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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Emerging Bacterial Pathogens Unit
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D
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M
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S
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Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit
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I
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S
EJune 30-July 3, 2013 - 34
th
Congress of European Society of
Mycobacteriology
www.esmcongress.com
Emerging
Emerging
Bacterial
Bacterial
Pathogens
Pathogens
Unit Unit