Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study.
The present update on the global distribution of Mycobacterium tuberculosis complex spoligotypes provides both the octal and binary descriptions of the spoligotypes for M. tuberculosis complex, including Mycobacterium bovis, from >90 countries (13,008 patterns grouped into 813 shared types containing 11,708 isolates and 1,300 orphan patterns). A number of potential indices were developed to summarize the information on the biogeographical specificity of a given shared type, as well as its geographical spreading (matching code and spreading index, respectively). To facilitate the analysis of hundreds of spoligotypes each made up of a binary succession of 43 bits of information, a number of major and minor visual rules were also defined. A total of six major rules (A to F) with the precise description of the extra missing spacers (minor rules) were used to define 36 major clades (or families) of M. tuberculosis. Some major clades identified were the East African-Indian (EAI) clade, the Beijing clade, the Haarlem clade, the Latin American and Mediterranean (LAM) clade, the Central Asian (CAS) clade, a European clade of IS6110 low banders (X; highly prevalent in the United States and United Kingdom), and a widespread yet poorly defined clade (T). When the visual rules defined above were used for an automated labeling of the 813 shared types to define nine superfamilies of strains (Mycobacterium africanum, Beijing, M. bovis, EAI, CAS, T, Haarlem, X, and LAM), 96.9% of the shared types received a label, showing the potential for automated labeling of M. tuberculosis families in well-defined phylogeographical families. Intercontinental matches of shared types among eight continents and subcontinents (Africa, North America, Central America, South America, Europe, the Middle East and Central Asia, and the Far East) are analyzed and discussed.
Filliol
Ingrid
I
Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe.
Driscoll
Jeffrey R
JR
van Soolingen
Dick
D
Kreiswirth
Barry N
BN
Kremer
Kristin
K
Valétudie
Georges
G
Dang
Duc Anh
DA
Barlow
Rachael
R
Banerjee
Dilip
D
Bifani
Pablo J
PJ
Brudey
Karine
K
Cataldi
Angel
A
Cooksey
Robert C
RC
Cousins
Debby V
DV
Dale
Jeremy W
JW
Dellagostin
Odir A
OA
Drobniewski
Francis
F
Engelmann
Guido
G
Ferdinand
Séverine
S
Gascoyne-Binzi
Deborah
D
Gordon
Max
M
Gutierrez
M Cristina
MC
Haas
Walter H
WH
Heersma
Herre
H
Kassa-Kelembho
Eric
E
Ho
Minh Ly
ML
Makristathis
Athanasios
A
Mammina
Caterina
C
Martin
Gerald
G
Moström
Peter
P
Mokrousov
Igor
I
Narbonne
Valérie
V
Narvskaya
Olga
O
Nastasi
Antonino
A
Niobe-Eyangoh
Sara Ngo
SN
Pape
Jean W
JW
Rasolofo-Razanamparany
Voahangy
V
Ridell
Malin
M
Rossetti
M Lucia
ML
Stauffer
Fritz
F
Suffys
Philip N
PN
Takiff
Howard
H
Texier-Maugein
Jeanne
J
Vincent
Véronique
V
de Waard
Jacobus H
JH
Sola
Christophe
C
Rastogi
Nalin
N
D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D030561:Databases, Nucleic Acid; D006801:Humans; D017720:Molecular Epidemiology; D009163:Mycobacterium bovis / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology
D004269:DNA, Bacterial; D021901:DNA, Intergenic