Upload
others
View
11
Download
0
Embed Size (px)
Citation preview
Alessandra CarattoliIstituto Superiore di Sanità, Roma IT
Public health perspectives on antimicrobial resistance plasmids in Enterobacteriaceae
Molecular epidemiology of antimicrobial resistance: the
targets• AR gene
• transposon
• plasmid
• bacterial clone
replication stability conjugation resistance mobile elements other genes
Rep
licas
e
Inse
rtion
sequ
ence
Parti
tioni
ngR
estri
ctio
nen
zym
e
reso
lvas
e
Self-conjugative systemRes
ista
nce
gene
Toxi
n-an
titox
in
Met
hyla
se
Large (30-300 kb) self-conjugative plasmid
Small (<30 kb) mobilizable plasmidoriV oriT
Inse
rtion
sequ
ence
mob
A/B
mob
C
repA
/B/C
itero
ns
Res
ista
nce
Inse
rtion
sequ
ence
oriV
Resistance
objective:to trace resistance plasmids
PLASMID TYPING AND SUBTYPING
1st level: PCR
PCR Multiplex(bp)
PCR Simplex(bp)
1 2 3 4 5
HI1471
HI2644
I1139
X376
L/M785
N559
FIA462
FIB702
W242
Y765
P534
FIC262
A/C465
T750
FIIS270
FII270
K155
B/O147
PCR-Based Replicon Typing (PBRT):plasmids are detected using replicase genes as targets
PBRT-KIT
M1
•HI1 (534)•HI2 (308)•I1α (159)
M2
•M (741)•N (514)•I2 (316)•B/O (159)
M3
•FIB (683)•FIA (462)•W (242)
M4
•L (854)•P (534)•X3 (284)•I1γ (161)
M5
•T (750)•A/C (418)•FIIS (259-260)
M6
•U (843)•X1 (370)•R (251)•FIIK (142-148)
M7
•Y (765)•X2 (376)•FIC (262)•K (160)
M8
•HIB-M (570)•FIB-M (440)•FII (258-262)
objective:to trace resistance plasmids
PLASMID TYPING AND SUBTYPING
2nd level: PCR-sequencing of the amplicon
pDLST(plasmid double locus sequence typing)
smr 0018 (1118 bp)smr 0199 (536 bp)
IncHI2 (multiplex PCR)
hipAsmr 0092smr 0183
repI: replicase gene
ardA: type I restriction-modification enzyme
trbA: involved in maintenance and plasmid transfer
sogS: DNA primase
pilL: type IV pilus biogenesis
IncI1 IncHI2
FII: The copA region of the FII replicon FIA: The region comprising the iterons and the replication protein repE gene of the FIA replicon FIB: The replication protein repB gene of the FIB replicon FIC: The copA region of the FIC replicon
IncF IncN
repN: replicase gene traJ: mobilization of the plasmid during the conjugative transfer korA: negatively regulating the synthesis of the conjugal pilus and mating pore during the conjugation process
García-Fernández et al. 2011Villa et al. 2010
García-Fernández & Carattoli. 2010García-Fernández et al. 2008
IncHI1 HCM1 043; HCM1 064; HCM1 099; HCM1 116; HCM1 178ac; HCM1 259 Phan MD& Wain J
Plasmid MultiLocus Sequence Typinghttp://pubmlst.org/plasmid/
objective:to trace resistance plasmids
PLASMID TYPING AND SUBTYPING
3rd level: whole genome sequencing (WGS)
PlasmidFinder and pMLST in silico
http://cge.cbs.dtu.dk/services/PlasmidFinder/http://cge.cbs.dtu.dk/services/pMLST/
In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing A Carattoli et al., AAC 58: 3895-3903
I1 plasmids and ESBLs
Plasmid transmission among bacteria from animals and humans
avian commensal E. coli (AFEC) avian pathogenic E. coli (APEC) retail poultry E. coli (RPEC)human commensal E. coli (HFEC) uropathogenic E. coli (UPEC)
Replicon AFEC %(n=92)
APEC %(n=422)
RPEC %(n=200)
HFEC %(n=101)
UPEC %(n=200)
I1 17.4 41.0 34.5 6.9 6.5
Occurrence of IncI1 plasmid replicons among various E. coliisolates- PBRT
Johnson TJ et al.,Plasmid Replicon Typing of Commensal and Pathogenic Escherichia coli Isolates. 2007 AEM 73: 1976–83
pMLST identified related IncI1 plasmids in isolatesfrom animal and human sources
CC‐3, CC‐7: CTX‐M‐1
CC‐12: CMY‐2
CC‐5: TEM‐52 TEM‐20
CC31: CTX‐M‐15
CC‐3, CC‐7: CTX‐M‐1Leverstein-van Hall et al CMI 2011
The birth of a resistance gene:CTX-M comes from Kluyvera
Rodríguez M M et al. Antimicrob. Agents Chemother. 2004;48:4895-4897
CTX-M
0
14.7
2468101214
CTX-M-43 (DQ102702)Toho-1 (D37830)CTX-M-31 (AJ567481)CTX-M-35 (AB176532)CTX-M-2 (X92507)CTX-M-20 (AJ416344)CTX-M-4 (Y14156)CTX-M-7 (AJ005045)CTX-M-6 (AJ005044)KLUA-5 (AJ427463)KLUA-12 (AJ427469)KLUA-4 (AJ427462)KLUA-3 (AJ427461)KLUA-1 (AJ272538)KLUA-8 (AJ427465)KLUA-9 (AJ427466)KLUA-11 (AJ427468)CTX-M-5 (U95364)KLUA-6 (AJ427464)KLUA-2 (AJ251722)KLUA-10 (AJ427467)CTX-M-25 (AF518567)CTX-M-39 (AY954516)CTX-M-26 (AY157676)CTX-M-41 (DQ023162)CTX-M-8 (AF189721)KLUG-1 (AF501233)CTX-M-40 (AY750914)CTX-M-1 (X92506)CTX-M-32 (AJ557142)CTX-M-36 (AB177384)CTX-M-29 (AY267213)CTX-M-30 (AY292654)CTX-M-11 (AJ310929)CTX-M-33 (AY238472)CTX-M-15 (AY044436)=UOE-1CTX-M-28 (AJ549244)CTX-M-23 (AF488377)CTX-M-42 (DQ061159)CTX-M-22 (AY080894)CTX-M-3 (Y10278)CTX-M-12 (AF305837)CTX-M-10 (AF255298)CTX-M-34 (AY515297)CTX-M-37 (AY649755)KLUC-1 (AY026417)CTX-M-38 (AY822595)Toho-2 (D89862)CTX-M-19 (AF325134)CTX-M-24 (AY143430)CTX-M-9 (AF174129)CTX-M-16 (AY029068)CTX-M-27 (AY156923)CTX-M-14 (AF252622)=M-18=Toh3=UOE-2CTX-M-17 (AY033516)CTX-M-13 (AF252623)CTX-M-21 (AJ416346)
pMLST identified related IncI1 plasmids in isolatesfrom animal and human sources
CC‐3, CC‐7: CTX‐M‐1
CC‐12: CMY‐2
CC‐5: TEM‐52 TEM‐20
CC31: CTX‐M‐15
CC‐3, CC‐7: CTX‐M‐1Leverstein-van Hall et al CMI 2011
The travels of CTX-M-1 and CTX-M-15
CC7-CTX-M-1CC3-CTX-M-1 CC31-CTX-M-15
Characterization of Epidemic IncI1-I Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella entericafrom Animals and Humans. H. Smith et al., 2015, AAC 9:5357-65
pMLST-I1 plasmid validation by WGS
Another example:diversity of plasmids at the origin of dissemination of NDM-1 carbapenemase
Worldwide dissemination of the NDM-type carbapenemases in Gram-negative bacteria. Dortet et al., Biomed Res Int. 2014;2014:249856
The carbapenemase threat in the animal world: the wrong culpritPoirel L, et al., J Antimicrob Chemother. 2014 Jul;69(7):2007-8.
NDM-type carbapenemase dissemination
EARSS 2015Escherichia coliResistance to carbapenems R+I
Plasmids without frontiers: IncA/C plasmids associated with NDM-1
Escherichia coliKlebsiella pneumoniaeProvidencia stuartii
Identification of NDM-positive IncA/C plasmids. A. Carattoli 2016, unpublished blaNDM-1 + armA + blaCMY-16
Milvus migransfosA3
fosphomycin resistancesuspected
origin in Asiatic regions
Ho et al., JAM 2013China:cattle, pigs, chickens,dogs, cats, and rodents
Plasmids without frontiers• MCR-1: plasmid mediated colistin resistanceAnimal reservoir?Human origin?Food-related transmission?Hospital, community, travels?
Species Source Country Year Beta-lactamases Plasmid Reference
E. coli Poultry ChinaDenmarkFranceAlgeriaMalaysia
2005-2015 CTX-M-1CMY-2 SHV-12
I2X4 HI2NT
Liu et al., LID 2016Hasman et al., EurSurv 2015Olaitan et al., LID 2016Petrillo et al., LID 2016Perrin-Guyomard et al., EurSurv 2016
E. coli Cattle FranceBelgiumJapan
2005-2015 CTX-M-1CTX-M-27
I2PHI2NT
Haenni et al., LID 2016Suzuki et al., LID 2016Malhotra-Kumar et al., LID 2016Perrin-Guyomard et al., EurSurv 2016
E. coliSalmonella
Swine ChinaBelgiumGermanyLaosMalaysiaJapanVietnam
2010-2013 CTX-M-1CTX-M-27CTX-M-55
I2HI2 X4NT
Liu et al., LID 2016Olaitan et al., LID 2016Petrillo et al., LID 2016Falgenhauer et al., LID 2016Suzuki et al., LID 2016Malhotra-Kumar et al., LID 2016Perrin-Guyomard et al., EurSurv 2016
E. coliSalmonella
Food ChinaSwitzerlandPortugalFrance
2011-2014 CTX-M-55CTX-M-65NDM-9
I2P X4NT
Liu et al., LID 2016Tse et al., LID 2016Petrillo et al., LID 2016Webb et al., LID 2016Malhotra-Kumar et al., LID 2016Yao et al., LID 2016Zurfuh et al., AAC 2016
E. coli Water SwitzerlandMalaysia
2012-2013 SHV-12 NT Petrillo et al., LID 2016Zurfuh et al., AAC 2016
More MCR-1 findings in animals, food, environment
Species Country Year Beta-lactamases Plasmid Reference
E. coli K. pneumoniae
ChinaDenmarkSwitzerlandTunisiaCambodiaPerùBoliviaGermanyLaosThailandiaVietnam
2012-2015 CMY-2VIM-1KPC-2CTX-M-1CTX-M-14CTX-M-15CTX-M-65CTX-M-55
I2HI2NT
Liu et al., LID 2016Hasman et al., EurSurv 2015Poirel et al., LID 2016Arcilla et al., LID 2016Stoesser et al., LID 2016Falgenhauer et al., LID 2016Olaitan et al., LID 2016Du et al., LID 2016
More MCR-1 findings in humans
Map of IncI2 plasmid pHNSHP45 carrying mcr-1 from Escherichia coli in ChinaLiu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu LF, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu JH, Shen J. Lancet Infect Dis. 2016 Feb;16(2):161-8
IncI2 plasmid associated with mcr-1
Horizontal transmissionMultifocal bacterial strainsSuccessfull broad-host range plasmidsEpidemic plasmids