An#bio#c Use in Animals in the News Kennedy, Nov 15, 2013, Science Since: • WHO • FDA • President Obama
Antibiotics and their Resistance Gene Path to Humans
Aug 17, 2015
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
An#bio#c Use in Animals in the News
Kennedy, Nov 15, 2013, Science
Since: • WHO • FDA • President Obama
Increasing an#bio#c resistance genes in soil
in soil bacteria may be another factor impacting our battleagainst global AR.
AcknowledgmentsWe thank T. Schwartz and H. J. Monstein for providing DNAstandards, and William Sloan for comments on the manu-script. C.W.K., J.D., and D.W.G. were funded by ECOSERV,an EU Marie Curie Excellence Programme (MEXT-CT-2006-023469).
Supporting Information AvailableAdditional information on the regression analysis of log-transformed 16S-rRNA gene abundances versus time (TableS1); the abundance of 16S-rRNA genes and ARG for eachsample-year and sample-site (Table S2); exponential ratecoefficients for ARG genes and heavy metals based on unitized
data from 1940 to 2008 (Table S3); antibiotic production levelsin the United States (kton per year) from 1950 to 1986 (FigureS1); heavy metals over time among soils based on unitizeddata from 1940 to 2008 (Figure S2); and utilization of selectedantibiotics in agriculture in The Netherlands between 1997and 2007 (Figure S3). This information is available free ofcharge via the Internet at http://pubs.acs.org/.
Literature Cited(1) Committee on Human Health Risk Assessment of using Sub-
therapeutic Antibiotics in Animal Feeds. Human Health Riskswith the Subtherapeutic Use of Penicillin or Tetracyclines inAnimal Feed; Institute of Medicine, Division of Health Promotionand Disease Prevention: National Academy Press, Washington,DC, 1989.
(2) Martinez, J. L. Antibiotics and antibiotic resistance genes innatural environments. Science 2008, 321, 365–367.
(3) Bergstrom, C. T.; Feldgarden, M., The Ecology and Evolutionof Antibiotic-Resistant Bacteria In Evolution in Health andDisease; Stearns, S., Koella, J., Eds.; Karen Bush/J&J, 2008.
(4) Taubes, G. The bacteria fight back. Science 2008, 321, 356–361.(5) Frost, A. J., Antibiotics and animal production In Microbiology
of Animals and Animal Products; Woolcock, J. B., Ed. Elsevier:Amsterdam, 1991; pp 181-194.
(6) Sarmah, A. K.; Meyer, M. T.; Boxall, A. B. A. A global perspectiveon the use, sales, exposure pathways, occurrence, fate and effectsof veterinary antibiotics (VAs) in the environment.Chemosphere2006, 65, 725–759.
(7) Levy, S. B. Factors impacting on the problem of antibioticresistance. J. Antimicrob. Chemother. 2002, 49 (1), 25–30.
(8) Ungemach, F. R. Figures on quantities of antibacterials usedfor different purposes in the EU countries and interpretation.Acta Vet. Scand. 2000, 89–98.
(9) Commission of the European Communities. Report from thecommission to the council on the basis of member states’ reportson the implementation of the council recommendation (2002/77/EC) on the prudent use of antimicrobial agents in humanmedicine; Council of the European Union: Brussels, Belgium,2002.
(10) Swan Report. Report of the joint committee on the use ofantibiotics in animal husbandry and veterinary medicine;H.M.S.O.: London, UK, 1969.
(11) Kummerer, K. Resistance in the environment. J. Antimicrob.Chemother. 2004, 54 (2), 311–320.
(12) Davies, J. Inactivation of antibiotics and the dissemination ofresistance genes. Science 1994, 264 (5157), 375–382.
(13) Clark, I. M.; Hirsch, P. R. Survival of bacterial DNA and culturablebacteria in archived soils from the Rothamsted Broadbalkexperiment. Soil Biol. Biochem. 2008, 40 (5), 1090–1102.
(14) Dolfing, J.; Vos, A.; Bloem, J.; Ehlert, P. A. I.; Naumova, N. B.;Kuikman, P. J. Microbial diversity in archived soils.Science 2004,306 (5697), 813–813.
(15) Tzeneva, V. A.; Salles, J. F.; Naumova, N.; de Vos, W. M.; Kuikman,P. J.; Dolfing, J.; Smidt, H. Effect of soil sample preservation,compared to the effect of other environmental variables, onbacterial and eukaryotic diversity. Res. Microbiol. 2009, 160 (2),89–98.
(16) Yu, Y.; Lee, C.; Kim, J.; Hwang, S. Group-specific primer andprobe sets to detect methanogenic communities using quan-titative real-time polymerase chain reaction.Biotechnol. Bioeng.2005, 89 (6), 670–679.
(17) Peak, N.; Knapp, C. W.; Yang, R. K.; Hanfelt, M. M.; Smith, M. S.;Aga, D. S.; Graham, D. W. Abundance of six tetracyclineresistance genes in wastewater lagoons at cattle feedlots withdifferent antibiotic use strategies. Environ. Microbiol. 2007, 9(1), 143–151.
(18) Smith, M. S.; Yang, R. K.; Knapp, C. W.; Niu, Y. F.; Peak, N.;Hanfelt, M. M.; Galland, J. C.; Graham, D. W. Quantification oftetracycline resistance genes in feedlot lagoons by real-timePCR. Appl. Environ. Microbiol. 2004, 70 (12), 7372–7377.
(19) Patterson, A. J.; Colangeli, R.; Spigaglia, P.; Scott, K. P. Distributionof specific tetracycline and erythromycin resistance genes inenvironmental samples assessed by macroarray detection.Environ. Microbiol. 2007, 9 (3), 703–715.
(20) Volkmann, H.; Schwartz, T.; Bischoff, P.; Kirchen, S.; Obst, U.Detection of clinically relevant antibiotic-resistance genes inmunicipal wastewater using real-time PCR (TaqMan). J. Mi-crobiol. Meth. 2004, 56, 277–286.
FIGURE 2. Relative increase of antibiotic resistance genesamong soils collected at five sites in The Netherlands from1940 to 2008. All values have been normalized to 16S rRNAgene abundances. Normalized values were then groupedaccording to decade and unitized relative to mean observedvalues from 1970 to 1979 for each site. Normalization andunitization were required to account for differences inbacterial abundances among sites and place data from eachsite into a common unit of measure. Each time seriesrepresents the unbiased sum of standardized values from allfive sites. Table S2 provides detailed data for each site.mecA, blaOXA-1, vanA and ampC were analyzed, but werebelow detection limits. Shaded areas are the best-fit curvesfor each class of detected antibiotics assuming a first-ordermodel, which represents the basal level of resistance geneswithin the soils. Inset rate coefficients are for each class ofantibiotic. Rate coefficients for each individual detectedgene are provided in Table S3.
586 9 ENVIRONMENTAL SCIENCE & TECHNOLOGY / VOL. 44, NO. 2, 2010
Knapp et al., 2010, ES&T
Tim Johnson, MSU Robert Sted9eld, MSU Syed Hashsham, MSU Jim Cole, MSU Torey LooB*, USDA Heather Allen, USDA Thad Stanton, USDA Yong-‐Guan Zhu**, CAS Jianqiang Su, CAS *PNAS, 2012 **PNAS, 2013
Acknowledgements
From 1940 to 2008 in 5 soil series in The Netherlands Hence, environmental selection is increasing
An#bio#cs and their resistance gene paths to humans (outside the clinic)
• Hospital wastes • Disposal from home use, WWTP • Manufacturing and formula#on facili#es • Agriculture
• Fruit produc#on (minor % of an#bio#c use) • Animal produc#on (pigs, chickens)
• Waste water, especially reuse in the Southwest • Manure compost (to fields, organic fer#lizers, vegetables)
• Farm workers • Dust
Needed: Resistance gene, mobile element,
recep#ve pathogen and an#bio#c (or co-‐) selec#on Goal: slow the rate of MDR pathogens
A
B
C
An#bio#c deac#va#on Efflux pump Cellular protec#on Other/ unknown
Aminoglycoside Beta Lactam FCA MLSB Tetracycline Vancomycin Other/ efflux
0
20
40
60
80
100
CP
M
BJP
M
JX
PM
PT
PM
CS
BJM
C
JX
MC
PT
MC
BJS
C
JX
SC
PT
SC
No
. R
esis
tan
ce
Gen
es D
ete
cte
d
CP
BM
JM
PM
CS
BC
JC
PC
BS
JS
PS
Nearly 100 resistance genes detected
CM
A
B
C
An#bio#c deac#va#on Efflux pump Cellular protec#on Other/ unknown
Aminoglycoside Beta Lactam FCA MLSB Tetracycline Vancomycin Other/ efflux
0
20
40
60
80
100
CP
M
BJP
M
JX
PM
PT
PM
CS
BJM
C
JX
MC
PT
MC
BJS
C
JX
SC
PT
SC
No
. R
es
ista
nc
e
Ge
ne
s D
ete
cte
d
CP
BM
JM
PM
CS
BC
JC
PC
BS
JS
PS
Macrolide, lincosamide, streptogramin Quinolones, amphenicols
In 3 commercial Chinese pig farms
Transposons, an#bio#cs, and metals correlate with resistance
Resistance genes gene#cally mobile?
Emergence of integrons JOURNAL OF BACTERIOLOGY, July 2008, p. 5095–5100 Vol. 190, No. 140021-9193/08/$08.00!0 doi:10.1128/JB.00152-08Copyright © 2008, American Society for Microbiology. All Rights Reserved.
The Evolution of Class 1 Integrons and the Rise ofAntibiotic Resistance!†
Michael Gillings,1* Yan Boucher,2 Maurizio Labbate,2 Andrew Holmes,3 Samyuktha Krishnan,1Marita Holley,1 and H. W. Stokes2
Department of Biological Sciences1 and Department of Chemistry and Biomolecular Sciences,2 Macquarie University, Sydney,NSW 2109, Australia, and School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia3
Received 29 January 2008/Accepted 7 May 2008
Class 1 integrons are central players in the worldwide problem of antibiotic resistance, because they cancapture and express diverse resistance genes. In addition, they are often embedded in promiscuous plasmidsand transposons, facilitating their lateral transfer into a wide range of pathogens. Understanding the origin ofthese elements is important for the practical control of antibiotic resistance and for exploring how lateral genetransfer can seriously impact on, and be impacted by, human activities. We now show that class 1 integrons canbe found on the chromosomes of nonpathogenic soil and freshwater Betaproteobacteria. Here they exhibitstructural and sequence diversity, an absence of antibiotic resistance genes, and a phylogenetic signature oflateral transfer. Some examples are almost identical to the core of the class 1 integrons now found inpathogens, leading us to conclude that environmental Betaproteobacteria were the original source of thesegenetic elements. Because these elements appear to be readily mobilized, their lateral transfer into humancommensals and pathogens was inevitable, especially given that Betaproteobacteria carrying class 1 integronsare common in natural environments that intersect with the human food chain. The strong selection pressureimposed by the human use of antimicrobial compounds then ensured their fixation and global spread into newspecies.
The rapid appearance and rise of the class 1 integron is oneof the most stunning examples of evolution in action, driven bythe power of natural selection. Class 1 integrons appeared in anumber of different locations, and on different plasmids andtransposons, coincident with the widespread use of antibiotics(5, 29). They are now found in 40 to 70% of gram-negativepathogens isolated from clinical contexts (7, 18) and at similarfrequencies in pathogens and commensals isolated from live-stock (6, 10). The rapid spread of class 1 integrons throughgram-negative and, more recently, into gram-positive specieshas been facilitated by their location on mobile DNA elements,such as plasmids and transposons, coupled with the selectiveadvantage conferred by their associated antibiotic resistancegenes (5, 26, 35). They have created a worldwide crisis in themanagement of bacterial infections.
There are at least 90 distinct integron classes, mostly locatedon chromosomes, and about 10% of sequenced bacterial ge-nomes carry these elements (3, 19). All integrons capture mo-bile gene cassettes using site-specific recombination mediatedby an integron-integrase (intI) (12). This integrase type cata-lyzes recombination between a primary recombination site(attI) and a corresponding 59-base element site (59-be or attC)carried on mobile gene cassettes. Through this activity, chro-mosomal integrons can accumulate up to hundreds of cassettesin a tandem array extending from attI, thus contributing exten-
sively to the diversity of bacterial genomes (9, 14, 27). Chro-mosomal integrons do exhibit intragenomic, intercellular, andinterspecies movement over evolutionary time frames but aregenerally stable in particular phylogenetic lineages (3, 9, 14, 19,20, 27).
The first integrons to be described, classes 1, 2, and 3, exhibita number of features not typical of the more numerically dom-inant chromosomal integron classes. They are carried on trans-posons and/or plasmids and most commonly contain from 0 to6 cassettes drawn from a pool of about 100 cassettes in total,almost all of which encode antibiotic resistance determinants(24, 30). There is experimental evidence (26) that the antibioticresistance genes found in class 1, 2, and 3 integrons wereacquired by capturing gene cassettes from the vast pool ofdiverse cassettes that are prevalent in microbial communities(3, 19, 21, 28).
While potential sources of resistance genes may have beenidentified, the origin of the class 1 recombination platform,now so abundant in clinical pathogens, is not known. Since theclass 1 integron has had a major role in the spread of antibioticresistance and led to worldwide difficulties in controlling bac-terial infection, understanding the origin of these elements isimportant both for practical control of antibiotic resistance andfor exploring the means by which bacterial lateral gene transfercan seriously impact on, and be impacted by, human activities.
Clues to this origin lie in features that are common to class1 integrons from clinical contexts. The nucleotide sequencesfor their integrase genes (intI1) are identical, or nearly so,strongly suggesting that these elements were derived from avery recent common ancestor. Here we will use the term “clin-ical” class 1 integrons to refer to the group of integrons whichshare this nucleotide sequence and are commonly found in
* Corresponding author. Mailing address: Biological Sciences, Mac-quarie University, Sydney, NSW 2109, Australia. Phone: 61 2 98508199. Fax: 61 2 9850 9237. E-mail: [email protected].
† Supplemental material for this article may be found at http://jb.asm.org/.
! Published ahead of print on 16 May 2008.
5095
on Decem
ber 5, 2013 by Macquarie U
niversity Libraryhttp://jb.asm
.org/D
ownloaded from
were conjugated into a human commensal or pathogen. Thisfirst cassette may have encoded qacE, since it is a commonfeature of clinical class 1 integrons, and quaternary ammoniumcompounds have a longer history of use than antibiotics. Onceresident in the human population, the chances of evolutionarysuccess for such an element were vastly improved. The abilityof class 1 integrons to access antibiotic resistance cassettes,coupled with the enhanced mobility conferred by the plasmid/transposon combination, allowed the rapid spread and struc-tural diversification of clinical class 1 integrons, while still re-taining the class 1 core that participated in the originalmobilization event (Fig. 2).
A key prediction of this model is that representatives of therecipient Tn402-like element should still be recoverable. Suchan element should carry flanking sequences that are present inclinical class 1 integrons but lacking in their betaproteobacte-rial ancestors. We have found such an element in a survey offecal bacteria from healthy volunteers. An isolate of Entero-bacter cloacae was recovered which contained a putative trans-poson (Tn6008) carrying IRi and part of the 5!-CS, extendingup to the ISPa7 insertion point (Fig. 1A; see also Fig. S1 in thesupplemental material). It also carried IRt and tniA (althoughnot of the Tn402 type) but did not carry intI1 or any gene
cassettes. Consequently, Tn6008 is a representative of the kindof element into which a chromosomal class 1 integron wasoriginally inserted. Recombination between a Tn6008-like el-ement and a betaproteobacterial class 1 integron at the ISPa7insertion point would generate the 5!-CS typical of clinicalclass1 integrons (Fig. 1; see also Fig. S1 in the supplementalmaterial). Tn6008 is from a commensal bacterium that alsocauses nosocomial infections, reinforcing the ease with whichmobile elements can move between environments and provid-ing a plausible route for entry of betaproteobacterial class 1integrons into human commensal flora. This E. cloacae isolatewas recovered in the absence of antibiotic selection, under-scoring the fact that the current antibiotic resistance epidemiccannot be fully understood by only examining hospital isolatesrecovered using antibiotic resistance media.
While Tn6008 represents the kind of element into which aclass 1 integron might have been inserted, it is not the imme-diate ancestor of clinical class 1 integrons, since it lacks therequired set of transposition genes. However, further clues tothe most immediate past event that linked the class 1 integronto a Tn402-like transposon can be found in the Thauera, Hy-drogenophaga, and Aquabacterium integrons. Their left-handboundaries agree with the model described above. In addition,these integrons also have a common right-hand boundary, 44bases beyond the recombination point of the last gene cassettein each of their arrays. The 44 nucleotides leading up to thisboundary are identical, or very nearly so, to a region of Tn402in the same relative position (see Fig. S3 in the supplementalmaterial). Thus, we predict that the Tn402-like transposon thatcaptured the class 1 integron lacked these 44 bases, since theywere brought into the transposon when the class 1 integron wascaptured.
Why was the class 1 integron the most successful in pene-trating and propagating in the clinical environment? We pos-tulate that the predisposition of class 1 integrons for mobili-zation and their presence in a bacterial group that iswidespread and relatively abundant in water supplies weresignificant factors in their preeminent role in the integron-borne antibiotic resistance epidemic. However, given the ap-parent ubiquity of integrons in the environment, the selectionof an integron with the ability to sequester antibiotic resistancegenes was probably inevitable once antibiotics began to bewidely used. In support of this idea, the other two integrons ofclinical importance, classes 2 and 3, may also have recentenvironmental ancestors. A functional class 2 integron contain-ing four gene cassettes, none of which encodes antibiotic re-sistance, has been isolated from Providencia stuartii (1). Simi-larly, a chromosomal class 3 integron has recently beenrecovered from Delftia (34). This genus is also in the Betapro-teobacteria, and the class 3 integrases are the sister group ofclass 1 integrases. Finally, the Vibrio salmonicida resistanceplasmid pRVS1 carries a tetracycline resistance gene cassetteassociated with an integron-integrase gene that is 99% identi-cal to the chromosomal integrase in Pseudoalteromonas halo-planktis (32). Consequently, even if we could eliminate allintegron-borne antibiotic resistance determinants from the hu-man environment, new antibiotic resistance integrons wouldinevitably be selected from the vast pool of integrons and genecassettes that are always endemic in natural environments.
FIG. 2. Model for the origin and subsequent divergence of the class1 integrons that are now widely disseminated in pathogens and humancommensals. Stages in the hypothetical evolution are as follows. (Aand B) The common ancestor of clinical class 1 integrons was a mem-ber of an integron pool that was repeatedly acquired by diverse Beta-proteobacteria but not other lineages (Fig. 1) (21). (C and D) Onebetaproteobacterial chromosomal integron inserted/recombined into aTn402-like element. This event occurred prior to, or concomitant with,the antibiotic era. Capture of qacE probably occurred around the sametime. (E) sul1 and orf5 were captured. (F) Deletions, insertions, andother rearrangements involving qacE, sul1, and adjacent sequencegenerated the 3!-conserved segment (3!-CS). (G) Deletions and inser-tions involving tni generated Tn402 transposition-incompetent inte-grons, which conferred various antibiotic resistance phenotypes due totheir diverse cassette arrays. (H) trans-mediated Tn402-like transposi-tion events moved integrons into diverse plasmids and other trans-posons, such as the Tn21 family (22). These events generated furtherdiversity and accelerated the penetration of class 1 integrons into awide variety of pathogens and commensals.
VOL. 190, 2008 EVOLUTION OF CLASS 1 INTEGRONS 5099
on Decem
ber 5, 2013 by Macquarie U
niversity Libraryhttp://jb.asm
.org/D
ownloaded from
Sequencing of the is6100-‐intI1 cluster
26−0D26−14D31−0D31−14D32−0D32−14D34−0D34−14D35−0D35−14D35−3D37−0D37−14DF104F2
F312F6A1A2A3
BM1BM2BM3BC1BC2BC3BS1BS2BS4JM1JM2JM3JC1JC2JC3JS1JS3JS4PM1PM2PM3PC1PC2PC3PS1PS2PS3
allRefSeq
X16S_O
TU_033_144
X16S_O
TU_192_215
X16S_O
TU_007_253
X16S_O
TU_050_258
X16S_O
TU_226_362
X16S_O
TU_010_417
X16S_O
TU_006_462
X16S_O
TU_014_565
X16S_O
TU_002_717
X16S_O
TU_038_745
X16S_O
TU_042_845
X16S_O
TU_019_1300
X16S_O
TU_037_2335
X16S_O
TU_001_4276
X16S_O
TU_000_64949
AG10_O
TU_217_201
AG10_O
TU_027_206
AG10_O
TU_053_208
AG10_O
TU_220_212
AG10_O
TU_051_220
AG10_O
TU_008_221
AG10_O
TU_060_222
AG10_O
TU_005_232
AG10_O
TU_046_247
AG10_O
TU_013_250
AG10_O
TU_280_252
AG10_O
TU_222_300
AG10_O
TU_227_332
AG10_O
TU_091_54305
AG10_O
TU_002_67731
Tn21_O
TU_014_46
Tn21_O
TU_011_52
Tn21_O
TU_019_54
Tn21_O
TU_012_58
Tn21_O
TU_057_59
Tn21_O
TU_069_60
Tn21_O
TU_003_65
Tn21_O
TU_008_66
Tn21_O
TU_023_68
Tn21_O
TU_010_69
Tn21_O
TU_030_77
Tn21_O
TU_013_86
Tn21_O
TU_031_108
Tn21_O
TU_009_115
Tn21_O
TU_000_23582
tet9_O
TU_013_195
tet9_O
TU_045_202
tet9_O
TU_054_203
tet9_O
TU_059_219
tet9_O
TU_040_228
tet9_O
TU_016_239
tet9_O
TU_010_247
tet9_O
TU_023_253
tet9_O
TU_079_254
tet9_O
TU_021_255
tet9_O
TU_049_268
tet9_O
TU_072_291
tet9_O
TU_032_303
tet9_O
TU_067_365
tet9_O
TU_000_91714
tet8_O
TU_0968_419
tet8_O
TU_0169_495
tet8_O
TU_0341_500
tet8_O
TU_0452_746
tet8_O
TU_0176_781
tet8_O
TU_0191_932
tet8_O
TU_0210_1235
tet8_O
TU_0055_1256
tet8_O
TU_0001_1434
tet8_O
TU_3831_1620
tet8_O
TU_1476_1884
tet8_O
TU_0002_3895
tet8_O
TU_0110_8573
tet8_O
TU_0034_18627
tet8_O
TU_0000_31950
tet7_O
TU_0232_101
tet7_O
TU_0240_107
tet7_O
TU_0327_140
tet7_O
TU_0042_154
tet7_O
TU_0101_251
tet7_O
TU_0034_287
tet7_O
TU_0149_393
tet7_O
TU_0008_926
tet7_O
TU_0012_1203
tet7_O
TU_0024_1782
tet7_O
TU_0007_2652
tet7_O
TU_0010_3721
tet7_O
TU_0005_3821
tet7_O
TU_0004_7401
tet7_O
TU_0002_16351
tet6_O
TU_045_183
tet6_O
TU_015_188
tet6_O
TU_056_190
tet6_O
TU_065_198
tet6_O
TU_005_199
tet6_O
TU_006_216
tet6_O
TU_023_222
tet6_O
TU_050_224
tet6_O
TU_025_253
tet6_O
TU_040_281
tet6_O
TU_021_296
tet6_O
TU_003_396
tet6_O
TU_093_3645
tet6_O
TU_008_4647
tet6_O
TU_001_72686
IncP_O
TU_0164_351
IncP_O
TU_0807_352
IncP_O
TU_0542_377
IncP_O
TU_0043_522
IncP_O
TU_0004_528
IncP_O
TU_0001_548
IncP_O
TU_1384_600
IncP_O
TU_1088_660
IncP_O
TU_0895_748
IncP_O
TU_0032_825
IncP_O
TU_0003_1046
IncP_O
TU_0826_1059
IncP_O
TU_0747_1240
IncP_O
TU_0000_2904
IncP_O
TU_0002_3852
IncN_O
TU_0023_228
IncN_O
TU_0090_233
IncN_O
TU_0036_242
IncN_O
TU_0060_245
IncN_O
TU_0100_255
IncN_O
TU_0108_256
IncN_O
TU_0123_260
IncN_O
TU_0017_262
IncN_O
TU_0049_294
IncN_O
TU_0007_313
IncN_O
TU_0002_328
IncN_O
TU_0236_1238
IncN_O
TU_0253_1327
IncN_O
TU_1759_25082
IncN_O
TU_0001_73797
ILMA_OTU
_00633_240
ILMA_OTU
_17867_250
ILMA_OTU
_17773_295
ILMA_OTU
_30002_303
ILMA_OTU
_00000_308
ILMA_OTU
_00742_321
ILMA_OTU
_06873_323
ILMA_OTU
_00183_518
ILMA_OTU
_00686_597
ILMA_OTU
_00959_686
ILMA_OTU
_00012_742
ILMA_OTU
_02617_777
ILMA_OTU
_01472_786
ILMA_OTU
_00935_800
ILMA_OTU
_00001_1402
GapA.F_OTU
_0018_432
GapA.F_OTU
_0113_437
GapA.F_OTU
_0089_438
GapA.F_OTU
_0031_444
GapA.F_OTU
_0009_450
GapA.F_OTU
_0027_462
GapA.F_OTU
_0054_470
GapA.F_OTU
_0048_476
GapA.F_OTU
_0069_513
GapA.F_OTU
_0172_551
GapA.F_OTU
_0007_582
GapA.F_OTU
_0056_609
GapA.F_OTU
_0111_883
GapA.F_OTU
_5528_2015
GapA.F_OTU
_0000_145966
dfrA1_OTU
_061_151
dfrA1_OTU
_069_153
dfrA1_OTU
_005_157
dfrA1_OTU
_014_165
dfrA1_OTU
_016_171
dfrA1_OTU
_018_180
dfrA1_OTU
_004_182
dfrA1_OTU
_038_186
dfrA1_OTU
_043_189
dfrA1_OTU
_010_192
dfrA1_OTU
_009_206
dfrA1_OTU
_015_288
dfrA1_OTU
_011_1949
dfrA1_OTU
_003_4460
dfrA1_OTU
_000_61459
dfra2_OTU
_030_61
dfra2_OTU
_026_70
dfra2_OTU
_021_74
dfra2_OTU
_015_77
dfra2_OTU
_016_85
dfra2_OTU
_019_86
dfra2_OTU
_004_88
dfra2_OTU
_013_89
dfra2_OTU
_012_90
dfra2_OTU
_023_107
dfra2_OTU
_000_113
dfra2_OTU
_031_124
dfra2_OTU
_005_127
dfra2_OTU
_010_159
dfra2_OTU
_001_37786
AG7_OTU
_0051_294
AG7_OTU
_0019_300
AG7_OTU
_0103_308
AG7_OTU
_0046_315
AG7_OTU
_0001_317
AG7_OTU
_0037_319
AG7_OTU
_0024_323
AG7_OTU
_0030_325
AG7_OTU
_0006_352
AG7_OTU
_0005_367
AG7_OTU
_0053_407
AG7_OTU
_0038_472
AG7_OTU
_0043_844
AG7_OTU
_0296_913
IS26_O
TU_035_371
IS26_O
TU_005_372
IS26_O
TU_021_373
IS26_O
TU_011_381
IS26_O
TU_019_383
IS26_O
TU_032_387
IS26_O
TU_009_390
IS26_O
TU_066_392
IS26_O
TU_010_399
IS26_O
TU_031_408
IS26_O
TU_029_415
IS26_O
TU_027_473
IS26_O
TU_003_491
IS26_O
TU_042_565
IS26_O
TU_000_142450
tet1_O
TU_0271_274
tet1_O
TU_0382_278
tet1_O
TU_0009_290
tet1_O
TU_0205_293
tet1_O
TU_0265_297
tet1_O
TU_0692_314
tet1_O
TU_0269_386
tet1_O
TU_0241_387
tet1_O
TU_0203_402
tet1_O
TU_0003_550
tet1_O
TU_0578_3063
tet1_O
TU_0278_5767
tet1_O
TU_0001_22800
tet1_O
TU_0252_23738
tet1_O
TU_0000_78220
Tn23_O
TU_026_133
Tn23_O
TU_021_136
Tn23_O
TU_089_140
Tn23_O
TU_045_143
Tn23_O
TU_038_146
Tn23_O
TU_047_153
Tn23_O
TU_059_165
Tn23_O
TU_022_169
Tn23_O
TU_008_184
Tn23_O
TU_006_195
Tn23_O
TU_013_208
Tn23_O
TU_020_220
Tn23_O
TU_205_373
Tn23_O
TU_053_455
Tn23_O
TU_000_50722
tnpA_O
TU_029_99
tnpA_O
TU_005_101
tnpA_O
TU_035_108
tnpA_O
TU_012_117
tnpA_O
TU_040_126
tnpA_O
TU_088_139
tnpA_O
TU_047_165
tnpA_O
TU_013_176
tnpA_O
TU_023_211
tnpA_O
TU_157_302
tnpA_O
TU_004_316
tnpA_O
TU_056_410
tnpA_O
TU_090_570
tnpA_O
TU_003_1136
tnpA_O
TU_000_31244
mefA_OTU
_0041_568
mefA_OTU
_0121_573
mefA_OTU
_2454_666
mefA_OTU
_1233_782
mefA_OTU
_5205_816
mefA_OTU
_0126_931
mefA_OTU
_2529_952
mefA_OTU
_1379_966
mefA_OTU
_3811_3455
mefA_OTU
_0282_3812
mefA_OTU
_1414_7479
mefA_OTU
_0034_10700
mefA_OTU
_0071_15229
mefA_OTU
_0951_19579
mefA_OTU
_0000_137471
is1216_OTU
_032_167
is1216_OTU
_027_177
is1216_OTU
_009_181
is1216_OTU
_006_182
is1216_OTU
_013_184
is1216_OTU
_012_192
is1216_OTU
_017_194
is1216_OTU
_090_202
is1216_OTU
_043_223
is1216_OTU
_025_242
is1216_OTU
_002_258
is1216_OTU
_019_259
is1216_OTU
_007_306
is1216_OTU
_171_322
is1216_OTU
_001_68327
AG7_OTU
_0000_106398
AG6_OTU
_0016_590
AG6_OTU
_0013_595
AG6_OTU
_0042_602
AG6_OTU
_0080_629
AG6_OTU
_0025_650
AG6_OTU
_0152_659
AG6_OTU
_0026_677
AG6_OTU
_0004_681
AG6_OTU
_0001_699
AG6_OTU
_0003_718
AG6_OTU
_0005_777
AG6_OTU
_0012_864
AG6_OTU
_0019_998
AG6_OTU
_0031_1073
AG6_OTU
_0000_236839
tet2_O
TU_0024_298
tet2_O
TU_0057_300
tet2_O
TU_0077_315
tet2_O
TU_0062_318
tet2_O
TU_0003_330
tet2_O
TU_0070_337
tet2_O
TU_0002_338
tet2_O
TU_0030_352
tet2_O
TU_0019_383
tet2_O
TU_0007_387
tet2_O
TU_0014_853
tet2_O
TU_0004_4858
tet2_O
TU_0005_8612
tet2_O
TU_0001_20063
tet2_O
TU_0000_100930
tet5_O
TU_0050_373
tet5_O
TU_0009_450
tet5_O
TU_0024_462
tet5_O
TU_0001_467
tet5_O
TU_0091_497
tet5_O
TU_0144_514
tet5_O
TU_0002_571
tet5_O
TU_0004_627
tet5_O
TU_0010_761
tet5_O
TU_0075_949
tet5_O
TU_0019_1669
tet5_O
TU_0003_1970
tet5_O
TU_0015_2209
tet5_O
TU_0005_9848
tet5_O
TU_0000_114770
tet4_O
TU_032_328
tet4_O
TU_053_330
tet4_O
TU_028_333
tet4_O
TU_023_337
tet4_O
TU_026_346
tet4_O
TU_010_348
tet4_O
TU_047_362
tet4_O
TU_012_363
tet4_O
TU_034_386
tet4_O
TU_039_388
tet4_O
TU_007_422
tet4_O
TU_008_620
tet4_O
TU_009_4144
tet4_O
TU_002_14530
tet4_O
TU_000_124412
tet3_O
TU_0087_895
tet3_O
TU_0009_969
tet3_O
TU_0015_1162
tet3_O
TU_0052_1409
tet3_O
TU_0003_1462
tet3_O
TU_0050_1469
tet3_O
TU_0011_1778
tet3_O
TU_0031_1861
tet3_O
TU_0006_1908
tet3_O
TU_0056_2050
tet3_O
TU_0016_2145
tet3_O
TU_0005_8110
tet3_O
TU_0004_16405
tet3_O
TU_0002_38959
tet3_O
TU_0001_47127
tp614_OTU
_0071_296
tp614_OTU
_0029_300
tp614_OTU
_0003_303
tp614_OTU
_0039_305
tp614_OTU
_0053_318
tp614_OTU
_0010_323
tp614_OTU
_0020_327
tp614_OTU
_0016_343
tp614_OTU
_0109_350
tp614_OTU
_0235_351
tp614_OTU
_0077_415
tp614_OTU
_0005_593
tp614_OTU
_0346_1757
tp614_OTU
_0006_12571
tp614_OTU
_0000_120359
IS613_OTU
_1637_368
IS613_OTU
_0339_380
IS613_OTU
_1603_611
IS613_OTU
_0021_632
IS613_OTU
_0012_1839
IS613_OTU
_0015_2788
IS613_OTU
_0018_3195
IS613_OTU
_0006_3739
IS613_OTU
_0036_4977
IS613_OTU
_0007_5099
IS613_OTU
_0054_8962
IS613_OTU
_0001_9580
IS613_OTU
_0366_13919
IS613_OTU
_0000_29617
IS613_OTU
_0009_29731
CHL1_O
TU_025_151
CHL1_O
TU_043_161
CHL1_O
TU_031_166
CHL1_O
TU_022_177
CHL1_O
TU_051_181
CHL1_O
TU_020_184
CHL1_O
TU_034_187
CHL1_O
TU_023_190
CHL1_O
TU_017_198
CHL1_O
TU_030_207
CHL1_O
TU_021_214
CHL1_O
TU_042_223
CHL1_O
TU_009_232
CHL1_O
TU_026_234
CHL1_O
TU_000_70169
AG9_OTU
_043_215
AG9_OTU
_021_216
AG9_OTU
_029_230
AG9_OTU
_055_244
AG9_OTU
_047_251
AG9_OTU
_027_254
AG9_OTU
_023_256
AG9_OTU
_022_261
AG9_OTU
_037_262
AG9_OTU
_034_269
AG9_OTU
_007_279
AG9_OTU
_004_289
AG9_OTU
_010_332
AG9_OTU
_001_371
AG9_OTU
_000_101290
AG8_OTU
_0051_189
AG8_OTU
_0081_195
AG8_OTU
_0002_196
AG8_OTU
_0012_200
AG8_OTU
_0231_211
AG8_OTU
_0004_219
AG8_OTU
_0022_223
AG8_OTU
_0098_233
AG8_OTU
_0044_250
AG8_OTU
_0435_264
AG8_OTU
_0441_274
AG8_OTU
_0011_551
AG8_OTU
_0105_4053
AG8_OTU
_0039_32404
AG8_OTU
_0000_53087
IS4_OTU
_0029_256
IS4_OTU
_0004_258
IS4_OTU
_0025_261
IS4_OTU
_0045_265
IS4_OTU
_0003_271
IS4_OTU
_0002_273
IS4_OTU
_0033_283
IS4_OTU
_0037_289
IS4_OTU
_0007_296
IS4_OTU
_0088_306
IS4_OTU
_0013_320
IS4_OTU
_0817_330
IS4_OTU
_0042_344
IS4_OTU
_0001_407
IS4_OTU
_0000_97897
AG5_OTU
_017_126
AG5_OTU
_015_128
AG5_OTU
_040_137
AG5_OTU
_005_139
AG5_OTU
_003_155
AG5_OTU
_051_168
AG5_OTU
_056_170
AG5_OTU
_010_189
AG5_OTU
_011_190
AG5_OTU
_002_201
AG5_OTU
_009_217
AG5_OTU
_035_230
AG5_OTU
_023_238
AG5_OTU
_001_6133
AG5_OTU
_000_49696
sul2_O
TU_0017_306
sul2_O
TU_0013_326
sul2_O
TU_0006_333
sul2_O
TU_0043_342
sul2_O
TU_0026_343
sul2_O
TU_0010_351
sul2_O
TU_0005_360
sul2_O
TU_0052_367
sul2_O
TU_0024_369
sul2_O
TU_0034_374
sul2_O
TU_0011_419
sul2_O
TU_0020_458
sul2_O
TU_0032_462
sul2_O
TU_0053_2646
sul2_O
TU_0000_133284
qac_OTU
_014_279
qac_OTU
_038_292
qac_OTU
_040_301
qac_OTU
_021_302
qac_OTU
_012_307
qac_OTU
_008_312
qac_OTU
_043_326
qac_OTU
_004_328
qac_OTU
_042_336
qac_OTU
_019_347
qac_OTU
_022_397
qac_OTU
_003_402
qac_OTU
_005_411
qac_OTU
_034_432
qac_OTU
_000_113511
tet10_OTU
_067_160
tet10_OTU
_082_162
tet10_OTU
_103_164
tet10_OTU
_097_166
tet10_OTU
_085_177
tet10_OTU
_073_179
tet10_OTU
_122_181
tet10_OTU
_112_187
tet10_OTU
_100_193
tet10_OTU
_087_244
tet10_OTU
_111_250
tet10_OTU
_127_296
tet10_OTU
_096_402
tet10_OTU
_001_10703
tet10_OTU
_000_62329
AG4_OTU
_0018_206
AG4_OTU
_0472_207
AG4_OTU
_0399_208
AG4_OTU
_0001_211
AG4_OTU
_0035_219
AG4_OTU
_0014_243
AG4_OTU
_0421_253
AG4_OTU
_0469_275
AG4_OTU
_0084_518
AG4_OTU
_0706_580
AG4_OTU
_0098_745
AG4_OTU
_0197_869
AG4_OTU
_0063_1406
AG4_OTU
_0000_55356
AG4_OTU
_0002_68636
AG3_OTU
_0065_339
AG3_OTU
_0033_345
AG3_OTU
_0035_352
AG3_OTU
_0070_364
AG3_OTU
_0063_372
AG3_OTU
_0026_394
AG3_OTU
_0069_399
AG3_OTU
_0020_402
AG3_OTU
_0045_413
AG3_OTU
_0002_432
AG3_OTU
_0006_449
AG3_OTU
_0027_451
AG3_OTU
_0012_509
AG3_OTU
_0019_512
AG3_OTU
_0000_139305
AG2_OTU
_0006_338
AG2_OTU
_0043_340
AG2_OTU
_0010_373
AG2_OTU
_0050_374
AG2_OTU
_0002_391
AG2_OTU
_0004_395
AG2_OTU
_0036_411
AG2_OTU
_0030_436
AG2_OTU
_0039_472
AG2_OTU
_0051_498
AG2_OTU
_0044_554
AG2_OTU
_0075_656
AG2_OTU
_0090_1243
AG2_OTU
_0024_4531
AG2_OTU
_0000_143382
AG1_OTU
_008_140
AG1_OTU
_058_149
AG1_OTU
_005_153
AG1_OTU
_060_156
AG1_OTU
_003_157
AG1_OTU
_054_162
AG1_OTU
_049_166
AG1_OTU
_020_173
AG1_OTU
_013_179
AG1_OTU
_076_190
AG1_OTU
_077_192
AG1_OTU
_001_226
AG1_OTU
_017_232
AG1_OTU
_002_4023
AG1_OTU
_000_59698
qINT.3_O
TU_003_266
qINT.3_O
TU_005_269
qINT.3_O
TU_053_276
qINT.3_O
TU_033_288
qINT.3_O
TU_002_292
qINT.3_O
TU_019_301
qINT.3_O
TU_022_306
qINT.3_O
TU_036_308
qINT.3_O
TU_011_313
qINT.3_O
TU_042_318
qINT.3_O
TU_021_328
qINT.3_O
TU_007_330
qINT.3_O
TU_004_365
qINT.3_O
TU_012_411
qINT.3_O
TU_000_112559
IS6100_O
TU_043_195
IS6100_O
TU_009_210
IS6100_O
TU_067_213
IS6100_O
TU_008_229
IS6100_O
TU_027_233
IS6100_O
TU_064_237
IS6100_O
TU_055_240
IS6100_O
TU_003_241
IS6100_O
TU_060_250
IS6100_O
TU_014_257
IS6100_O
TU_029_268
IS6100_O
TU_006_278
IS6100_O
TU_018_340
IS6100_O
TU_036_414
IS6100_O
TU_001_99440
IncW
_OTU
_0122_114
IncW
_OTU
_0069_116
IncW
_OTU
_0061_117
IncW
_OTU
_0152_118
IncW
_OTU
_0066_123
IncW
_OTU
_0151_128
IncW
_OTU
_0131_137
IncW
_OTU
_0114_141
IncW
_OTU
_0225_163
IncW
_OTU
_0034_171
IncW
_OTU
_0040_381
IncW
_OTU
_0162_421
IncW
_OTU
_0008_811
IncW
_OTU
_0003_1350
IncW
_OTU
_0001_36993
−10
−8−6
−4−2
0Value
Col
or K
ey
is6100 intI1 aadA5 aadA aadA. aadA2 tetR qacE∆1 sul2 aadA9 is4 strA strB cmlA1
allRefSeq A1 A2 A3
BM1
BM2
BM3
BC1
BC2
BC3
BS1
BS2
BS4
JM1
JM2
JM3
JC1
JC2
JC3
JS1
JS3
JS4
PM1
PM2
PM3
PC1
PC2
PC3
PS1
PS2
PS3
AG2_OTU_0036_411AG3_OTU_0020_402qINT.3_OTU_036_308AG3_OTU_0002_432IS6100_OTU_064_237qINT.3_OTU_005_269qINT.3_OTU_033_288AG3_OTU_0070_364IS6100_OTU_060_250IS4_OTU_0045_265qINT.3_OTU_022_306qINT.3_OTU_019_301qINT.3_OTU_053_276IS26_OTU_031_408IS6100_OTU_014_257tet9_OTU_054_203IS26_OTU_029_415sul2_OTU_0005_360dfrA1_OTU_009_206IS26_OTU_011_381dfrA1_OTU_014_165IS26_OTU_005_372qac_OTU_021_302AG2_OTU_0010_373IS26_OTU_021_373AG3_OTU_0035_352qac_OTU_040_301qINT.3_OTU_011_313tet9_OTU_040_228qac_OTU_043_326AG3_OTU_0045_413IS6100_OTU_008_229IS6100_OTU_027_233tet9_OTU_023_253AG3_OTU_0026_394AG2_OTU_0002_391IS6100_OTU_006_278qINT.3_OTU_003_266qac_OTU_022_397IS6100_OTU_055_240AG3_OTU_0069_399tet9_OTU_079_254AG3_OTU_0006_449IS26_OTU_032_387IS26_OTU_009_390tet5_OTU_0050_373AG4_OTU_0472_207AG9_OTU_055_244AG9_OTU_023_256tet9_OTU_045_202is1216_OTU_012_192tet9_OTU_032_303AG3_OTU_0033_345qINT.3_OTU_002_292IS6100_OTU_003_241IS6100_OTU_043_195tet9_OTU_010_247qINT.3_OTU_042_318AG4_OTU_0469_275qINT.3_OTU_004_365qac_OTU_034_432AG3_OTU_0019_512AG9_OTU_010_332AG7_OTU_0024_323qac_OTU_019_347qINT.3_OTU_021_328AG3_OTU_0027_451IS26_OTU_003_491qINT.3_OTU_012_411qac_OTU_005_411dfrA1_OTU_015_288tet9_OTU_067_365sul2_OTU_0026_343sul2_OTU_0024_369sul2_OTU_0010_351sul2_OTU_0006_333IS6100_OTU_009_210AG3_OTU_0063_372dfrA1_OTU_043_189AG9_OTU_027_254IS26_OTU_066_392AG2_OTU_0006_338AG4_OTU_0421_253AG4_OTU_0197_869IS26_OTU_027_473AG6_OTU_0080_629AG6_OTU_0003_718AG6_OTU_0042_602IS26_OTU_035_371AG6_OTU_0025_650AG9_OTU_007_279AG6_OTU_0013_595AG6_OTU_0026_677AG6_OTU_0001_699AG9_OTU_022_261AG6_OTU_0005_777AG6_OTU_0016_590AG9_OTU_021_216IS26_OTU_010_399dfrA1_OTU_069_153tet1_OTU_0205_293tet5_OTU_0009_450AG6_OTU_0012_864AG6_OTU_0019_998AG6_OTU_0031_1073tet5_OTU_0001_467AG6_OTU_0004_681CHL1_OTU_031_166CHL1_OTU_022_177CHL1_OTU_026_234CHL1_OTU_009_232CHL1_OTU_030_207tet1_OTU_0269_386tet1_OTU_0203_402AG9_OTU_001_371is1216_OTU_027_177AG9_OTU_047_251AG9_OTU_004_289IS4_OTU_0004_258IS4_OTU_0013_320IS4_OTU_0003_271tet1_OTU_0271_274tet1_OTU_0265_297tet2_OTU_0030_352tet2_OTU_0019_383tet2_OTU_0077_315tet2_OTU_0014_853tet2_OTU_0062_318tet2_OTU_0024_298tet2_OTU_0057_300AG9_OTU_037_262IS4_OTU_0033_283tet10_OTU_127_296tet1_OTU_0241_387AG6_OTU_0152_659mefA_OTU_1233_782tet1_OTU_0692_314tet1_OTU_0578_3063tet1_OTU_0003_550qINT.3_OTU_007_330IS26_OTU_019_383tet9_OTU_072_291is1216_OTU_043_223IS4_OTU_0002_273tet9_OTU_059_219AG3_OTU_0012_509tet4_OTU_023_337tet4_OTU_012_363tet4_OTU_034_386tet4_OTU_039_388tet4_OTU_009_4144tet4_OTU_028_333tet4_OTU_026_346tet4_OTU_010_348tet4_OTU_007_422CHL1_OTU_020_184tet4_OTU_032_328CHL1_OTU_017_198CHL1_OTU_023_190CHL1_OTU_051_181CHL1_OTU_034_187CHL1_OTU_043_161tet4_OTU_053_330CHL1_OTU_021_214CHL1_OTU_042_223CHL1_OTU_025_151dfra2_OTU_000_113AG1_OTU_058_149AG1_OTU_017_232AG1_OTU_005_153AG5_OTU_017_126AG5_OTU_005_139sul2_OTU_0053_2646dfra2_OTU_030_61dfra2_OTU_015_77tet2_OTU_0002_338tet2_OTU_0007_387tet3_OTU_0002_38959tet8_OTU_0002_3895tet2_OTU_0005_8612tet2_OTU_0001_20063mefA_OTU_0951_19579tet1_OTU_0252_23738AG8_OTU_0000_53087dfra2_OTU_023_107dfra2_OTU_031_124dfra2_OTU_016_85dfra2_OTU_004_88dfra2_OTU_005_127tet10_OTU_001_10703dfra2_OTU_026_70dfra2_OTU_010_159dfra2_OTU_019_86tet1_OTU_0278_5767tet5_OTU_0144_514AG4_OTU_0063_1406AG4_OTU_0018_206Tn23_OTU_022_169is1216_OTU_090_202dfra2_OTU_012_90dfra2_OTU_013_89IncW_OTU_0001_36993AG2_OTU_0075_656IS613_OTU_0009_29731tnpA_OTU_000_31244Tn23_OTU_038_146Tn23_OTU_020_220Tn23_OTU_013_208Tn23_OTU_021_136Tn23_OTU_045_143Tn23_OTU_089_140Tn23_OTU_047_153Tn23_OTU_006_195Tn23_OTU_008_184Tn23_OTU_026_133Tn23_OTU_059_165AG8_OTU_0012_200AG8_OTU_0011_551AG4_OTU_0014_243IncN_OTU_1759_25082AG7_OTU_0043_844tet6_OTU_001_72686AG10_OTU_002_67731IncW_OTU_0066_123IncW_OTU_0131_137IncW_OTU_0152_118IncW_OTU_0061_117IncW_OTU_0122_114IncW_OTU_0114_141IncW_OTU_0151_128IncW_OTU_0162_421IncW_OTU_0008_811IncW_OTU_0069_116IncW_OTU_0225_163tnpA_OTU_056_410dfrA1_OTU_011_1949mefA_OTU_0121_573ILMA_OTU_01472_786IncW_OTU_0040_381IncP_OTU_0032_825AG8_OTU_0105_4053tet10_OTU_112_187tet7_OTU_0012_1203AG1_OTU_013_179tet7_OTU_0007_2652AG1_OTU_002_4023tet7_OTU_0232_101tet8_OTU_0452_746tet7_OTU_0327_140tet7_OTU_0042_154tet7_OTU_0008_926tet8_OTU_0001_1434tet7_OTU_0024_1782IncW_OTU_0034_171IncP_OTU_0002_3852AG4_OTU_0084_518tet7_OTU_0010_3721tet7_OTU_0034_287tet7_OTU_0240_107AG5_OTU_010_189AG5_OTU_011_190AG5_OTU_002_201AG5_OTU_009_217AG5_OTU_023_238AG5_OTU_003_155AG5_OTU_035_230AG5_OTU_051_168AG5_OTU_015_128AG5_OTU_056_170AG1_OTU_003_157AG1_OTU_060_156AG1_OTU_049_166tet10_OTU_073_179AG1_OTU_008_140AG1_OTU_054_162AG1_OTU_020_173AG1_OTU_076_190AG1_OTU_077_192AG1_OTU_001_226dfrA1_OTU_016_171dfrA1_OTU_018_180AG2_OTU_0043_340AG2_OTU_0090_1243tet8_OTU_0176_781tet8_OTU_0191_932tet8_OTU_0341_500tet8_OTU_0210_1235tet8_OTU_0110_8573mefA_OTU_0034_10700mefA_OTU_0282_3812tet8_OTU_0055_1256tet7_OTU_0149_393X16S_OTU_192_215qac_OTU_014_279qac_OTU_004_328is1216_OTU_032_167sul2_OTU_0013_326sul2_OTU_0034_374qac_OTU_012_307qac_OTU_008_312sul2_OTU_0017_306sul2_OTU_0043_342AG2_OTU_0030_436AG2_OTU_0039_472is1216_OTU_009_181IS4_OTU_0007_296qac_OTU_003_402sul2_OTU_0032_462tet9_OTU_021_255qac_OTU_042_336IS6100_OTU_018_340AG2_OTU_0051_498IS6100_OTU_036_414is1216_OTU_007_306IS26_OTU_042_565is1216_OTU_017_194sul2_OTU_0020_458is1216_OTU_025_242AG7_OTU_0037_319AG2_OTU_0050_374sul2_OTU_0011_419AG2_OTU_0044_554qac_OTU_038_292IS6100_OTU_029_268is1216_OTU_006_182is1216_OTU_019_259tet9_OTU_016_239tet9_OTU_013_195AG10_OTU_227_332AG10_OTU_222_300AG10_OTU_220_212tet10_OTU_067_160tet10_OTU_087_244tet10_OTU_111_250tet10_OTU_100_193tet10_OTU_096_402tet10_OTU_085_177tet10_OTU_082_162tet1_OTU_0382_278sul2_OTU_0052_367AG10_OTU_217_201IS6100_OTU_067_213AG10_OTU_280_252AG9_OTU_034_269IS4_OTU_0042_344AG7_OTU_0006_352IS4_OTU_0088_306AG7_OTU_0030_325AG7_OTU_0051_294is1216_OTU_002_258is1216_OTU_013_184AG3_OTU_0065_339AG7_OTU_0038_472AG7_OTU_0001_317X16S_OTU_014_565AG9_OTU_043_215dfrA1_OTU_010_192dfrA1_OTU_061_151IS4_OTU_0001_407dfrA1_OTU_038_186X16S_OTU_019_1300AG9_OTU_029_230IS4_OTU_0029_256AG7_OTU_0005_367AG7_OTU_0019_300IS4_OTU_0037_289AG7_OTU_0053_407IS4_OTU_0025_261AG4_OTU_0001_211tet4_OTU_047_362X16S_OTU_033_144tet10_OTU_097_166tet10_OTU_122_181tet10_OTU_103_164AG5_OTU_040_137AG4_OTU_0035_219X16S_OTU_050_258AG4_OTU_0098_745mefA_OTU_0071_15229AG8_OTU_0039_32404mefA_OTU_0000_137471dfra2_OTU_001_37786Tn23_OTU_000_50722IncN_OTU_0001_73797Tn21_OTU_000_23582tet4_OTU_002_14530tet3_OTU_0001_47127AG7_OTU_0103_308X16S_OTU_007_253AG7_OTU_0046_315X16S_OTU_010_417X16S_OTU_001_4276X16S_OTU_037_2335X16S_OTU_000_64949AG9_OTU_000_101290tet4_OTU_000_124412sul2_OTU_0000_133284AG10_OTU_091_54305AG6_OTU_0000_236839AG3_OTU_0000_139305IS6100_OTU_001_99440IS26_OTU_000_142450tet9_OTU_000_91714IS4_OTU_0000_97897tet5_OTU_0000_114770dfrA1_OTU_000_61459AG2_OTU_0000_143382AG5_OTU_000_49696tet8_OTU_0000_31950AG2_OTU_0024_4531AG2_OTU_0004_395CHL1_OTU_000_70169qac_OTU_000_113511AG4_OTU_0002_68636AG7_OTU_0000_106398is1216_OTU_001_68327tet7_OTU_0004_7401AG4_OTU_0000_55356tet1_OTU_0001_22800AG1_OTU_000_59698qINT.3_OTU_000_112559tet1_OTU_0000_78220dfrA1_OTU_005_157dfrA1_OTU_004_182AG4_OTU_0399_208dfrA1_OTU_003_4460tet10_OTU_000_62329tp614_OTU_0000_120359tet2_OTU_0000_100930tet8_OTU_0034_18627tet7_OTU_0002_16351IS613_OTU_0366_13919GapA.F_OTU_0000_145966tet3_OTU_0005_8110X16S_OTU_038_745X16S_OTU_042_845GapA.F_OTU_0007_582GapA.F_OTU_0069_513GapA.F_OTU_0018_432GapA.F_OTU_0089_438GapA.F_OTU_0031_444GapA.F_OTU_0027_462GapA.F_OTU_0048_476GapA.F_OTU_0054_470GapA.F_OTU_0056_609GapA.F_OTU_0172_551GapA.F_OTU_0009_450GapA.F_OTU_0113_437IncN_OTU_0007_313IncN_OTU_0023_228IncN_OTU_0123_260IncN_OTU_0060_245tp614_OTU_0053_318IncN_OTU_0049_294IncN_OTU_0108_256IncN_OTU_0236_1238tp614_OTU_0016_343tp614_OTU_0010_323tp614_OTU_0020_327tp614_OTU_0039_305tp614_OTU_0071_296tp614_OTU_0003_303tp614_OTU_0109_350tp614_OTU_0005_593tp614_OTU_0029_300tp614_OTU_0077_415tp614_OTU_0006_12571AG8_OTU_0231_211AG8_OTU_0441_274AG8_OTU_0435_264Tn21_OTU_031_108Tn21_OTU_014_46Tn21_OTU_008_66Tn21_OTU_013_86Tn21_OTU_012_58Tn21_OTU_011_52Tn21_OTU_019_54Tn21_OTU_057_59Tn21_OTU_030_77tet5_OTU_0002_571Tn21_OTU_023_68Tn21_OTU_069_60Tn21_OTU_003_65tet2_OTU_0070_337Tn21_OTU_009_115tet6_OTU_050_224tet6_OTU_003_396tet6_OTU_065_198tet6_OTU_023_222tet6_OTU_040_281tet6_OTU_006_216tet6_OTU_045_183tet6_OTU_015_188tet6_OTU_005_199tet6_OTU_021_296tet6_OTU_056_190tet6_OTU_008_4647tnpA_OTU_029_99tnpA_OTU_035_108tnpA_OTU_047_165tnpA_OTU_088_139tnpA_OTU_040_126tnpA_OTU_012_117tnpA_OTU_013_176mefA_OTU_2454_666mefA_OTU_1414_7479tnpA_OTU_023_211IncN_OTU_0100_255IncN_OTU_0036_242IncN_OTU_0253_1327IncN_OTU_0090_233IncN_OTU_0017_262tet6_OTU_025_253AG8_OTU_0004_219AG8_OTU_0044_250Tn23_OTU_053_455AG8_OTU_0098_233tet3_OTU_0056_2050mefA_OTU_0126_931tp614_OTU_0346_1757IS613_OTU_0015_2788AG8_OTU_0022_223AG8_OTU_0002_196AG8_OTU_0051_189IncN_OTU_0002_328GapA.F_OTU_0111_883AG8_OTU_0081_195tnpA_OTU_003_1136Tn23_OTU_205_373tnpA_OTU_157_302tnpA_OTU_090_570IncP_OTU_0000_2904ILMA_OTU_06873_323IS613_OTU_0036_4977tet3_OTU_0006_1908tet3_OTU_0015_1162tet3_OTU_0003_1462tet5_OTU_0003_1970tet5_OTU_0075_949tet5_OTU_0010_761Tn21_OTU_010_69tet3_OTU_0011_1778IS613_OTU_1637_368IS613_OTU_0339_380dfra2_OTU_021_74tet1_OTU_0009_290ILMA_OTU_02617_777tet3_OTU_0031_1861tet3_OTU_0050_1469tet3_OTU_0016_2145tet4_OTU_008_620tet3_OTU_0009_969tet5_OTU_0005_9848tet3_OTU_0052_1409tet2_OTU_0004_4858is1216_OTU_171_322mefA_OTU_0041_568tet3_OTU_0004_16405AG5_OTU_001_6133ILMA_OTU_00000_308ILMA_OTU_00633_240ILMA_OTU_00183_518tnpA_OTU_005_101IncP_OTU_1088_660IncP_OTU_0001_548IncP_OTU_1384_600GapA.F_OTU_5528_2015IncP_OTU_0004_528IncP_OTU_0807_352ILMA_OTU_00742_321ILMA_OTU_00001_1402ILMA_OTU_30002_303AG7_OTU_0296_913IncP_OTU_0826_1059IS613_OTU_0021_632tp614_OTU_0235_351ILMA_OTU_00935_800IncP_OTU_0542_377AG4_OTU_0706_580mefA_OTU_2529_952IncW_OTU_0003_1350tnpA_OTU_004_316ILMA_OTU_17773_295ILMA_OTU_17867_250IncP_OTU_0043_522X16S_OTU_226_362mefA_OTU_3811_3455mefA_OTU_5205_816IncP_OTU_0895_748IncP_OTU_0164_351IncP_OTU_0747_1240IncP_OTU_0003_1046tet8_OTU_0968_419tet7_OTU_0101_251IS4_OTU_0817_330tet6_OTU_093_3645AG10_OTU_051_220AG10_OTU_005_232AG10_OTU_046_247AG10_OTU_027_206AG10_OTU_008_221tet5_OTU_0004_627mefA_OTU_1379_966tet5_OTU_0019_1669AG10_OTU_060_222AG10_OTU_013_250AG10_OTU_053_208tet5_OTU_0091_497tet5_OTU_0024_462tet3_OTU_0087_895tet5_OTU_0015_2209IS613_OTU_0001_9580X16S_OTU_006_462IS613_OTU_0012_1839IS613_OTU_0007_5099IS613_OTU_0018_3195IS613_OTU_0006_3739IS613_OTU_0000_29617tet8_OTU_3831_1620ILMA_OTU_00686_597IS613_OTU_0054_8962ILMA_OTU_00012_742tet8_OTU_1476_1884X16S_OTU_002_717ILMA_OTU_00959_686tet8_OTU_0169_495tet7_OTU_0005_3821tet9_OTU_049_268tet2_OTU_0003_330IS613_OTU_1603_611
−10 −8 −6 −4 −2 0Value
Color Key
ARG allele percentage 0.1 0.4 1.5 6 25 100
PS PC PM JS JC JM BS BC BM Cntl Soil
Ref
• 90% of the 125,000 intl! sequences were iden:cal in both USA and China pig samples. •The next highest variant was only 0.3%
1 15
Are an#bio#c resistances in non-‐an#bio#c exposed animals?
• A baby mammoth Lluba discovered in a frozen bog is one of the best preserved mammoths ever found. • Lived 41,800 years ago • We sampled along the gut for resistance genes.
• Feral pigs from South Carolina barrier islands.
Two cases:
Waking Lyuba, the Baby Mammoth, aBer 41,800 years
She was found by a reindeer breeder and herder in 2007 on the Yamal Peninsula of Arc#c Russia
Dan Fisher, U of Michigan
Lyuba in the Laboratory
Lyuba was only 30 days old, about 110 lbs when she died of suffoca#on in mud. She had milk and fecal mager, presumably from her mother, in her stomach
Dissec#ng Lyuba’s gut
Does she have an#bio#c resistance genes?
S1
S2
S2_PS3
S4
S5
L6
Streptomyces_antibiotics_ATP-binding-protein_oleC_1000
Multi_genera_acrAB_triclosan-resis_1of2_1000
Plasmid_pIM13_ermIM_methylase_1000
Escherichia_coli_uidA_F1, R2
Streptomyces_venezuelae_erm30_pikR2_methylt_1001
mdth_10of72
emrD_18of64
Streptococcus_agalactiae_LnuC_1001
Multi_genera_tetracycline-resistance_tet4_3of25_1003
tolC_8of66
Multi_genera_Beta-lactamase-C-penicillin_beta-blaCMY_32of82_F1002
Neisseria_meningitidis_Z2491_MC58_FAM18_mtrD_drug-efflux4of4_1001
Multi_genera_blaCTX_5of43_1000
Multi_genera_chloramphenicol-resistance_chlo-rarD_9of12_1001
Staph_aureus_qacB_2_1000
Salmonella_sp_acridine_efflux-pump_1of3_1001
Multi_genera_vgaB_1000
Vibrio_sp._no6_tet(34)_tet-resis-determinant_1000
Multi_genera_Tetracycline-resistance_tet_4of74(2)_1004
bl2_len_146of172
Mulgi_genera_tetD_2_1000
oprJ_2of6
Camplyobacter_spp_streptothricine-acetyl-transferase_acety-sat_3_1002
Multi_genera_tetG_4of4_1000
tolC_7of66
Multi_genera_SHV-beta-lactamase_bet-blaSHV_4of94_1002
Plasmid_pNG2_ermCD_erythromycin-resistance_1001
Multi_genera_erythromycin-res_mphA_1of2_1000
vanYD_2of6
bl2be_oxy1_32of59
aac3iv_4of6
Multi_genera_transposase_beta-tnpA_2of23_1001
Multi_genera_transposase_bet-tnpA_20of30_1001
Multi_genera_streptomycin-resistance_strB_9_F1002
Pseudomonas_entomophila_L48_TtgA_efflux_3of3_1002
oprD_5of7
Salmonella_sp_acridine_efflux-pump_2of3_1000
Mycobacterium_tuberculosis_pyrazinamidase_pyaz-pncA_26_1000
Multi_genera_Beta-lactamase- C-penicillin_beta-blaCMY_5of82_1001
pbp2b(penA)_98of99
Pseudomonas_spp_mexF_1of2_1001
Multi_genera_AAC-3-VI_gent-aac4_2_1001
Multi_genera_Beta-lactamase-C-penicillin_beta-blaCMY_6of82(2)_1000
Enterococcus_spp_vanC_1000
vanC, fox5, aacC, mexF, penA, blaCMY2, pncA, acrA, oprD
^gA, strB, Tn24, Tn22, aacC4, blaOXY
vanYD, mphA, ermX, blaTEM, tolC, tetG, sat4, oprJ
tetD, blaSHV, tetD, tet(34), vgaB
acrA, qacA, rarD, blaCTX-‐M
mtrD
blaCMY2, tolC, tetR, lnuC, emrD
yceL/mdtH, pikR2, uidA, plasmid?, acrR, oleC
Genes GENERAL TREND
BETA LACTAMASE RND EFFLUX
TRANSPOSASE BL, RND, AG
RND EFFLUX MLSB
TET EFFLUX
EFFLUX
RND EFFLUX
EFFLUX, BL, TET, MLSB
EFFLUX, MLSB
S = small intes#ne L = large intes#ne
RND = mul#drug efflux pumps; BL = beta lactam; AG = aminoglycoside, MLSB = macrolide, licosamide, and streptogramin B; TET = tetracycline resistances. The presence of these genes needs to be confirmed via sequencing, especially vanC.
Are an#bio#c resistances in non-‐an#bio#c exposed animals?
• In baby mammoth Lluba who lived 41,800 years ago • Feral pigs from South Carolina barrier islands.
Intl1 not detected in either sample! But in all samples from Iowa and Chinese pigs, and with no SNPs
Two cases:
Super car is already in acfon globally
What are the Environmental Issues ?
• Are the an#bio#c resistances genes linked to mobile gene#c elements?
• Are mul#ple resistance traits also linked?
• Important to co-‐selec#on • Important to risk for spread of mul#-‐drug resistances
(are we building the super drug resistance microbes)
• This is a global issue (obvious) • Spread of Chinese-‐style facili#es • An#bio#c produc#on facili#es • Un-‐ or poorly-‐ regulated use, disposal, and human food chain
What are the MSU Resources for ARG Studies?
• 300 Plus an#bio#c resistance primers pairs, validated • Expanding mobile gene#c element (MGE) primer pairs • Virulence and marker gene#cs for targeted pathogens • Wafergen, highly parallel qPCR,system, 5186 assays/chip
For quan#ta#on of ARGs: (Hashsham, Stedfeldt, Tiedje)
Database of ARG genes: ( Cole, Tiedje) • Monthly HMM search of GenBank (by RDP) • Joint project with U of Hong Kong on structured ARG DB State-‐of-‐art analy#cal methods, LC-‐MS-‐MS for quan#ta#on
of pharmaceu#cals. (Liu)
Developing sequenced-‐based tracking of ARGs: (Stedfeldt, RTSF)
Related Documents
