Bacteria Subsisting on Antibiotics Gautam Dantas Church Lab CEGS Annual Grantee Meeting - 2008

Bacteria Subsisting on Antibiotics

Gautam Dantas Church Lab

CEGS Annual Grantee Meeting - 2008

Agency for healthcare research and quality, 2006

US reported MRSA infections [1000’s]

in US: MRSA kills more people than AIDS

2006: 18,964

2006: 14,627

Mechanisms of antibiotic resistance

antibiotic modification efflux target modification

resistance gene origin hypothesis: antibiotic resistance genes originated as

producer self immunity and was transferred to human pathogens

Proc. Nat. Acad. Sci. 70:2276 (1973)

Science 312:374 (2006)

many antibiotics are produced in the environment, but it is likely that they

undergo further biological transformations

G. Dantas., M. Sommer et al. Science 320:100 (2008)

GROWTH NO GROWTH

Bacteria subsisting on antibiotics are widely distributed in the environment

Antibiotic eaters are phylogenetically diverse


microbes subsisting on antibiotics are phylogenetically

diverse

they comprise of 3 out the 4 major phyla of human microbiomes

27% of the phylogenetic nearest named isolates are

pathogens

compared to antibiotic producer organisms

they constitute a more accessible reservoir of

resistance

Bacteria subsisting on antibiotics are extremely resistant



using functional genomic selections we have identified more than 150 unique antibiotic resistance genes

from antibiotic eaters

Gentamicin resistance from eater vs. Salmonella enterica subsp. enterica serovar Typhimurium genomic island I

Experiments by: G. Dantas, M. Sommer. Unpublished data

resistance genes from some antibiotic catabolizers are identical to resistance

genes of pathogens at the nucleotide level

best genetic support for producer hypothesis:

>gi|27461214|gb|AY082011.1| Enterococcus faecium strain 10/96A vanD gene cluster, complete sequence; and ISEfa4 insertion sequence element

>gi|4104707:67-693 Streptomyces toyocaensis D-ala-D-ala dipeptidase (vanXst) gene, complete cds; and unknown gene

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY 42: 2215 (1998), Science 312:374 (2006),

Nature Reviews Microbiology 5:175 (2007)

Producer vs. Pathogen

best homology between resistance gene from producer and pathogen: 66% identity @ nucleotide level

homology between resistance gene from eater and

pathogen: 98.5%, 99.9%, 99.9%, 100% identity @ nucleotide level

some antibiotic resistance genes acquired by pathogens by HGT may have originated from

antibiotic eaters

Acknowledgements

Morten SommerGeorge Church John AachDuhee BangJay Lee Church Lab

Rantimi Oluwasegun (Cornell)

Jay Shendure (U.W.)Lynn Bry (BWH Pathology) Roberto Kolter (HMS)Peter Girguis, Hellen White

(Harvard)Will Haas (HMS)Wayne Curtis (Penn State)David Ellison

publications about antibiotic resistance

Experimental Design resuspend in minimal media

4x filter 500uL Innoculum

11 soils X 18 antibiotics

toothpick passage 1

toothpick passage 2

plate on solid (100,1,0.01uL, no

carbon)

liquid passage of

clones restreak

Experiments by: G. Dantas, M. Sommer, R. Oluwasegun.

11 soils: pristine, farm, urban

18 antibiotics: chemical class:

beta-lactams quinolones

sulfonamides amphenicols

aminoglycosides glycopeptides

amino-acid derivorigin:

natural productssemi-synthetic

synthetic compounds

Penicillin Catabolism in Action



Penicillin Catabolism in Action

some antibiotic resistance genes acquired by pathogens by HGT may have

originated from antibiotic eaters

>gi|94960156|gb|DQ519091.1| Acinetobacter baumannii strain DB60079/01 class I integron


>dbj|AB207867.1| Escherichia coli transposon Tn2610, complete sequence

gi|83627312|dbj|AB207867.1|_Es TCCGGTGCGGGGACGGCTGCTCAGTGTTGCGCCTGTGTTCGCACGTTCGTGE_AB95Da04_01_mgRes1_R.trim.f ---------------------------------TCTGTTCGCACGTTCGT * ***************gi|83627312|dbj|AB207867.1|_Es ATCGGTGCGTTCTGATCTTCGCGTCAGACATTGCCGCGGCGCGGGCACAAGE_AB95Da04_01_mgRes1_R.trim.f ATCGGTGCGTTCTGATCTTCGCGTCAGACATTGCCGCGGCGCGGGCACAA **************************************************gi|83627312|dbj|AB207867.1|_Es CAAAAAGCCCGGCATCGCTGCCGGGCTCCGGCCCCGTCCTTGGGGCCTTGGE_AB95Da04_01_mgRes1_R.trim.f CAAAAAGCCCGGCATCGCTGCCGGGCTCCGGCCCCGTCCTTGGGGCCTTG **************************************************gi|83627312|dbj|AB207867.1|_Es ATGTCGGGTCGTTGCCGGGATCGGACCGCGCTGGCGCGGTCCGGTTCCCTGE_AB95Da04_01_mgRes1_R.trim.f ATGTCGGGTCGTTGCCGGGATCGGACCGCGCTGGCGCGGTCCGGTTCCCT **************************************************gi|83627312|dbj|AB207867.1|_Es GACGACCGGGCCAACCGGATCAGAAATCCATGCCGCCCATGCCGCCCATAGE_AB95Da04_01_mgRes1_R.trim.f GACGACCGGGCCAACCGGATCAGAAATCCATGCCGCCCATGCCGCCCATA **************************************************gi|83627312|dbj|AB207867.1|_Es CCGCCAGCACCCGGCATGGCCGGCTCTTCCTTCTTCGGCACTTCGGCCACGE_AB95Da04_01_mgRes1_R.trim.f CCGCCAGCACCCGGCATGGCCGGCTCTTCCTTCTTCGGCACTTCGGCCAC **************************************************gi|83627312|dbj|AB207867.1|_Es GACCACTTCGGTCGTGATCGCAAGGCCGGCGACGGAAGCGGCGTGCTGCAGE_AB95Da04_01_mgRes1_R.trim.f GACCACTTCGGTCGTGATCGCAAGGCCGGCGACGGAAGCGGCGTGCTGCA **************************************************gi|83627312|dbj|AB207867.1|_Es GGGCCGAGCGGGTCACCTTGGTCGGGTCCAGGATGCCCATGGCGATCATGGE_AB95Da04_01_mgRes1_R.trim.f GGGCCGAGCGGGTCACCTTGGTCGGGTCCAGGATGCCCATGGCGATCATG **************************************************gi|83627312|dbj|AB207867.1|_Es TCGCCGAACTCGCCGGTGGCGGCGTTGTAGCCGTAGCTGCCTTCGCCGGCGE_AB95Da04_01_mgRes1_R.trim.f TCGCCGAACTCGCCGGTGGCGGCGTTGTAGCCGTAGCTGCCTTCGCCGGC **************************************************gi|83627312|dbj|AB207867.1|_Es CTTGACGTTGGCCACGATCACGCTCGGTTCTTCACCGGCGTTGGCCACGAGE_AB95Da04_01_mgRes1_R.trim.f CTTGACGTTGGCCACGATCACGCTCGGTTCTTCACCGGCGTTGGCCACGA **************************************************gi|83627312|dbj|AB207867.1|_Es TGGCGCGCAGCGGGGCTTCCAGCGCACGGCGGGTGATGGCGATGCCCAGGGE_AB95Da04_01_mgRes1_R.trim.f TGGCGCGCAGCGGGGCTTCCAGCGCACGGCGGGTGATGGCGATGCCCAGG **************************************************gi|83627312|dbj|AB207867.1|_Es TTCTGGTCTTCGTTGATGCCCTGCCAGGGCAGATCCGTGCACAGCACCTTGE_AB95Da04_01_mgRes1_R.trim.f TTCTGGTCTTCGTTGATGCCCTGCCAGGGCAGATCCGTGCACAGCACCTT **************************************************gi|83627312|dbj|AB207867.1|_Es GCCGTAGAAGAACAGCAAGGCCGCCAATGCCTGACGATGCGTGGAGACCGGE_AB95Da04_01_mgRes1_R.trim.f GCCGTAGAAGAACAGCAAGGCCGCCAATGCCTGACGATGCGTGGAGACCG **************************************************gi|83627312|dbj|AB207867.1|_Es AAACCTTGCGCTCGTTCGCCAGCCAGGACAGAAATGCCTCGACTTCGCTGGE_AB95Da04_01_mgRes1_R.trim.f AAACCTTGCGCTCGTTCGCCAGCCAGGACAGAAATGCCTCGACTTCGCTG **************************************************gi|83627312|dbj|AB207867.1|_Es CTGCCCAAGGTTGCCGGGTGACGCACACCGTGGAAACGGATGAAGGCACGGE_AB95Da04_01_mgRes1_R.trim.f CTGCCCAAGGTTGCCGGGTGACGCACACCGTGGAAACGGATGAAGGCACG **************************************************gi|83627312|dbj|AB207867.1|_Es AACCCAGTGGACATAAGCCTGTTCGGTTGGTAAGCTGTAATGCAAGTAGCGE_AB95Da04_01_mgRes1_R.trim.f AACCCAGTGGACATAAGCCT------------------------------ ********************




>gi|4583495|gb|AF133140.1| Pseudomonas sp. plasmid pPSTG2


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Bacteria Subsisting on Antibiotics Gautam Dantas Church Lab CEGS Annual Grantee Meeting - 2008