Abstract

Forsomethingascomplexandmultifacetedasbacterialantibioticresistance(AR),ourdrugevaluation paradigmisstrikinglynarrowandhomogenous:MIC/MBCtestinginstandardizedbacteriologicmedia.We haveshownthatthisdrugevaluationparadigmisinadequate,evenmisleading,aschangesinthemedia conditionsoftheprocedureleadtodramaticallydifferentresults.Amoreholisticdefinitionofantibiotictherapy thatcentersonunderstandingantibioticactivityinsynergywithhostinnateimmunefactorssuchascationic antimicrobialpeptides(AMPs),serumandphagocyticcells(e.g.neutrophils)revealstherapeuticoptions unrecognizedinstandardtesting.TheproposedU01programrepresentsagroundbreakingapproachtouse systemsbiologyapproachesandinformmoreeffectiveantibioticutilizationinthecontextofhostinnate immunity.Weproposeto:1)buildaniterativesystemsbiologyworkflowthatintegratesmultipleexperimental andcomputationalapproachestogiveacomprehensiveassessmentofAR?and2)applythisworkflowtohigh prioritypathogenstosystematicallyelucidateARmechanismsandtheirconditiondependency.Theiterative workflowincludes:(i)omicsandphysiologicaldatageneration.Clinicallyisolatedstrainsoftheselected pathogenswillbegrownunderconventionaltesting(bacteriologicmedia)andmorephysiologicconditions (tissueculturemedia,serum,andinpresenceofAMPsandneutrophils)toprobeforadvantageousgainof activity.Theomicsdatatypescollectedare:DNAresequencing,RNAseq,andmetabolomics.(ii) Bioinformaticsanddatamodelinganalysisinvolvesthreeapproaches:bigdataanalysisfordataset dimensionalityandcoarsegrainedvariabledependenciesassessment,genomescalemodelingfor mechanisticelucidationandanalysis,andmachinelearningthatusesARrelatedmetadatatoclassifythe overallbiologicalfunctions.ThisanalysiswillleadtounderstandingofARmechanisms.(iii)Multiscale validationfromanimalmodels,tolaboratoryevolution,tocytology,togeneexpressionalteration,tostructural proteinanalysisofputativetargets.Thevalidationthusrangesfromhostbehaviortoatomisticdetailof ligandtargetinteractions.Theiterativeloopthencloses,comparingcomputationalpredictiontoexperimental outcomes.Falsenegativeandfalsepositivepredictionsarethenalgorithmicallyanalyzedbyahypothesis generatingfamilyofalgorithmsthatthenmakessuggestionsaboutwhatconditionstouseinthenextiteration oftheloop.Thepathogensthatwewillfocusonaremethicillinresistant?Staphylococcusaureus?(MRSA),the carbapenemresistantEnterobacteriaceae(CRE)Klebsiella?pneumoniae?and?Acinetobacterbaumannii,?and Pseudomonasaeruginosa?.Theteamofinvestigatorshasmadethefoundationalobservationsandledthe developmentofthetechnologiesonwhichtheiterativeworkflowisbased.Amultiandgenomescalemethods ofsystemsbiologyfulfillsrequirementsofRFAAI14064towhichitresponds.

Public Health Relevance

Thecurrentevaluationofantibioticdrugcandidatesindrugdiscoveryandinclinicalmedicineisconductedin laboratorymediathatignorestheactualphysiologicconditionsinthehostandthehostimmunesystem.We havediscoveredpotentantimicrobialactivitiesofexistingantibioticsagainsthighly?drugresistantsuperbugs? thatarecurrentlyignoredbutrevealedinsynergywiththehumanimmunesystem.Thisprogramproposesa holisticandcomprehensivesystemsbiologyapproachtosystematicallydiscovernoveltreatmentopportunities andunderlyingmechanismsusinganoveliterativedatageneration,analysis,andmodelingworkflow.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01AI124316-04
Application #
9653953
Study Section
Special Emphasis Panel (ZAI1)
Program Officer
Shabman, Reed Solomon
Project Start
2016-03-15
Project End
2021-02-28
Budget Start
2019-03-01
Budget End
2020-02-29
Support Year
4
Fiscal Year
2019
Total Cost
Indirect Cost

  Institution

Name
University of California, San Diego
Department
Pediatrics
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093

  Publications

Choudhary, Kumari S; Mih, Nathan; Monk, Jonathan et al. (2018) The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Front Microbiol 9:1082
Fang, Xin; Monk, Jonathan M; Mih, Nathan et al. (2018) Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst Biol 12:66
Reynolds, Kirk A; Luhavaya, Hanna; Li, Jie et al. (2018) Isolation and structure elucidation of lipopeptide antibiotic taromycin B from the activated taromycin biosynthetic gene cluster. J Antibiot (Tokyo) 71:333-338
Seif, Yara; Kavvas, Erol; Lachance, Jean-Christophe et al. (2018) Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun 9:3771
Pekar, Jonathan E; Phaneuf, Patrick; Szubin, Richard et al. (2018) Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiol Resour Announc 7:
Kumaraswamy, Monika; Collignon, Sean; Do, Carter et al. (2018) Decontaminating surfaces with atomized disinfectants generated by a novel thickness-mode lithium niobate device. Appl Microbiol Biotechnol 102:6459-6467
Choe, Donghui; Szubin, Richard; Dahesh, Samira et al. (2018) Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. Sci Rep 8:2215
Norsigian, Charles J; Kavvas, Erol; Seif, Yara et al. (2018) iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Front Genet 9:121
Kumaraswamy, Monika; Do, Carter; Sakoulas, George et al. (2018) Listeria monocytogenes endocarditis: case report, review of the literature, and laboratory evaluation of potential novel antibiotic synergies. Int J Antimicrob Agents 51:468-478
Askarian, Fatemeh; Wagner, Theresa; Johannessen, Mona et al. (2018) Staphylococcus aureus modulation of innate immune responses through Toll-like (TLR), (NOD)-like (NLR) and C-type lectin (CLR) receptors. FEMS Microbiol Rev 42:656-671

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