@article {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/102703,
    title ="Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics",
    author = "Meirelles, Lucas A. and Perry, Elena K.",
    
    
    
    
    month = "April",
    year = "2020",
    
    
    
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20200421-132753787",
    note = "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nPosted April 20, 2020. \n\nWe thank members of the Newman lab and Shashank Gandhi for constructive feedback throughout the project and on the manuscript. We also thank Steven Wilbert for assistance with image analysis, David Basta for providing the plasmid used for lptA deletion, and The Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech and Igor Antoshechkin for support during library preparation and sequencing of the Tn-seq samples. Finally, we thank John LiPuma (CFF Burkholderia cepacia Research Laboratory and Repository at the University of Michigan) for providing clinical Burkholderia strains. Grants to D.K.N. from the NIH (1R01AI127850-01A1) and ARO (W911NF-17-1-0024) supported this work. E.K.P. was supported by a National Science Foundation Graduate Research Fellowship under Grant No. DGE-1745301. \n\nAuthor contributions: These authors contributed equally and are listed alphabetically: Lucas A. Meirelles and Elena K. Perry. Study conception: L.A.M., E.K.P., D.K.N. Study design: L.A.M., E.K.P., M.B., D.K.N. Tn-seq: L.A.M, M.B. Tolerance experiments: L.A.M. Resistance experiments: E.K.P. Manuscript preparation: E.K.P., L.A.M., M.B., D.K.N. Study supervision and funding: D.K.N. \n\nThe authors declare no competing interests. \n\nData and materials availability: Tn-seq data have been deposited at GEO under accession number GSE148769. Whole genome sequencing data for Δphz and ciprofloxacin-resistant mutants of P. aeruginosa and B. multivorans AU42096 have been deposited at NCBI under accession number PRJNA625945. All other data that support the findings of this study are available from the corresponding author upon reasonable request.",
    revision_no = "21",
    abstract = "As antibiotic-resistant infections become increasingly prevalent worldwide, understanding the factors that lead to antimicrobial treatment failure is essential to optimizing the use of existing drugs. Opportunistic human pathogens in particular typically exhibit high levels of intrinsic antibiotic resistance and tolerance1, leading to chronic infections that can be nearly impossible to eradicate2. We asked whether the recalcitrance of these organisms to antibiotic treatment could be driven in part by their evolutionary history as environmental microbes, which frequently produce or encounter natural antibiotics3,4. Using the opportunistic pathogen Pseudomonas aeruginosa as a model, we demonstrate that the self-produced natural antibiotic pyocyanin (PYO) activates bacterial defenses that confer collateral tolerance to certain synthetic antibiotics, including in a clinically-relevant growth medium. Non-PYO-producing opportunistic pathogens isolated from lung infections similarly display increased antibiotic tolerance when they are co-cultured with PYO-producing P. aeruginosa. Furthermore, we show that beyond promoting bacterial survival in the presence of antibiotics, PYO can increase the apparent rate of mutation to antibiotic resistance by up to two orders of magnitude. Our work thus suggests that bacterial production of natural antibiotics in infections could play an important role in modulating not only the immediate efficacy of clinical antibiotics, but also the rate at which antibiotic resistance arises in multispecies bacterial communities.",
}
@article {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/91271,
    title ="Refinement of metabolite detection in cystic fibrosis sputum reveals heme negatively correlates with lung function",
    author = "Glasser, Nathaniel R. and Hunter, Ryan C.",
    
    
    
    
    month = "November",
    year = "2018",
    
    
    
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526010",
    note = "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. \n\nThe MWCFC Sputum Biomarker investigators included Frederick R Adler, Fadi Asfour, Barbara A Chatfield, Jessica A Francis, John R Hoidal, Judy L Jensen, Yanping Li, Theodore G Liou, Kristyn A Packer, Jane Vroom (University of Utah); Natalia Argel, Peggy Radford (Phoenix Children’s Hospital); Perry S Brown, Dixie Durham (St. Luke’s Cystic Fibrosis Center of Idaho); Cori L Daines, Osmara Molina (University of Arizona); Barbara Glover, Craig Nakamura, Ryan Yoshikawa (Cystic Fibrosis Center, Las Vegas); Theresa Heynekamp, Abby J Redway (University of New Mexico); Ruth Keogh (London School of Hygiene and Tropical Medicine); Carol M Kopecky, Scott D Sagel (Children's Hospital Colorado, University of Colorado School of Medicine); Noah Lechtzin (Johns Hopkins University School of Medicine); Jerimiah Lysinger, Shawna Sprandel (Montana Cystic Fibrosis Center, Billings Clinic); Katie R Poch, Jennifer L Taylor-Cousar (National Jewish Health); Alexandra L Quittner (Miami Children's Research Institute, Nicklaus Children's Hospital); John P Clancy (University of Cincinnati); J Stuart Elborn (Queen’s University, Belfast and Royal Brompton Hospital, London); Kenneth N Olivier (Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart Lung and Blood Institute, National Institutes of Health). We thank Dr. Nathan Dalleska at the Environmental Analysis Center (Caltech) for analytical support.",
    revision_no = "11",
    abstract = "Pseudomonas aeruginosa lung infections are a leading cause of morbidity and mortality in cystic fibrosis (CF) patients (1, 2). Our laboratory has studied a class of small molecules produced by P. aeruginosa known as phenazines, including pyocyanin and its biogenic precursor phenazine 1 carboxylic acid (PCA). As phenazines are known virulence factors (3), we and others have explored the possibility of using phenazine concentrations as a marker for disease progression (4, 5, 6). Previously, we reported that sputum concentrations of pyocyanin and PCA negatively correlate with lung function in cystic fibrosis patients (6). Our study used high performance liquid chromatography (HPLC) to quantify phenazines by UV vis absorbance after extraction from lung sputum. Since our initial study, methods for metabolite analysis have advanced considerably, aided in large part by usage of mass spectrometry (LC MS) and tandem mass spectrometry (LC MS/MS). Because a more recent study employing LC MS/MS revealed a surprising decoupling of P. aeruginosa metabolites in sputum and the detection of P. aeruginosa through culturing or microbiome profiles (4), we decided to check whether we could reproduce our previous findings by analyzing sputum samples from a different patient cohort with a new LC MS instrument in our laboratory. Our new samples were provided by the Mountain West CF Consortium Sputum Biomarker study (7). In the course of performing our new analyses, comparison of our old HPLC data to our new LC MS data led us to realize that the peak previously assigned to PCA instead originates from heme, and the peak assigned to pyocyanin originates from an as yet unknown compound. This correction only affects the measurements of phenazines in sputum, and we are confident in the phenazine measurements from isolated cultures and the 16S rRNA gene sequencing data from that study (6). Here we outline the basis for our correction and present additional data showing that heme concentration negatively correlates with lung function in cystic fibrosis patients.",
}
@article {CaltechAUTHORS_https://authors.library.caltech.edu/id/eprint/90009,
    title ="Extended hopanoid lipids promote bacterial motility, surface attachment, and root nodule development in the Bradyrhizobium diazoefficiens-Aeschynomene afraspera symbiosis",
    author = "Belin, Brittany J. and Tookmanian, Elise T.",
    
    
    
    
    month = "September",
    year = "2018",
    
    
    
    url = "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224832",
    note = "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license. \n\nThis work was supported by grants from the HHMI (D.K.N.), NASA (NNX12AD93G, D.K.N.), Jane Coffin Childs Memorial Fund (B.J.B.), NIH (K99GM126141, B.J.B.), and Ford Foundation Predoctoral Fellowship (J.d.A.), and Army Research Office (W911NF-18-1-0254, GW). We thank Dr. Eric Giraud for his generous gift of A. afraspera seeds and training on Aeschynomene symbioses and Drs. Hans-Martin Fischer and Raphael Ledermann for plasmids and technical advice for the genetic transformation of B. diazoefficiens. Dr. Nathan Dalleska of the Environmental Analysis Center at Caltech was instrumental in providing training and support for GC-MS analysis of acetylene reduction. We are grateful to Dr. Gargi Kulkarni and other members of the Newman lab, as well as Drs. Elliot Meyerowitz and Rob Phillips, for their collegiality and thoughtful discussions about this work. We are indebted to Ms. Shannon Park and Ms. Kristy Nguyen for providing the administrative assistance that allows us to focus on our research.",
    revision_no = "15",
    abstract = "Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Roughly 10% of bacteria contain genes involved in hopanoid biosynthesis, and these genes are particularly conserved in plant-associated organisms. We previously found that the extended class of hopanoids (C35) in the nitrogen-fixing soil bacterium Bradyrhizobium diazoefficiens promotes its root nodule symbiosis with the tropical legume Aeschynomene afraspera. By quantitatively modeling root nodule development, we identify independent roles for hopanoids in the initiation of root nodule formation and in determining the rate of root nodule maturation. In vitro studies demonstrate that extended hopanoids support B. diazoefficiens motility and surface attachment, which may correlate with stable root colonization in planta. Confocal microscopy of maturing root nodules reveals that root nodules infected with extended hopanoid-deficient B. diazoefficiens contain unusually low densities of bacterial symbionts, indicating that extended hopanoids are necessary for persistent, high levels of host infection. This work identifies extended hopanoids as regulators of the efficiency of Bradyrhizobia nitrogen-fixing symbioses, agriculturally and economically significant associations with growing importance in a changing climate.",
}