1
|
Chopyk J, Cobián Güemes AG, Ramirez-Sanchez C, Attai H, Ly M, Jones MB, Liu R, Liu C, Yang K, Tu XM, Abeles SR, Nelson K, Pride DT. Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household. BMC Microbiol 2023; 23:206. [PMID: 37528343 PMCID: PMC10394940 DOI: 10.1186/s12866-023-02949-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/19/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The microbiome of the human gut serves a role in a number of physiological processes, but can be altered through effects of age, diet, and disturbances such as antibiotics. Several studies have demonstrated that commonly used antibiotics can have sustained impacts on the diversity and the composition of the gut microbiome. The impact of the two most overused antibiotics, azithromycin, and amoxicillin, in the human microbiome has not been thoroughly described. In this study, we recruited a group of individuals and unrelated controls to decipher the effects of the commonly used antibiotics amoxicillin and azithromycin on their gut microbiomes. RESULTS We characterized the gut microbiomes by metagenomic sequencing followed by characterization of the resulting microbial communities. We found that there were clear and sustained effects of the antibiotics on the gut microbial community with significant alterations in the representations of Bifidobacterium species in response to azithromycin (macrolide antibiotic). These results were supported by significant increases identified in putative antibiotic resistance genes associated with macrolide resistance. Importantly, we did not identify these trends in the unrelated control individuals. There were no significant changes observed in other members of the microbial community. CONCLUSIONS As we continue to focus on the role that the gut microbiome plays and how disturbances induced by antibiotics might affect our overall health, elucidating members of the community most affected by their use is of critical importance to understanding the impacts of common antibiotics on those who take them. Clinical Trial Registration Number NCT05169255. This trial was retrospectively registered on 23-12-2021.
Collapse
Affiliation(s)
- Jessica Chopyk
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Ana Georgina Cobián Güemes
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | | | - Hedieh Attai
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Melissa Ly
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Marcus B Jones
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Roland Liu
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA
| | - Chenyu Liu
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, 92093, USA
| | - Kun Yang
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, 92093, USA
| | - Xin M Tu
- Division of Biostatistics and Bioinformatics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, San Diego, CA, 92093, USA
| | - Shira R Abeles
- Department of Medicine, University of California San Diego, San Diego, CA, 92093, USA
| | - Karen Nelson
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - David T Pride
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, MC 0612, La Jolla, San Diego, CA, 92093-0612, USA.
- Department of Medicine, University of California San Diego, San Diego, CA, 92093, USA.
| |
Collapse
|
2
|
Rajagopal VM, Watanabe K, Mbatchou J, Ayer A, Quon P, Sharma D, Kessler MD, Praveen K, Gelfman S, Parikshak N, Otto JM, Bao S, Chim SM, Pavlopoulos E, Avbersek A, Kapoor M, Chen E, Jones MB, Leblanc M, Emberson J, Collins R, Torres J, Morales PK, Tapia-Conyer R, Alegre J, Berumen J, Shuldiner AR, Balasubramanian S, Abecasis GR, Kang HM, Marchini J, Stahl EA, Jorgenson E, Sanchez R, Liedtke W, Anderson M, Cantor M, Lederer D, Baras A, Coppola G. Rare coding variants in CHRNB2 reduce the likelihood of smoking. Nat Genet 2023:10.1038/s41588-023-01417-8. [PMID: 37308787 DOI: 10.1038/s41588-023-01417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/04/2023] [Indexed: 06/14/2023]
Abstract
Human genetic studies of smoking behavior have been thus far largely limited to common variants. Studying rare coding variants has the potential to identify drug targets. We performed an exome-wide association study of smoking phenotypes in up to 749,459 individuals and discovered a protective association in CHRNB2, encoding the β2 subunit of the α4β2 nicotine acetylcholine receptor. Rare predicted loss-of-function and likely deleterious missense variants in CHRNB2 in aggregate were associated with a 35% decreased odds for smoking heavily (odds ratio (OR) = 0.65, confidence interval (CI) = 0.56-0.76, P = 1.9 × 10-8). An independent common variant association in the protective direction ( rs2072659 ; OR = 0.96; CI = 0.94-0.98; P = 5.3 × 10-6) was also evident, suggesting an allelic series. Our findings in humans align with decades-old experimental observations in mice that β2 loss abolishes nicotine-mediated neuronal responses and attenuates nicotine self-administration. Our genetic discovery will inspire future drug designs targeting CHRNB2 in the brain for the treatment of nicotine addiction.
Collapse
Affiliation(s)
| | | | | | - Ariane Ayer
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Peter Quon
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | | | | | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | - Jonathan Emberson
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jason Torres
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Pablo Kuri Morales
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, Mexico
| | - Roberto Tapia-Conyer
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico, Mexico
| | - Jesus Alegre
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico, Mexico
| | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM), Mexico, Mexico
| | | | | | | | - Hyun M Kang
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | - Eli A Stahl
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA.
| | | |
Collapse
|
3
|
Manderstedt E, Lind‐Halldén C, Halldén C, Elf J, Svensson PJ, Engström G, Melander O, Baras A, Lotta LA, Zöller B, Abecasis G, Baras A, Cantor M, Coppola G, Economides A, Lotta LA, Overton JD, Reid JG, Shuldiner A, Beechert C, Forsythe C, Fuller ED, Gu Z, Lattari M, Lopez A, Overton JD, Schleicher TD, Padilla MS, Widom L, Wolf SE, Pradhan M, Manoochehri K, Ulloa RH, Bai X, Balasubramanian S, Blumenfeld A, Boutkov B, Eom G, Habegger L, Hawes A, Khalid S, Krasheninina O, Lanche R, Mansfield AJ, Maxwell EK, Nafde M, O’Keeffe S, Orelus M, Panea R, Polanco T, Rasool A, Reid JG, Salerno W, Staples JC, Jones MB, Mighty J, Mitnaul LJ. Genetic variation of the blood coagulation regulator tissue factor pathway inhibitor and venous thromboembolism among middle‐aged and older adults: A population‐based cohort study. Res Pract Thromb Haemost 2022; 6:e12842. [PMID: 36381289 PMCID: PMC9644338 DOI: 10.1002/rth2.12842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background Tissue factor is the main initiator of blood coagulation, and tissue factor pathway inhibitor (TFPI) is the primary inhibitor of the initiation of blood coagulation. The genetic variation of TFPI and the relation to venous thromboembolism (VTE), that is, venous thrombosis and pulmonary embolism, remains to be clarified. This exome sequencing study aimed to determine the molecular epidemiology of the TFPI gene and the relation to VTE in a large population‐based cohort of middle‐aged and older adults. Methods The exomes of TFPI were analyzed for variants in 28,794 subjects without previous VTE (born 1923–1950, 60% women), who participated in the Malmö Diet and Cancer Study (1991–1996). Patients were followed until the first event of VTE, death, or 2018. Qualifying variants were defined as loss‐of‐function or nonbenign (PolyPhen‐2) missense variants with minor allele frequency less than 0.1%. Results No common variant was associated with VTE. Nine rare variants (two loss‐of‐function and seven nonbenign missense) were classified as qualifying and included in collapsing analysis. Prevalence of qualifying variants was 0.09%. Five individuals with VTE compared to 17 individuals without VTE carried one qualifying variant. Cox multivariate regression analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking and alcohol consumption, rs6025, rs1799963, and ancestry showed a hazard ratio of 2.9 (95% CI, 1.2–7.1) for rare qualifying variants. Conclusion Rare qualifying TFPI variants were associated with VTE, suggesting that rare variants in TFPI contribute to the development of VTE. The qualifying TFPI gene variants were very rare, suggesting a constrained gene.
Collapse
Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and Bioscience Kristianstad University Kristianstad Sweden
| | - Christina Lind‐Halldén
- Department of Environmental Science and Bioscience Kristianstad University Kristianstad Sweden
| | - Christer Halldén
- Department of Environmental Science and Bioscience Kristianstad University Kristianstad Sweden
| | - Johan Elf
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Peter J. Svensson
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Gunnar Engström
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Olle Melander
- Department of Clinical Sciences Lund University, Skåne University Hospital Malmö Sweden
| | - Aris Baras
- Regeneron Genetics Center Tarrytown New York USA
| | | | - Bengt Zöller
- Center for Primary Health Care Research Lund University and Region Skåne Malmö Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Vujkovic M, Ramdas S, Lorenz KM, Guo X, Darlay R, Cordell HJ, He J, Gindin Y, Chung C, Myers RP, Schneider CV, Park J, Lee KM, Serper M, Carr RM, Kaplan DE, Haas ME, MacLean MT, Witschey WR, Zhu X, Tcheandjieu C, Kember RL, Kranzler HR, Verma A, Giri A, Klarin DM, Sun YV, Huang J, Huffman JE, Creasy KT, Hand NJ, Liu CT, Long MT, Yao J, Budoff M, Tan J, Li X, Lin HJ, Chen YDI, Taylor KD, Chang RK, Krauss RM, Vilarinho S, Brancale J, Nielsen JB, Locke AE, Jones MB, Verweij N, Baras A, Reddy KR, Neuschwander-Tetri BA, Schwimmer JB, Sanyal AJ, Chalasani N, Ryan KA, Mitchell BD, Gill D, Wells AD, Manduchi E, Saiman Y, Mahmud N, Miller DR, Reaven PD, Phillips LS, Muralidhar S, DuVall SL, Lee JS, Assimes TL, Pyarajan S, Cho K, Edwards TL, Damrauer SM, Wilson PW, Gaziano JM, O'Donnell CJ, Khera AV, Grant SFA, Brown CD, Tsao PS, Saleheen D, Lotta LA, Bastarache L, Anstee QM, Daly AK, Meigs JB, Rotter JI, Lynch JA, Rader DJ, Voight BF, Chang KM. A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation. Nat Genet 2022; 54:761-771. [PMID: 35654975 PMCID: PMC10024253 DOI: 10.1038/s41588-022-01078-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/18/2022] [Indexed: 02/05/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a growing cause of chronic liver disease. Using a proxy NAFLD definition of chronic elevation of alanine aminotransferase (cALT) levels without other liver diseases, we performed a multiancestry genome-wide association study (GWAS) in the Million Veteran Program (MVP) including 90,408 cALT cases and 128,187 controls. Seventy-seven loci exceeded genome-wide significance, including 25 without prior NAFLD or alanine aminotransferase associations, with one additional locus identified in European American-only and two in African American-only analyses (P < 5 × 10-8). External replication in histology-defined NAFLD cohorts (7,397 cases and 56,785 controls) or radiologic imaging cohorts (n = 44,289) replicated 17 single-nucleotide polymorphisms (SNPs) (P < 6.5 × 10-4), of which 9 were new (TRIB1, PPARG, MTTP, SERPINA1, FTO, IL1RN, COBLL1, APOH and IFI30). Pleiotropy analysis showed that 61 of 77 multiancestry and all 17 replicated SNPs were jointly associated with metabolic and/or inflammatory traits, revealing a complex model of genetic architecture. Our approach integrating cALT, histology and imaging reveals new insights into genetic liability to NAFLD.
Collapse
Affiliation(s)
- Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shweta Ramdas
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kim M Lorenz
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Rebecca Darlay
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Heather J Cordell
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Robert P Myers
- Gilead Sciences, Inc., Foster City, CA, USA
- The Liver Company, Palo Alto, CA, USA
| | - Carolin V Schneider
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Joseph Park
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kyung Min Lee
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Marina Serper
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rotonya M Carr
- Division of Gastroenterology, University of Washington, Seattle, WA, USA
| | - David E Kaplan
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary E Haas
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew T MacLean
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Walter R Witschey
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiang Zhu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Catherine Tcheandjieu
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel L Kember
- Mental Illness Research Education and Clinical Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Henry R Kranzler
- Mental Illness Research Education and Clinical Center, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Anurag Verma
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayush Giri
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Derek M Klarin
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yan V Sun
- Atlanta VA Medical Center, Decatur, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Jie Huang
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | | | - Kate Townsend Creasy
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicholas J Hand
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Michelle T Long
- Department of Medicine, Section of Gastroenterology, Boston University School of Medicine, Boston, MA, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Matthew Budoff
- Department of Cardiology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ruey-Kang Chang
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald M Krauss
- Departments of Pediatrics and Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Silvia Vilarinho
- Section of Digestive Diseases, Department of Internal Medicine, and Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Joseph Brancale
- Section of Digestive Diseases, Department of Internal Medicine, and Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - K Rajender Reddy
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Jeffrey B Schwimmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Arun J Sanyal
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Naga Chalasani
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathleen A Ryan
- Program for Personalized and Genomic Medicine, Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elisabetta Manduchi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yedidya Saiman
- Department of Medicine, Section of Hepatology, Lewis Katz School of Medicine at Temple University, Temple University Hospital, Philadelphia, PA, USA
| | - Nadim Mahmud
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Donald R Miller
- Center for Healthcare Organization and Implementation Research, Bedford VA Healthcare System, Bedford, MA, USA
- Center for Population Health, Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Lawrence S Phillips
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Endocrinology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sumitra Muralidhar
- Office of Research and Development, Veterans Health Administration, Washington, DC, USA
| | - Scott L DuVall
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jennifer S Lee
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Todd L Edwards
- Nashville VA Medical Center, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter W Wilson
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
| | - Christopher J O'Donnell
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Amit V Khera
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Struan F A Grant
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Danish Saleheen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Non-Communicable Diseases, Karachi, Sindh, Pakistan
| | | | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quentin M Anstee
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ann K Daly
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Julie A Lynch
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- College of Nursing and Health Sciences, University of Massachusetts, Lowell, MA, USA
| | - Daniel J Rader
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
5
|
Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE. Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. Cell Metab 2019; 30:607. [PMID: 31484056 PMCID: PMC8025688 DOI: 10.1016/j.cmet.2019.08.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
6
|
Abstract
11 tests were selected from two microcomputer-based performance test batteries because previously these tests exhibited rapid stability (<10 min. of practice) and high retest reliability efficiencies (r>0.707 for each 3 min. of testing). The battery was administered three times to each of 108 college students (48 men and 60 women) and a factor analysis was performed. Two of the three identified factors appear to be related to information processing (“encoding” and “throughput/ decoding”), and the third named an “output/speed” factor. The spatial, memory, and verbal tests loaded on the “encoding” factor and included Grammatical Reasoning, Pattern Comparison, Continuous Recall, and Matrix Rotation. The “throughput/ decoding” tests included perceptual/numerical tests like Math Processing, Code Substitution, and Pattern Comparison. The output speed factor was identified by Tapping and Reaction Time tests. The Wonderlic Personnel Test was group administered before the first and after the last administration of the performance tests. The multiple Rs in the total sample between combined Wonderlic as a criterion and less than 5 min. of microcomputer testing on Grammatical Reasoning and Math Processing as predictors ranged between 0.41 and 0.52 on the three test administrations. Based on these results, the authors recommend a core battery which, if time permits, would consist of two tests from each factor. Such a battery is now known to permit stable, reliable, and efficient assessment.
Collapse
|
7
|
Zhu Q, Dupont CL, Jones MB, Pham KM, Jiang ZD, DuPont HL, Highlander SK. Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. Microbiome 2018; 6:201. [PMID: 30409177 PMCID: PMC6225641 DOI: 10.1186/s40168-018-0579-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/17/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease. RESULTS We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays. Abnormal and diverse taxonomic profiles in TD samples were revealed. WGS reads were assembled and the resulting contigs were visualized using multiple query types. A semi-manual workflow was applied to isolate independent genomes from metagenomic pools. A total of 565 genome bins were extracted, 320 of which were complete enough to be characterized as cellular genomes; 160 were viral genomes. We made predictions of the etiology of disease for many of the individual subjects based on the properties and features of the recovered genomes. Multiple patients with low-diversity metagenomes were predominated by one to several E. coli strains. Functional annotation allowed prediction of pathogenic type in many cases. Five patients were co-infected with E. coli and other members of Enterobacteriaceae, including Enterobacter, Klebsiella, and Citrobacter; these may represent blooms of organisms that appear following secretory diarrhea. New "dark matter" microbes were observed in multiple samples. In one, we identified a novel TM7 genome that phylogenetically clustered with a sludge isolate; it carries genes encoding potential virulence factors. In multiple samples, we observed high proportions of putative novel viral genomes, some of which form clusters with the ubiquitous gut virus, crAssphage. The total relative abundance of viruses was significantly higher in healthy travelers versus TD patients. CONCLUSION Our study highlights the strength of assembly-based metagenomics, especially the manually curated, visualization-assisted binning of contigs, in resolving unusual and under-characterized pathogenic profiles of human-associated microbiomes. Results show that TD may be polymicrobial, with multiple novel cellular and viral strains as potential players in the diarrheal disease.
Collapse
Affiliation(s)
- Qiyun Zhu
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
- Department of Pediatrics, University of California San Diego, 9500 Gillman Drive #0763, La Jolla, CA 92093 USA
| | | | - Marcus B. Jones
- Human Longevity, Inc., 4570 Executive Drive, La Jolla, CA 92121 USA
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591 USA
| | - Kevin M. Pham
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
- 2132 Calaveras Ave, Davis, CA 95616 USA
| | - Zhi-Dong Jiang
- University of Texas School of Public Health, 7000 Fannin St., Houston, TX 77030 USA
| | - Herbert L. DuPont
- University of Texas School of Public Health, 7000 Fannin St., Houston, TX 77030 USA
| | - Sarah K. Highlander
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
- Pathogen and Microbiome Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86005 USA
| |
Collapse
|
8
|
Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE. Host Genetic Control of the Oral Microbiome in Health and Disease. Cell Host Microbe 2018; 22:269-278.e3. [PMID: 28910633 DOI: 10.1016/j.chom.2017.08.013] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/30/2017] [Accepted: 08/18/2017] [Indexed: 12/11/2022]
Abstract
Host-associated microbial communities are influenced by both host genetics and environmental factors. However, factors controlling the human oral microbiome and their impact on disease remain to be investigated. To determine the combined and relative effects of host genotype and environment on oral microbiome composition and caries phenotypes, we profiled the supragingival plaque microbiome of 485 dizygotic and monozygotic twins aged 5-11. Oral microbiome similarity always increased with shared host genotype, regardless of caries state. Additionally, although most of the variation in the oral microbiome was determined by environmental factors, highly heritable oral taxa were identified. The most heritable oral bacteria were not associated with caries state, did not tend to co-occur with other taxa, and decreased in abundance with age and sugar consumption frequency. Thus, while the human oral microbiome composition is influenced by host genetic background, potentially cariogenic taxa are likely not controlled by genetic factors.
Collapse
Affiliation(s)
- Andres Gomez
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Josh L Espinoza
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Derek M Harkins
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Pamela Leong
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michelle Bockmann
- School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Manolito Torralba
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Claire Kuelbs
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Rohith Kodukula
- JCVI Summer Intern Program, Torrey Pines High School, San Diego, CA 9213, USA
| | - Jason Inman
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Toby Hughes
- School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeffrey M Craig
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Sarah K Highlander
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Chris L Dupont
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Karen E Nelson
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA; Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA.
| |
Collapse
|
9
|
Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS. Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease. Clin Transl Gastroenterol 2018; 9:e132. [PMID: 29345635 PMCID: PMC5795019 DOI: 10.1038/ctg.2017.58] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/15/2017] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals. Genetic risk scores, computed on 159 single nucleotide variants, and human leukocyte antigen (HLA) types differentiated IBD patients from healthy controls. RESULTS Genetic risk was associated with the need for use of biologics in IBD and, modestly, with the composition of the gut microbiome. As compared with healthy controls, IBD patients had hallmarks of stool microbiome dysbiosis, with loss of a diversified core microbiome, enrichment and depletion of specific bacteria, and enrichment of bacterial virulence factors. CONCLUSIONS We show that genetic risk may have a role in early risk stratification in the care of IBD patients and propose that expression of virulence factors in a dysbiotic microbiome may contribute to pathogenesis in IBD.
Collapse
Affiliation(s)
| | - Weizhong Li
- Human Longevity Inc., San Diego, CA, USA
- J. Craig Venter Institute, La Jolla, CA, USA
| | | | | | - Parambir S Dulai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | | | | | | | - J Craig Venter
- Human Longevity Inc., San Diego, CA, USA
- J. Craig Venter Institute, La Jolla, CA, USA
| | | | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | | | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
10
|
Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE. Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. Cell Metab 2017; 25:1054-1062.e5. [PMID: 28467925 PMCID: PMC5502730 DOI: 10.1016/j.cmet.2017.04.001] [Citation(s) in RCA: 610] [Impact Index Per Article: 87.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/21/2016] [Accepted: 03/30/2017] [Indexed: 02/07/2023]
Abstract
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis). We identified a set of 40 features (p < 0.006), which included 37 bacterial species that were used to construct a Random Forest classifier model to distinguish mild/moderate NAFLD from advanced fibrosis. The model had a robust diagnostic accuracy (AUC 0.936) for detecting advanced fibrosis. This study provides preliminary evidence for a fecal-microbiome-derived metagenomic signature to detect advanced fibrosis in NAFLD.
Collapse
Affiliation(s)
- Rohit Loomba
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Epidemiology, Department of Family and Preventive Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | | | - Weizhong Li
- Human Longevity, San Diego, CA 92121, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Tao Long
- Human Longevity, San Diego, CA 92121, USA
| | | | - Archana Bhatt
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Parambir Singh Dulai
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cyrielle Caussy
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Richele Bettencourt
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | | | - Claude B Sirlin
- Liver Imaging Group, Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernd Schnabl
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | | | - Chi-Hua Chen
- Liver Imaging Group, Department of Radiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David A Brenner
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Shibu Yooseph
- Human Longevity, San Diego, CA 92121, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - J Craig Venter
- Human Longevity, San Diego, CA 92121, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Karen E Nelson
- Human Longevity, San Diego, CA 92121, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA
| |
Collapse
|
11
|
Jones MB, Nierman WC, Shan Y, Frank BC, Spoering A, Ling L, Peoples A, Zullo A, Lewis K, Nelson KE. Reducing the Bottleneck in Discovery of Novel Antibiotics. Microb Ecol 2017; 73:658-667. [PMID: 27896376 DOI: 10.1007/s00248-016-0889-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform. This is particularly troubling given the emergence of pan-resistant pathogens. The current practice in dealing with the problem of the background of known compounds is to use chemical dereplication of extracts to assess the relative novelty of a compound it contains. Dereplication typically requires scale-up, extraction, and often fractionation before an accurate mass and structure can be produced by MS analysis in combination with 2D NMR. Here, we describe a transcriptome analysis approach using RNA sequencing (RNASeq) to identify promising novel antimicrobial compounds from microbial extracts. Our pipeline permits identification of antimicrobial compounds that produce distinct transcription profiles using unfractionated cell extracts. This efficient pipeline will eliminate the requirement for purification and structure determination of compounds from extracts and will facilitate high-throughput screen of cell extracts for identification of novel compounds.
Collapse
Affiliation(s)
- Marcus B Jones
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA.
- Human Longevity, Inc, San Diego, CA, USA.
| | | | - Yue Shan
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Bryan C Frank
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Losee Ling
- NovoBiotic Pharmaceuticals, Cambridge, MA, USA
| | | | | | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA
| | - Karen E Nelson
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
- Human Longevity, Inc, San Diego, CA, USA
| |
Collapse
|
12
|
Ly M, Jones MB, Abeles SR, Santiago-Rodriguez TM, Gao J, Chan IC, Ghose C, Pride DT. Transmission of viruses via our microbiomes. Microbiome 2016; 4:64. [PMID: 27912785 PMCID: PMC5134127 DOI: 10.1186/s40168-016-0212-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/24/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts. RESULTS Here, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts. CONCLUSIONS Because bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household.
Collapse
Affiliation(s)
- Melissa Ly
- Department of Pathology, University of California, San Diego, 92093, USA
| | | | - Shira R Abeles
- Department of Medicine, University of California, San Diego, 92093, USA
| | | | - Jonathan Gao
- Department of Pathology, University of California, San Diego, 92093, USA
| | - Ivan C Chan
- Department of Pathology, University of California, San Diego, 92093, USA
| | | | - David T Pride
- Department of Pathology, University of California, San Diego, 92093, USA.
- Department of Medicine, University of California, San Diego, 92093, USA.
| |
Collapse
|
13
|
Anderson EL, Li W, Klitgord N, Highlander SK, Dayrit M, Seguritan V, Yooseph S, Biggs W, Venter JC, Nelson KE, Jones MB. A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome. Sci Rep 2016; 6:31731. [PMID: 27558918 PMCID: PMC4997331 DOI: 10.1038/srep31731] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/25/2016] [Indexed: 12/30/2022] Open
Abstract
As reports on possible associations between microbes and the host increase in number, more meaningful interpretations of this information require an ability to compare data sets across studies. This is dependent upon standardization of workflows to ensure comparability both within and between studies. Here we propose the standard use of an alternate collection and stabilization method that would facilitate such comparisons. The DNA Genotek OMNIgene∙Gut Stool Microbiome Kit was compared to the currently accepted community standard of freezing to store human stool samples prior to whole genome sequencing (WGS) for microbiome studies. This stabilization and collection device allows for ambient temperature storage, automation, and ease of shipping/transfer of samples. The device permitted the same data reproducibility as with frozen samples, and yielded higher recovery of nucleic acids. Collection and stabilization of stool microbiome samples with the DNA Genotek collection device, combined with our extraction and WGS, provides a robust, reproducible workflow that enables standardized global collection, storage, and analysis of stool for microbiome studies.
Collapse
Affiliation(s)
| | - Weizhong Li
- Human Longevity, Inc., San Diego, CA 92121, USA.,Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | | | - Mark Dayrit
- Human Longevity, Inc., San Diego, CA 92121, USA
| | | | - Shibu Yooseph
- Human Longevity, Inc., San Diego, CA 92121, USA.,Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - J Craig Venter
- Human Longevity, Inc., San Diego, CA 92121, USA.,Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Karen E Nelson
- Human Longevity, Inc., San Diego, CA 92121, USA.,Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | |
Collapse
|
14
|
Tran TM, Jones MB, Ongoiba A, Bijker EM, Schats R, Venepally P, Skinner J, Doumbo S, Quinten E, Visser LG, Whalen E, Presnell S, O'Connell EM, Kayentao K, Doumbo OK, Chaussabel D, Lorenzi H, Nutman TB, Ottenhoff THM, Haks MC, Traore B, Kirkness EF, Sauerwein RW, Crompton PD. Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria. Sci Rep 2016; 6:31291. [PMID: 27506615 PMCID: PMC4978957 DOI: 10.1038/srep31291] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/15/2016] [Indexed: 12/16/2022] Open
Abstract
Identifying molecular predictors and mechanisms of malaria disease is important for understanding how Plasmodium falciparum malaria is controlled. Transcriptomic studies in humans have so far been limited to retrospective analysis of blood samples from clinical cases. In this prospective, proof-of-principle study, we compared whole-blood RNA-seq profiles at pre-and post-infection time points from Malian adults who were either asymptomatic (n = 5) or febrile (n = 3) during their first seasonal PCR-positive P. falciparum infection with those from malaria-naïve Dutch adults after a single controlled human malaria infection (n = 5). Our data show a graded activation of pathways downstream of pro-inflammatory cytokines, with the highest activation in malaria-naïve Dutch individuals and significantly reduced activation in malaria-experienced Malians. Newly febrile and asymptomatic infections in Malians were statistically indistinguishable except for genes activated by pro-inflammatory cytokines. The combined data provide a molecular basis for the development of a pyrogenic threshold as individuals acquire immunity to clinical malaria.
Collapse
Affiliation(s)
- Tuan M Tran
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.,Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Marcus B Jones
- Genomic Medicine Group, J. Craig Venter Institute, Rockville, Maryland, USA
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Else M Bijker
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Remko Schats
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Pratap Venepally
- Genomic Medicine Group, J. Craig Venter Institute, Rockville, Maryland, USA
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Edwin Quinten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Elizabeth Whalen
- Systems Immunology Division, Benaroya Research Institute, Seattle, WA, USA
| | - Scott Presnell
- Systems Immunology Division, Benaroya Research Institute, Seattle, WA, USA
| | - Elise M O'Connell
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Ogobara K Doumbo
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Damien Chaussabel
- Systems Immunology Division, Benaroya Research Institute, Seattle, WA, USA.,Sidra Medical and Research Center, Doha, Qatar
| | - Hernan Lorenzi
- Infectious Diseases Group, J. Craig Venter Institute, Bethesda, Maryland, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariëlle C Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Ewen F Kirkness
- Genomic Medicine Group, J. Craig Venter Institute, Rockville, Maryland, USA
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| |
Collapse
|
15
|
Krol DJ, Jones MB, Williams M, Richards KG, Bourdin F, Lanigan GJ. The effect of renovation of long-term temperate grassland on N2O emissions and N leaching from contrasting soils. Sci Total Environ 2016; 560-561:233-240. [PMID: 27101460 DOI: 10.1016/j.scitotenv.2016.04.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 06/05/2023]
Abstract
Renovation of long-term grassland is associated with a peak in soil organic N mineralisation which, coupled with diminished plant N uptake can lead to large gaseous and leaching N losses. This study reports on the effect of ploughing and subsequent N fertilisation on the N2O emissions and DON/NO3(-) leaching, and evaluates the impact of ploughing technique on the magnitude and profile of N losses. This study was carried out on isolated grassland lysimeters of three Irish soils representing contrasting drainage properties (well-drained Clonakilty, moderately-drained Elton and poorly-drained Rathangan). Lysimeters were manually ploughed simulating conventional (CT) and minimum tillage (MT) as two treatments. Renovation of grassland increased N2O flux to a maximum of 0.9kgN2O-Nha(-1) from poorly-drained soil over four days after treatment. Although there was no difference between CT and MT in the post-ploughing period, the treatment influenced subsequent N2O after fertiliser applications. Fertilisation remained the major driver of N losses therefore reducing fertilisation rate post-planting to account for N mineralised through grassland renovation could reduce the losses in medium to longer term. Leaching was a significant loss pathway, with the cumulative drainage volume and N leached highly influenced by soil type. Overall, the total N losses (N2O+N leached) were lowest from poorly and moderately draining soil and highest for the well draining soil, reflecting the dominance of leaching on total N losses and the paramount importance of soil properties.
Collapse
Affiliation(s)
- D J Krol
- Teagasc, Johnstown Castle Environmental Research Centre, Wexford, Ireland.
| | - M B Jones
- Botany Department, Trinity College Dublin, Ireland
| | - M Williams
- Botany Department, Trinity College Dublin, Ireland
| | - K G Richards
- Teagasc, Johnstown Castle Environmental Research Centre, Wexford, Ireland
| | - F Bourdin
- Teagasc, Johnstown Castle Environmental Research Centre, Wexford, Ireland
| | - G J Lanigan
- Teagasc, Johnstown Castle Environmental Research Centre, Wexford, Ireland
| |
Collapse
|
16
|
Abeles SR, Jones MB, Santiago-Rodriguez TM, Ly M, Klitgord N, Yooseph S, Nelson KE, Pride DT. Microbial diversity in individuals and their household contacts following typical antibiotic courses. Microbiome 2016; 4:39. [PMID: 27473422 PMCID: PMC4967329 DOI: 10.1186/s40168-016-0187-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/22/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Antibiotics are a mainstay of treatment for bacterial infections worldwide, yet the effects of typical antibiotic prescriptions on human indigenous microbiota have not been thoroughly evaluated. We examined the effects of the two most commonly prescribed antibiotics (amoxicillin and azithromycin) in the USA to discern whether short-term antibiotic courses may have prolonged effects on human microbiota. RESULTS We sampled the feces, saliva, and skin specimens from a cohort of unrelated, cohabitating individuals over 6 months. An individual in each household was given an antibiotic, and the other a placebo to discern antibiotic impacts on microbiota, as well as determine whether antibiotic use might reshape the microbiota of each household. We observed household-specific patterns of microbiota on each body surface, which persevered despite antibiotic perturbations. While the gut microbiota within an individual became more dissimilar over time, there was no evidence that the use of antibiotics accelerated this process when compared to household members. There was a significant change in microbiota diversity in the gut and mouth in response to antibiotics, but analogous patterns were not observed on the skin. Those who received 7 days of amoxicillin generally had greater reductions in diversity compared to those who received 3 days, in contrast to those who received azithromycin. CONCLUSIONS As few as 3 days of treatment with the most commonly prescribed antibiotics can result in sustained reductions in microbiota diversity, which could have implications for the maintenance of human health and resilience to disease.
Collapse
Affiliation(s)
- Shira R Abeles
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA
| | | | - Tasha M Santiago-Rodriguez
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA
| | | | - Shibu Yooseph
- Human Longevity, Inc., San Diego, CA, 92121, USA
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Human Longevity, Inc., San Diego, CA, 92121, USA
- Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - David T Pride
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| |
Collapse
|
17
|
Yooseph S, Kirkness EF, Tran TM, Harkins DM, Jones MB, Torralba MG, O'Connell E, Nutman TB, Doumbo S, Doumbo OK, Traore B, Crompton PD, Nelson KE. Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection. BMC Genomics 2015; 16:631. [PMID: 26296559 PMCID: PMC4546150 DOI: 10.1186/s12864-015-1819-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/05/2015] [Indexed: 12/20/2022] Open
Abstract
Background In humans it is unknown if the composition of the gut microbiota alters the risk of Plasmodium falciparum infection or the risk of developing febrile malaria once P. falciparum infection is established. Here we collected stool samples from a cohort composed of 195 Malian children and adults just prior to an intense P. falciparum transmission season. We assayed these samples using massively parallel sequencing of the 16S ribosomal RNA gene to identify the composition of the gut bacterial communities in these individuals. During the ensuing 6-month P. falciparum transmission season we examined the relationship between the stool microbiota composition of individuals in this cohort and their prospective risk of both P. falciparum infection and febrile malaria. Results Consistent with prior studies, stool microbial diversity in the present cohort increased with age, although the overall microbiota profile was distinct from cohorts in other regions of Africa, Asia and North America. Age-adjusted Cox regression analysis revealed a significant association between microbiota composition and the prospective risk of P. falciparum infection; however, no relationship was observed between microbiota composition and the risk of developing febrile malaria once P. falciparum infection was established. Conclusions These findings underscore the diversity of gut microbiota across geographic regions, and suggest that strategic modulation of gut microbiota composition could decrease the risk of P. falciparum infection in malaria-endemic areas, potentially as an adjunct to partially effective malaria vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1819-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shibu Yooseph
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Ewen F Kirkness
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Tuan M Tran
- Laboratory of Immunogenetics, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
| | - Derek M Harkins
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Marcus B Jones
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Manolito G Torralba
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Elise O'Connell
- Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. elise.o'
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali.
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali.
| | - Boubacar Traore
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali.
| | - Peter D Crompton
- Laboratory of Immunogenetics, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
| | - Karen E Nelson
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| |
Collapse
|
18
|
Santiago-Rodriguez TM, Naidu M, Jones MB, Ly M, Pride DT. Identification of staphylococcal phage with reduced transcription in human blood through transcriptome sequencing. Front Microbiol 2015; 6:216. [PMID: 26074882 PMCID: PMC4447126 DOI: 10.3389/fmicb.2015.00216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/03/2015] [Indexed: 12/29/2022] Open
Abstract
Many pathogenic bacteria have bacteriophage and other mobile genetic elements whose activity during human infections has not been evaluated. We investigated the gene expression patterns in human subjects with invasive Methicillin Resistant Staphylococcus aureus (MRSA) infections to determine the gene expression of bacteriophage and other mobile genetic elements. We developed an ex vivo technique that involved direct inoculation of blood from subjects with invasive bloodstream infections into culture media to reduce any potential laboratory adaptation. We compared ex vivo to in vitro profiles from 10 human subjects to determine MRSA gene expression in blood. Using RNA sequencing, we found that there were distinct and significant differences between ex vivo and in vitro MRSA gene expression profiles. Among the major differences between ex vivo and in vitro gene expression were virulence/disease/defense and mobile elements. While transposons were expressed at higher levels ex vivo, lysogenic bacteriophage had significantly higher in vitro expression. Five subjects had MRSA with bacteriophage that were inhibited by the presence of blood in the media, supporting that the lysogeny state was preferred in human blood. Some of the phage produced also had reduced infectivity, further supporting that phage were inhibited by blood. By comparing the gene expression cultured in media with and without the blood of patients, we gain insights into the specific adaptations made by MRSA and its bacteriophage to life in the human bloodstream.
Collapse
Affiliation(s)
| | - Mayuri Naidu
- Department of Pathology, University of California San Diego, CA, USA
| | | | - Melissa Ly
- Department of Pathology, University of California San Diego, CA, USA
| | - David T Pride
- Department of Pathology, University of California San Diego, CA, USA ; Department of Medicine, University of California San Diego, CA, USA
| |
Collapse
|
19
|
Li J, Overall CC, Nakayasu ES, Kidwai AS, Jones MB, Johnson RC, Nguyen NT, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN. Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression. Front Microbiol 2015; 6:27. [PMID: 25713562 PMCID: PMC4322710 DOI: 10.3389/fmicb.2015.00027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/08/2015] [Indexed: 02/04/2023] Open
Abstract
The extracytoplasmic functioning sigma factor σE is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well-characterized, especially during infection. Here we used microarray to identify genes regulated by σE in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σE regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression of genes involved in Salmonella pathogenesis island (SPI)-1 type-three secretion system (TTSS), SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σE in at least one of the three conditions. An important finding is that σE up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σE is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between σE and SPI-2 genes, combined with the global regulatory effect of σE, may account for the lethality of rpoE-deficient Salmonella in murine infection.
Collapse
Affiliation(s)
- Jie Li
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Christopher C Overall
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Afshan S Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Marcus B Jones
- Department of Infectious Diseases, J. Craig Venter Institute Rockville, MD, USA
| | - Rudd C Johnson
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Nhu T Nguyen
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Eric D Cambronne
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| |
Collapse
|
20
|
Wright MS, Suzuki Y, Jones MB, Marshall SH, Rudin SD, van Duin D, Kaye K, Jacobs MR, Bonomo RA, Adams MD. Genomic and transcriptomic analyses of colistin-resistant clinical isolates of Klebsiella pneumoniae reveal multiple pathways of resistance. Antimicrob Agents Chemother 2015; 59:536-43. [PMID: 25385117 PMCID: PMC4291396 DOI: 10.1128/aac.04037-14] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/02/2014] [Indexed: 12/28/2022] Open
Abstract
The emergence of multidrug-resistant (MDR) Klebsiella pneumoniae has resulted in a more frequent reliance on treatment using colistin. However, resistance to colistin (Col(r)) is increasingly reported from clinical settings. The genetic mechanisms that lead to Col(r) in K. pneumoniae are not fully characterized. Using a combination of genome sequencing and transcriptional profiling by RNA sequencing (RNA-Seq) analysis, distinct genetic mechanisms were found among nine Col(r) clinical isolates. Col(r) was related to mutations in three different genes in K. pneumoniae strains, with distinct impacts on gene expression. Upregulation of the pmrH operon encoding 4-amino-4-deoxy-L-arabinose (Ara4N) modification of lipid A was found in all Col(r) strains. Alteration of the mgrB gene was observed in six strains. One strain had a mutation in phoQ. Common among these seven strains was elevated expression of phoPQ and unaltered expression of pmrCAB, which is involved in phosphoethanolamine addition to lipopolysaccharide (LPS). In two strains, separate mutations were found in a previously uncharacterized histidine kinase gene that is part of a two-component regulatory system (TCRS) now designated crrAB. In these strains, expression of pmrCAB, crrAB, and an adjacent glycosyltransferase gene, but not that of phoPQ, was elevated. Complementation with the wild-type allele restored colistin susceptibility in both strains. The crrAB genes are present in most K. pneumoniae genomes, but not in Escherichia coli. Additional upregulated genes in all strains include those involved in cation transport and maintenance of membrane integrity. Because the crrAB genes are present in only some strains, Col(r) mechanisms may be dependent on the genetic background.
Collapse
Affiliation(s)
| | - Yo Suzuki
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Steven H Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Susan D Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Keith Kaye
- Detroit Medical Center, Detroit, Michigan, USA
| | - Michael R Jacobs
- Department of Pathology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark D Adams
- J. Craig Venter Institute, La Jolla, California, USA
| |
Collapse
|
21
|
Jones MB, Montgomery CP, Boyle-Vavra S, Shatzkes K, Maybank R, Frank BC, Peterson SN, Daum RS. Genomic and transcriptomic differences in community acquired methicillin resistant Staphylococcus aureus USA300 and USA400 strains. BMC Genomics 2014; 15:1145. [PMID: 25527145 PMCID: PMC4630920 DOI: 10.1186/1471-2164-15-1145] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a human pathogen responsible for substantial morbidity and mortality through its ability to cause a number of human infections including bacteremia, pneumonia and soft tissue infections. Of great concern is the emergence and dissemination of methicillin-resistant Staphylococcus aureus strains (MRSA) that are resistant to nearly all β-lactams. The emergence of the USA300 MRSA genetic background among community associated S. aureus infections (CA-MRSA) in the USA was followed by the disappearance of USA400 CA-MRSA isolates. RESULTS To gain a greater understanding of the potential fitness advantages and virulence capacity of S. aureus USA300 clones, we performed whole genome sequencing of 15 USA300 and 4 USA400 clinical isolates. A comparison of representative genomes of the USA300 and USA400 pulsotypes indicates a number of differences in mobile genome elements. We examined the in vitro gene expression profiles by microarray hybridization and the in vivo transcriptomes during lung infection in mice of a USA300 and a USA400 MRSA strain by performing complete genome qRT-PCR analysis. The unique presence and increased expression of 6 exotoxins in USA300 (12- to 600-fold) compared to USA400 may contribute to the increased virulence of USA300 clones. Importantly, we also observed the up-regulation of prophage genes in USA300 (compared with USA400) during mouse lung infection (including genes encoded by both prophages ΦSa2usa and ΦSa3usa), suggesting that these prophages may play an important role in vivo by contributing to the elevated virulence characteristic of the USA300 clone. CONCLUSIONS We observed differences in the genetic content of USA300 and USA400 strains, as well as significant differences of in vitro and in vivo gene expression of mobile elements in a lung pneumonia model. This is the first study to document the global transcription differences between USA300 and USA400 strains during both in vitro and in vivo growth.
Collapse
Affiliation(s)
- Marcus B Jones
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Christopher P Montgomery
- Department of Pediatrics, Section of Critical Care, University of Chicago, Chicago, IL, 60637, USA.
| | - Susan Boyle-Vavra
- Department of Pediatrics, Section of Infectious Diseases, Chicago, IL, 60637, USA.
| | - Kenneth Shatzkes
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, 07103, USA.
| | - Rosslyn Maybank
- Battelle National Biodefense Institute, National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA.
| | - Bryan C Frank
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Scott N Peterson
- Sanford Burnham Medical Research Institute, 10901 N. Torrey Pines Rd, La Jolla, CA, 92037, USA.
| | - Robert S Daum
- Department of Pediatrics, Section of Critical Care, University of Chicago, Chicago, IL, 60637, USA. .,Department of Pediatrics, Section of Infectious Diseases, Chicago, IL, 60637, USA.
| |
Collapse
|
22
|
Nakano MM, Kominos-Marvell W, Sane B, Nader YM, Barendt SM, Jones MB, Zuber P. spxA2, encoding a regulator of stress resistance in Bacillus anthracis, is controlled by SaiR, a new member of the Rrf2 protein family. Mol Microbiol 2014; 94:815-27. [PMID: 25231235 DOI: 10.1111/mmi.12798] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2014] [Indexed: 12/22/2022]
Abstract
Spx, a member of the ArsC (arsenate reductase) protein family, is conserved in Gram-positive bacteria, and interacts with RNA polymerase to activate transcription in response to toxic oxidants. In Bacillus anthracis str. Sterne, resistance to oxidative stress requires the activity of two paralogues, SpxA1 and SpxA2. Suppressor mutations were identified in spxA1 mutant cells that conferred resistance to hydrogen peroxide. The mutations generated null alleles of the saiR gene and resulted in elevated spxA2 transcription. The saiR gene resides in the spxA2 operon and encodes a member of the Rrf2 family of transcriptional repressors. Derepression of spxA2 in a saiR mutant required SpxA2, indicating an autoregulatory mechanism of spxA2 control. Reconstruction of SaiR-dependent control of spxA2 was accomplished in Bacillus subtilis, where deletion analysis uncovered two cis-elements within the spxA2 regulatory region that are required for repression. Mutations to one of the sequences of dyad symmetry substantially reduced SaiR binding and SaiR-dependent repression of transcription from the spxA2 promoter in vitro. Previous studies have shown that spxA2 is one of the most highly induced genes in a macrophage infected with B. anthracis. The work reported herein uncovered a key regulator, SaiR, of the Spx system of stress response control.
Collapse
Affiliation(s)
- Michiko M Nakano
- Institute of Environmental Health, Oregon Health & Science University, Portland, OR, 97239, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Nakayasu ES, Tempel R, Cambronne XA, Petyuk VA, Jones MB, Gritsenko MA, Monroe ME, Yang F, Smith RD, Adkins JN, Heffron F. Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection. Mol Cell Proteomics 2013; 12:3297-309. [PMID: 23970565 DOI: 10.1074/mcp.m113.029850] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Francisella tularensis is a facultative intracellular bacterium that causes the deadly disease tularemia. Most evidence suggests that Francisella is not well recognized by the innate immune system that normally leads to cytokine expression and cell death. In previous work, we identified new bacterial factors that were hyper-cytotoxic to macrophages. Four of the identified hyper-cytotoxic strains (lpcC, manB, manC, and kdtA) had an impaired lipopolysaccharide (LPS) synthesis and produced an exposed lipid A lacking the O-antigen. These mutants were not only hyper-cytotoxic but also were phagocytosed at much higher rates compared with the wild type parent strain. To elucidate the cellular signaling underlying this enhanced phagocytosis and cell death, we performed a large-scale comparative phosphoproteomic analysis of cells infected with wild-type and delta-lpcC F. novicida. Our data suggest that not only actin but also intermediate filaments and microtubules are important for F. novicida entry into the host cells. In addition, we observed differential phosphorylation of tristetraprolin, a key component of the mRNA-degrading machinery that controls the expression of a variety of genes including many cytokines. Infection with the delta-lpcC mutant induced the hyper-phosphorylation and inhibition of tristetraprolin, leading to the production of cytokines such as IL-1beta and TNF-alpha that may kill the host cells by triggering apoptosis. Together, our data provide new insights for Francisella invasion and a post-transcriptional mechanism that prevents the expression of host immune response factors that control infection by this pathogen.
Collapse
Affiliation(s)
- Ernesto S Nakayasu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Deatherage Kaiser BL, Li J, Sanford JA, Kim YM, Kronewitter SR, Jones MB, Peterson CT, Peterson SN, Frank BC, Purvine SO, Brown JN, Metz TO, Smith RD, Heffron F, Adkins JN. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection. PLoS One 2013; 8:e67155. [PMID: 23840608 PMCID: PMC3694140 DOI: 10.1371/journal.pone.0067155] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 05/14/2013] [Indexed: 11/25/2022] Open
Abstract
The potential for commensal microorganisms indigenous to a host (the ‘microbiome’ or ‘microbiota’) to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics “systems” approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), and commensal gut microorganisms during intestinal infection with S. Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the infected 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and disrupting the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while promoting growth of Salmonella and Enterococcus). Alteration of the host microbiome population structure was highly correlated with gut environmental changes, including the accumulation of metabolites normally consumed by commensal microbiota. Finally, the less characterized phase of S. Typhimurium’s lifecycle was investigated, and both proteomic and glycomic evidence suggests S. Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut. The application of multiple omics measurements to Salmonella-induced intestinal inflammation provides insights into complex molecular strategies employed during pathogenesis between host, pathogen, and the microbiome.
Collapse
Affiliation(s)
- Brooke L. Deatherage Kaiser
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jie Li
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - James A. Sanford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Scott R. Kronewitter
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Marcus B. Jones
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Christine T. Peterson
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Scott N. Peterson
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Bryan C. Frank
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Joseph N. Brown
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| |
Collapse
|
25
|
Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong C, Hyduke DR, Metz TO, Adkins JN. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Mol Biosyst 2013; 9:1522-34. [PMID: 23559334 PMCID: PMC3665296 DOI: 10.1039/c3mb25598k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative pathogen that uses complex mechanisms to invade and proliferate within mammalian host cells. To investigate possible contributions of metabolic processes to virulence in S. Typhimurium grown under conditions known to induce expression of virulence genes, we used a metabolomics-driven systems biology approach coupled with genome-scale modeling. First, we identified distinct metabolite profiles associated with bacteria grown in either rich or virulence-inducing media and report the most comprehensive coverage of the S. Typhimurium metabolome to date. Second, we applied an omics-informed genome-scale modeling analysis of the functional consequences of adaptive alterations in S. Typhimurium metabolism during growth under our conditions. Modeling efforts highlighted a decreased cellular capability to both produce and utilize intracellular amino acids during stationary phase culture in virulence conditions, despite significant abundance increases for these molecules as observed by our metabolomics measurements. Furthermore, analyses of omics data in the context of the metabolic model indicated rewiring of the metabolic network to support pathways associated with virulence. For example, cellular concentrations of polyamines were perturbed, as well as the predicted capacity for secretion and uptake.
Collapse
Affiliation(s)
- Young-Mo Kim
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Brian J. Schmidt
- Department of Bioengineering, University of California at San Diego, San Diego, CA 92093
| | - Afshan S. Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239
| | | | - Brooke L. Deatherage Kaiser
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Heather M. Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Hugh D. Mitchell
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California at San Diego, San Diego, CA 92093
| | - Jason E. McDermott
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239
| | - Richard D. Smith
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | | | - Charles Ansong
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Daniel R. Hyduke
- Department of Bioengineering, University of California at San Diego, San Diego, CA 92093
| | - Thomas O. Metz
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Joshua N. Adkins
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352
| |
Collapse
|
26
|
Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN. Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling. Curr Top Microbiol Immunol 2013; 363:21-41. [PMID: 22886542 DOI: 10.1007/82_2012_247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Salmonella and Yersinia are two distantly related genera containing species with wide host-range specificity and pathogenic capacity. The metabolic complexity of these organisms facilitates robust lifestyles both outside of and within animal hosts. Using a pathogen-centric systems biology approach, we are combining a multi-omics (transcriptomics, proteomics, metabolomics) strategy to define properties of these pathogens under a variety of conditions including those that mimic the environments encountered during pathogenesis. These high-dimensional omics datasets are being integrated in selected ways to improve genome annotations, discover novel virulence-related factors, and model growth under infectious states. We will review the evolving technological approaches toward understanding complex microbial life through multi-omic measurements and integration, while highlighting some of our most recent successes in this area.
Collapse
Affiliation(s)
- Charles Ansong
- Biological Separations and Mass Spectroscopy Group, Pacific Northwest National Laboratory, PO Box 999, MSIN: K8-98, Richland, WA, 99352, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, Cho H, Brugarolas P, Gao YN, Peterson SN, Lan L, Bae T, He C. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proc Natl Acad Sci U S A 2013; 110:5010-5. [PMID: 23479646 PMCID: PMC3612684 DOI: 10.1073/pnas.1219446110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Quinone molecules are intracellular electron-transport carriers, as well as critical intra- and extracellular signals. However, transcriptional regulation of quinone signaling and its molecular basis are poorly understood. Here, we identify a thiol-stress-sensing regulator YodB family transcriptional regulator as a central component of quinone stress response of Staphylococcus aureus, which we have termed the quinone-sensing and response repressor (QsrR). We also identify and confirm an unprecedented quinone-sensing mechanism based on the S-quinonization of the essential residue Cys-5. Structural characterizations of the QsrR-DNA and QsrR-menadione complexes further reveal that the covalent association of menadione directly leads to the release of QsrR from operator DNA following a 10° rigid-body rotation as well as a 9-Å elongation between the dimeric subunits. The molecular level characterization of this quinone-sensing transcriptional regulator provides critical insights into quinone-mediated gene regulation in human pathogens.
Collapse
Affiliation(s)
- Quanjiang Ji
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Liang Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Marcus B. Jones
- Infectious Disease Group, Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850
| | - Fei Sun
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Xin Deng
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Haihua Liang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Hoonsik Cho
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | - Pedro Brugarolas
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Yihe N. Gao
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| | - Scott N. Peterson
- Infectious Disease Group, Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD 20850
| | - Lefu Lan
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408; and
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
| |
Collapse
|
28
|
Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim YM, McAteer K, Deatherage Kaiser BL, Dubois JL, Brewer HM, Frank BC, McDermott JE, Metz TO, Peterson SN, Smith RD, Motin VL, Adkins JN. A multi-omic systems approach to elucidating Yersinia virulence mechanisms. Mol Biosyst 2012; 9:44-54. [PMID: 23147219 DOI: 10.1039/c2mb25287b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The underlying mechanisms that lead to dramatic differences between closely related pathogens are not always readily apparent. For example, the genomes of Yersinia pestis (YP) the causative agent of plague with a high mortality rate and Yersinia pseudotuberculosis (YPT) an enteric pathogen with a modest mortality rate are highly similar with some species specific differences; however the molecular causes of their distinct clinical outcomes remain poorly understood. In this study, a temporal multi-omic analysis of YP and YPT at physiologically relevant temperatures was performed to gain insights into how an acute and highly lethal bacterial pathogen, YP, differs from its less virulent progenitor, YPT. This analysis revealed higher gene and protein expression levels of conserved major virulence factors in YP relative to YPT, including the Yop virulon and the pH6 antigen. This suggests that adaptation in the regulatory architecture, in addition to the presence of unique genetic material, may contribute to the increased pathogenecity of YP relative to YPT. Additionally, global transcriptome and proteome responses of YP and YPT revealed conserved post-transcriptional control of metabolism and the translational machinery including the modulation of glutamate levels in Yersiniae. Finally, the omics data was coupled with a computational network analysis, allowing an efficient prediction of novel Yersinia virulence factors based on gene and protein expression patterns.
Collapse
Affiliation(s)
- Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, P. O. Box 999, Richland, WA 99352, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Jeong DW, Cho H, Jones MB, Shatzkes K, Sun F, Ji Q, Liu Q, Peterson SN, He C, Bae T. The auxiliary protein complex SaePQ activates the phosphatase activity of sensor kinase SaeS in the SaeRS two-component system of Staphylococcus aureus. Mol Microbiol 2012; 86:331-48. [PMID: 22882143 DOI: 10.1111/j.1365-2958.2012.08198.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2012] [Indexed: 12/21/2022]
Abstract
In bacterial two-component regulatory systems (TCSs), dephosphorylation of phosphorylated response regulators is essential for resetting the activated systems to the pre-activation state. However, in the SaeRS TCS, a major virulence TCS of Staphylococcus aureus, the mechanism for dephosphorylation of the response regulator SaeR has not been identified. Here we report that two auxiliary proteins from the sae operon, SaeP and SaeQ, form a protein complex with the sensor kinase SaeS and activate the sensor kinase's phosphatase activity. Efficient activation of the phosphatase activity required the presence of both SaeP and SaeQ. When SaeP and SaeQ were ectopically expressed, the expression of coagulase, a sae target with low affinity for phosphorylated SaeR, was greatly reduced, while the expression of alpha-haemolysin, a sae target with high affinity for phosphorylated SaeR, was not, demonstrating a differential effect of SaePQ on sae target gene expression. When expression of SaePQ was abolished, most sae target genes were induced at an elevated level. Since the expression of SaeP and SaeQ is induced by the SaeRS TCS, these results suggest that the SaeRS TCS returns to the pre-activation state by a negative feedback mechanism.
Collapse
Affiliation(s)
- Do-Won Jeong
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol 2012; 8:558. [PMID: 22735334 PMCID: PMC3397418 DOI: 10.1038/msb.2012.21] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 05/09/2012] [Indexed: 12/11/2022] Open
Abstract
Macrophages are central players in immune response, manifesting divergent phenotypes to control inflammation and innate immunity through release of cytokines and other signaling factors. Recently, the focus on metabolism has been reemphasized as critical signaling and regulatory pathways of human pathophysiology, ranging from cancer to aging, often converge on metabolic responses. Here, we used genome-scale modeling and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to assess metabolic features that are critical for macrophage activation. We constructed a genome-scale metabolic network for the RAW 264.7 cell line to determine metabolic modulators of activation. Metabolites well-known to be associated with immunoactivation (glucose and arginine) and immunosuppression (tryptophan and vitamin D3) were among the most critical effectors. Intracellular metabolic mechanisms were assessed, identifying a suppressive role for de-novo nucleotide synthesis. Finally, underlying metabolic mechanisms of macrophage activation are identified by analyzing multi-omic data obtained from LPS-stimulated RAW cells in the context of our flux-based predictions. Our study demonstrates metabolism's role in regulating activation may be greater than previously anticipated and elucidates underlying connections between activation and metabolic effectors.
Collapse
Affiliation(s)
- Aarash Bordbar
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Monica L Mo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Bryan C Frank
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Daniel R Hyduke
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
31
|
Schrimpe-Rutledge AC, Jones MB, Chauhan S, Purvine SO, Sanford JA, Monroe ME, Brewer HM, Payne SH, Ansong C, Frank BC, Smith RD, Peterson SN, Motin VL, Adkins JN. Comparative omics-driven genome annotation refinement: application across Yersiniae. PLoS One 2012; 7:e33903. [PMID: 22479471 PMCID: PMC3313959 DOI: 10.1371/journal.pone.0033903] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/19/2012] [Indexed: 02/03/2023] Open
Abstract
Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes) protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.
Collapse
Affiliation(s)
| | - Marcus B. Jones
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Sadhana Chauhan
- University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - James A. Sanford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Heather M. Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Samuel H. Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bryan C. Frank
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Scott N. Peterson
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Vladimir L. Motin
- University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| |
Collapse
|
32
|
Sun F, Ji Q, Jones MB, Deng X, Liang H, Frank B, Telser J, Peterson SN, Bae T, He C. AirSR, a [2Fe-2S] cluster-containing two-component system, mediates global oxygen sensing and redox signaling in Staphylococcus aureus. J Am Chem Soc 2011; 134:305-14. [PMID: 22122613 DOI: 10.1021/ja2071835] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Oxygen sensing and redox signaling significantly affect bacterial physiology and host-pathogen interaction. Here we show that a Staphylococcus aureus two-component system, AirSR (anaerobic iron-sulfur cluster-containing redox sensor regulator, formerly YhcSR), responds to oxidation signals (O(2), H(2)O(2), NO, etc) by using a redox-active [2Fe-2S] cluster in the sensor kinase AirS. Mutagenesis studies demonstrate that the [2Fe-2S] cluster is essential for the kinase activity of AirS. We have also discovered that a homologue of IscS (SA1450) in S. aureus is active as a cysteine desulfurase, which enables the in vitro reconstitution of the [2Fe-2S] cluster in AirS. Phosphorylation assays show that the oxidized AirS with a [2Fe-2S](2+) cluster is the fully active form of the kinase but not the apo-AirS nor the reduced AirS possessing a [2Fe-2S](+) cluster. Overoxidation by prolonged exposure to O(2) or contact with H(2)O(2) or NO led to inactivation of AirS. Transcriptome analysis revealed that mutation of airR impacts the expression of ~355 genes under anaerobic conditions. Moreover, the mutant strain displayed increased resistance toward H(2)O(2), vancomycin, norfloxacin, and ciprofloxacin under anaerobic conditions. Together, our results show that S. aureus AirSR is a redox-dependent global regulatory system that plays important roles in gene regulation using a redox active Fe-S cluster under O(2)-limited conditions.
Collapse
Affiliation(s)
- Fei Sun
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Szkotak R, Niepa THR, Jawrani N, Gilbert JL, Jones MB, Ren D. Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis. AMB Express 2011; 1:39. [PMID: 22078549 PMCID: PMC3294250 DOI: 10.1186/2191-0855-1-39] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 11/11/2011] [Indexed: 12/22/2022] Open
Abstract
With the emergence and spread of multidrug resistant bacteria, effective methods to eliminate both planktonic bacteria and those embedded in surface-attached biofilms are needed. Electric currents at μA-mA/cm2 range are known to reduce the viability of bacteria. However, the mechanism of such effects is still not well understood. In this study, Bacillus subtilis was used as the model Gram-positive species to systematically investigate the effects of electrochemical currents on bacteria including the morphology, viability, and gene expression of planktonic cells, and viability of biofilm cells. The data suggest that weak electrochemical currents can effectively eliminate B. subtilis both as planktonic cells and in biofilms. DNA microarray results indicate that the genes associated with oxidative stress response, nutrient starvation, and membrane functions were induced by electrochemical currents. These findings suggest that ions and oxidative species generated by electrochemical reactions might be important for the killing effects of these currents.
Collapse
Affiliation(s)
- Robert Szkotak
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Tagbo H R Niepa
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Nikhil Jawrani
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Jeremy L Gilbert
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | | | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244, USA
| |
Collapse
|
34
|
Arpaia N, Godec J, Lau L, Sivick KE, McLaughlin LM, Jones MB, Dracheva T, Peterson SN, Monack DM, Barton GM. TLR signaling is required for Salmonella typhimurium virulence. Cell 2011; 144:675-88. [PMID: 21376231 DOI: 10.1016/j.cell.2011.01.031] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 12/06/2010] [Accepted: 01/10/2011] [Indexed: 01/02/2023]
Abstract
Toll-like receptors (TLRs) contribute to host resistance to microbial pathogens and can drive the evolution of virulence mechanisms. We have examined the relationship between host resistance and pathogen virulence using mice with a functional allele of the nramp-1 gene and lacking combinations of TLRs. Mice deficient in both TLR2 and TLR4 were highly susceptible to the intracellular bacterial pathogen Salmonella typhimurium, consistent with reduced innate immune function. However, mice lacking additional TLRs involved in S. typhimurium recognition were less susceptible to infection. In these TLR-deficient cells, bacteria failed to upregulate Salmonella pathogenicity island 2 (SPI-2) genes and did not form a replicative compartment. We demonstrate that TLR signaling enhances the rate of acidification of the Salmonella-containing phagosome, and inhibition of this acidification prevents SPI-2 induction. Our results indicate that S. typhimurium requires cues from the innate immune system to regulate virulence genes necessary for intracellular survival, growth, and systemic infection.
Collapse
Affiliation(s)
- Nicholas Arpaia
- Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Jones MB, Peterson SN, Benn R, Braisted JC, Jarrahi B, Shatzkes K, Ren D, Wood TK, Blaser MJ. Role of luxS in Bacillus anthracis growth and virulence factor expression. Virulence 2011; 1:72-83. [PMID: 21178420 DOI: 10.4161/viru.1.2.10752] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Quorum-sensing (QS), the regulation of bacterial gene expression in response to changes in cell density, involves pathways that synthesize signaling molecules (auto-inducers). The luxS/AI-2-mediated QS system has been identified in both gram-positive and gram-negative bacteria. Bacillus anthracis, the etiological agent of anthrax, possesses genes involved in luxS/AI-2-mediated QS, and deletion of luxS in B. anthracis Sterne strain 34F2 results in inhibition of AI-2 synthesis and a growth defect. In the present study, we created a ΔluxS B. anthracis strain complemented in trans by insertion of a cassette, including luxS and a gene encoding erythromycin resistance, into the truncated plcR regulator locus. The complemented ΔluxS strain has restored AI-2 synthesis and wild-type growth. A B. anthracis microarray study revealed consistent differential gene expression between the wild-type and ΔluxS strain, including downregulation of the B. anthracis S-layer protein gene EA1 and pXO1 virulence genes. These data indicate that B. anthracis may use luxS/AI-2-mediated QS to regulate growth, density-dependent gene expression and virulence factor expression.
Collapse
Affiliation(s)
- Marcus B Jones
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, MD, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Jones MB, Peterson SN, Benn R, Braisted JC, Jarrahi B, Shatzkes K, Ren D, Wood TK, Blaser MJ. Erratum to: Role of luxSin Bacillus anthracisgrowth and virulence factor expression. Virulence 2011. [DOI: 10.4161/viru.2.2.15095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
37
|
Festa RA, Jones MB, Butler-Wu S, Sinsimer D, Gerads R, Bishai WR, Peterson SN, Darwin KH. A novel copper-responsive regulon in Mycobacterium tuberculosis. Mol Microbiol 2010; 79:133-48. [PMID: 21166899 DOI: 10.1111/j.1365-2958.2010.07431.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this work we describe the identification of a copper-inducible regulon in Mycobacterium tuberculosis (Mtb). Among the regulated genes was Rv0190/MT0200, a paralogue of the copper metalloregulatory repressor CsoR. The five-locus regulon, which includes a gene that encodes the copper-protective metallothionein MymT, was highly induced in wild-type Mtb treated with copper, and highly expressed in an Rv0190/MT0200 mutant. Importantly, the Rv0190/MT0200 mutant was hyper-resistant to copper. The promoters of all five loci share a palindromic motif that was recognized by the gene product of Rv0190/MT0200. For this reason we named Rv0190/MT0200 RicR for regulated in copper repressor. Intriguingly, several of the RicR-regulated genes, including MymT, are unique to pathogenic Mycobacteria. The identification of a copper-responsive regulon specific to virulent mycobacterial species suggests copper homeostasis must be maintained during an infection. Alternatively, copper may provide a cue for the expression of genes unrelated to metal homeostasis, but nonetheless necessary for survival in a host.
Collapse
Affiliation(s)
- Richard A Festa
- New York University School of Medicine, Department of Microbiology, 550 First Avenue MSB 236, New York, NY 10016, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Safi H, Fleischmann RD, Peterson SN, Jones MB, Jarrahi B, Alland D. Allelic exchange and mutant selection demonstrate that common clinical embCAB gene mutations only modestly increase resistance to ethambutol in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2010; 54:103-8. [PMID: 19822701 PMCID: PMC2798522 DOI: 10.1128/aac.01288-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 10/07/2009] [Indexed: 11/20/2022] Open
Abstract
Mutations within codon 306 of the Mycobacterium tuberculosis embB gene modestly increase ethambutol (EMB) MICs. To identify other causes of EMB resistance and to identify causes of high-level resistance, we generated EMB-resistant M. tuberculosis isolates in vitro and performed allelic exchange studies of embB codon 406 (embB406) and embB497 mutations. In vitro selection produced mutations already identified clinically in embB306, embB397, embB497, embB1024, and embC13, which result in EMB MICs of 8 or 14 microg/ml, 5 microg/ml, 12 microg/ml, 3 microg/ml, and 4 microg/ml, respectively, and mutations at embB320, embB324, and embB445, which have not been identified in clinical M. tuberculosis isolates and which result in EMB MICs of 8 microg/ml, 8 microg/ml, and 2 to 8 microg/ml, respectively. To definitively identify the effect of the common clinical embB497 and embB406 mutations on EMB susceptibility, we created a series of isogenic mutants, exchanging the wild-type embB497 CAG codon in EMB-susceptible M. tuberculosis strain 210 for the embB497 CGG codon and the wild-type embB406 GGC codon for either the embB406 GCC, embB406 TGC, embB406 TCC, or embB406 GAC codon. These new mutants showed 6-fold and 3- to 3.5-fold increases in the EMB MICs, respectively. In contrast to the embB306 mutants, the isogenic embB497 and embB406 mutants did not have preferential growth in the presence of isoniazid or rifampin (rifampicin) at their MICs. These results demonstrate that individual embCAB mutations confer low to moderate increases in EMB MICs. Discrepancies between the EMB MICs of laboratory mutants and clinical M. tuberculosis strains with identical mutations suggest that clinical EMB resistance is multigenic and that high-level EMB resistance requires mutations in currently unknown loci.
Collapse
Affiliation(s)
- Hassan Safi
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, Pathogen Functional Genomics Center, J. Craig Venter Institute, Rockville, Maryland 20850
| | - Robert D. Fleischmann
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, Pathogen Functional Genomics Center, J. Craig Venter Institute, Rockville, Maryland 20850
| | - Scott N. Peterson
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, Pathogen Functional Genomics Center, J. Craig Venter Institute, Rockville, Maryland 20850
| | - Marcus B. Jones
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, Pathogen Functional Genomics Center, J. Craig Venter Institute, Rockville, Maryland 20850
| | - Behnam Jarrahi
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, Pathogen Functional Genomics Center, J. Craig Venter Institute, Rockville, Maryland 20850
| | - David Alland
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, Pathogen Functional Genomics Center, J. Craig Venter Institute, Rockville, Maryland 20850
| |
Collapse
|
39
|
Perry JA, Jones MB, Peterson SN, Cvitkovitch DG, Lévesque CM. Peptide alarmone signalling triggers an auto-active bacteriocin necessary for genetic competence. Mol Microbiol 2009; 72:905-17. [PMID: 19400789 DOI: 10.1111/j.1365-2958.2009.06693.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co-ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress-induced expression of the peptide pheromone competence-stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP-induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the 'death effector'. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness-enhancing genes in the oral biofilm.
Collapse
Affiliation(s)
- Julie A Perry
- Dental Research Institute, Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | | | | | | | | |
Collapse
|
40
|
Colangeli R, Helb D, Vilchèze C, Hazbón MH, Lee CG, Safi H, Sayers B, Sardone I, Jones MB, Fleischmann RD, Peterson SN, Jacobs WR, Alland D. Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis. PLoS Pathog 2007; 3:e87. [PMID: 17590082 PMCID: PMC1894825 DOI: 10.1371/journal.ppat.0030087] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 05/10/2007] [Indexed: 12/31/2022] Open
Abstract
Multi-drug tolerance is a key phenotypic property that complicates the sterilization of mammals infected with Mycobacterium tuberculosis. Previous studies have established that iniBAC, an operon that confers multi-drug tolerance to M. bovis BCG through an associated pump-like activity, is induced by the antibiotics isoniazid (INH) and ethambutol (EMB). An improved understanding of the functional role of antibiotic-induced genes and the regulation of drug tolerance may be gained by studying the factors that regulate antibiotic-mediated gene expression. An M. smegmatis strain containing a lacZ gene fused to the promoter of M. tuberculosis iniBAC (PiniBAC) was subjected to transposon mutagenesis. Mutants with constitutive expression and increased EMB-mediated induction of PiniBAC::lacZ mapped to the lsr2 gene (MSMEG6065), a small basic protein of unknown function that is highly conserved among mycobacteria. These mutants had a marked change in colony morphology and generated a new polar lipid. Complementation with multi-copy M. tuberculosis lsr2 (Rv3597c) returned PiniBAC expression to baseline, reversed the observed morphological and lipid changes, and repressed PiniBAC induction by EMB to below that of the control M. smegmatis strain. Microarray analysis of an lsr2 knockout confirmed upregulation of M. smegmatis iniA and demonstrated upregulation of genes involved in cell wall and metabolic functions. Fully 121 of 584 genes induced by EMB treatment in wild-type M. smegmatis were upregulated (“hyperinduced”) to even higher levels by EMB in the M. smegmatis lsr2 knockout. The most highly upregulated genes and gene clusters had adenine-thymine (AT)–rich 5-prime untranslated regions. In M. tuberculosis, overexpression of lsr2 repressed INH-mediated induction of all three iniBAC genes, as well as another annotated pump, efpA. The low molecular weight and basic properties of Lsr2 (pI 10.69) suggested that it was a histone-like protein, although it did not exhibit sequence homology with other proteins in this class. Consistent with other histone-like proteins, Lsr2 bound DNA with a preference for circular DNA, forming large oligomers, inhibited DNase I activity, and introduced a modest degree of supercoiling into relaxed plasmids. Lsr2 also inhibited in vitro transcription and topoisomerase I activity. Lsr2 represents a novel class of histone-like proteins that inhibit a wide variety of DNA-interacting enzymes. Lsr2 appears to regulate several important pathways in mycobacteria by preferentially binding to AT-rich sequences, including genes induced by antibiotics and those associated with inducible multi-drug tolerance. An improved understanding of the role of lsr2 may provide important insights into the mechanisms of action of antibiotics and the way that mycobacteria adapt to stresses such as antibiotic treatment. Understanding the cellular processes stimulated when Mycobacterium tuberculosis is treated with antibiotics may provide clues as to why months of therapy and use of several drugs simultaneously are required to prevent antibiotic resistance. Antibiotic treatment “turns on” or induces certain M. tuberculosis genes. These genes are of special interest because they appear to help M. tuberculosis survive the stress of antibiotic treatment. Our study of the regulation of antibiotic-induced genes, including iniBAC, in two mycobacterial species revealed that a small protein called Lsr2 controls iniBAC and other antibiotic-induced genes, especially ones related to the cell wall. Lsr2 binds to DNA in a relatively non-specific manner and appears to inhibit certain enzymes that must interact with DNA as part of their function. These properties differentiate Lsr2 from classical regulators of gene expression that bind to specific DNA sequences, and suggest that Lsr2 is a novel histone-like protein. These proteins regulate genes by changing the way DNA is shaped, and, indeed, we found that Lsr2 can change the shape of DNA by introducing a small number of coils into its structure. Our results suggest that Lsr2 is a major regulator of antibiotic-induced responses in mycobacteria.
Collapse
Affiliation(s)
- Roberto Colangeli
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Gold JA, Hoshino Y, Jones MB, Hoshino S, Nolan A, Weiden MD. Exogenous interferon-alpha and interferon-gamma increase lethality of murine inhalational anthrax. PLoS One 2007; 2:e736. [PMID: 17710136 PMCID: PMC1937023 DOI: 10.1371/journal.pone.0000736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 07/16/2007] [Indexed: 01/14/2023] Open
Abstract
Background Bacillus anthracis, the etiologic agent of inhalational anthrax, is a facultative intracellular pathogen. Despite appropriate antimicrobial therapy, the mortality from inhalational anthrax approaches 45%, underscoring the need for better adjuvant therapies. The variable latency between exposure and development of disease suggests an important role for the host's innate immune response. Type I and Type II Interferons (IFN) are prominent members of the host innate immune response and are required for control of intracellular pathogens. We have previously described a protective role for exogenous Type I and Type II IFNs in attenuating intracellular B.anthracis germination and macrophage cell death in vitro. Methodology and Principal Findings We sought to extend these findings in an in vivo model of inhalational anthrax, utilizing the Sterne strain (34F2) of B.anthracis. Mice devoid of STAT1, a component of IFN-α and IFN-γ signaling, had a trend towards increased mortality, bacterial germination and extrapulmonary spread of B.anthracis at 24 hrs. This was associated with impaired IL-6, IL-10 and IL-12 production. However, administration of exogenous IFN-γ, and to a lesser extent IFN-α, at the time of infection, markedly increased lethality. While IFNs were able to reduce the fraction of germinated spores within the lung, they increased both the local and systemic inflammatory response manifest by increases in IL-12 and reductions in IL-10. This was associated with an increase in extrapulmonary dissemination. The mechanism of IFN mediated inflammation appears to be in part due to STAT1 independent signaling. Conclusions In conclusion, while endogenous IFNs are essential for control of B.anthracis germination and lethality, administration of exogenous IFNs appear to increase the local inflammatory response, thereby increasing mortality.
Collapse
Affiliation(s)
- Jeffrey A Gold
- Division of Pulmonary and Critical Care Medicine, Oregon Health and Sciences University, Portland, Oregon, United States of America.
| | | | | | | | | | | |
Collapse
|
42
|
Cirz RT, Jones MB, Gingles NA, Minogue TD, Jarrahi B, Peterson SN, Romesberg FE. Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin. J Bacteriol 2006; 189:531-9. [PMID: 17085555 PMCID: PMC1797410 DOI: 10.1128/jb.01464-06] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Staphylococcus aureus infections can be difficult to treat due to both multidrug resistance and the organism's remarkable ability to persist in the host. Persistence and the evolution of resistance may be related to several complex regulatory networks, such as the SOS response, which modifies transcription in response to environmental stress. To understand how S. aureus persists during antibiotic therapy and eventually emerges resistant, we characterized its global transcriptional response to ciprofloxacin. We found that ciprofloxacin induces prophage mobilization as well as significant alterations in metabolism, most notably the up-regulation of the tricarboxylic acid cycle. In addition, we found that ciprofloxacin induces the SOS response, which we show, by comparison of a wild-type strain and a non-SOS-inducible lexA mutant strain, includes the derepression of 16 genes. While the SOS response of S. aureus is much more limited than those of Escherichia coli and Bacillus subtilis, it is similar to that of Pseudomonas aeruginosa and includes RecA, LexA, several hypothetical proteins, and a likely error-prone Y family polymerase whose homologs in other bacteria are required for induced mutation. We also examined induced mutation and found that either the inability to derepress the SOS response or the lack of the LexA-regulated polymerase renders S. aureus unable to evolve antibiotic resistance in vitro in response to UV damage. The data suggest that up-regulation of the tricarboxylic acid cycle and induced mutation facilitate S. aureus persistence and evolution of resistance during antibiotic therapy.
Collapse
Affiliation(s)
- Ryan T Cirz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
This paper investigates the effect of surfactants during tear film deposition and subsequent thinning. The surfactants occur naturally on the surface of the tear film in the form of a lipid layer. A lubrication model is developed that describes lipid spreading and film height evolution. It is shown that lipids may play an important role in drawing the tear film up the cornea during the opening phase of the blink. Further, nonuniform distributions of lipids may lead to a rapid thinning of the tear film behind the advancing lipid front (shock). Experiments using a fluorescein dye technique and using a tearscope were undertaken in order to visualise the motion of the lipid layer and any associated shocks immediately after a blink. It is found that the lipid layer continues to spread upwards on the cornea after the opening phase of the blink, in agreement with the model. Using the experimental data, lipid particles were tracked in order to determine the surface velocity and these results are compared to the model predictions.
Collapse
Affiliation(s)
- M B Jones
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
| | | | | | | | | |
Collapse
|
44
|
Bjørnstad A, Larsen BK, Skadsheim A, Jones MB, Andersen OK. The potential of ecotoxicoproteomics in environmental monitoring: biomarker profiling in mussel plasma using ProteinChip array technology. J Toxicol Environ Health A 2006; 69:77-96. [PMID: 16291563 DOI: 10.1080/15287390500259277] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
New global technologies, allowing simultaneous analysis of thousands of genes, proteins, and metabolites (so-called "omics" technologies), are being adopted rapidly by industry, academia, and regulatory agencies. This study evaluated the potential of proteomics in ecotoxicological research (i.e., ecotoxicoproteomics). Filter-feeding mussels (Mytilus edulis) were exposed continuously for 3 wk to oil, or oil spiked with alkylphenols and extra polycyclic aromatic hydrocarbons. The influence of chronic exposure on mussel plasma protein expression was investigated utilizing ProteinChip array technology in combination with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF MS). Results indicated that exposure to spiked oil had a more significant effect on protein expression in mussels than oil alone. In total, 83 mass peaks (intact or modified proteins/peptides) were significantly altered by spiked oil, while 49 were altered by oil. In exposed organisms, the majority of peaks were upregulated compared to controls (i.e., 69% in oil and 71% in spiked oil). Some peaks (32 in total) were affected by both treatments; however, the degree of response was higher in the spiked oil group for 25 of the 32 commonly affected features. Additionally, certain peaks revealed exposure- or gender-specific responses. Multivariate analysis with regression tree-based methods detected protein patterns associated with exposure that correctly classified masked samples with 90-95% accuracy. Similarly, 92% of females and 85% of males were correctly classified (independent of exposure). Results indicate that proteomics have the potential to make a valuable contribution to environmental monitoring and risk assessment.
Collapse
|
45
|
Abstract
This paper investigates the deposition of the tear film on the cornea of the human eye. The tear film is laid down by the motion of the upper eyelid and then subsequently flows and thins. Of particular interest is the stability of the tear layer and the development of dry patches on the cornea. While there has been significant research on the behaviour of tear films between blinks, this paper focuses on understanding the mechanisms which control the shape and thickness of the deposited film and how this affects the subsequent film behaviour. Numerical and analytical methods are applied to a lubrication model which includes the effects of surface tension, viscosity, gravity and evaporation. The model reveals the importance of the eyelid velocity, motion of the surface lipid layer and the storage of tear film between blinks.
Collapse
Affiliation(s)
- M B Jones
- School of Mathematical Sciences, Queensland University of Technology, Australia.
| | | | | | | | | | | |
Collapse
|
46
|
Warren R, Bauer A, Greif C, Wigger-Alberti W, Jones MB, Roddy MT, Seymour JL, Hansmann MA, Elsner P. Transepidermal Water Loss Dynamics of Human Vulvar and Thigh Skin. Skin Pharmacol Physiol 2005; 18:139-43. [PMID: 15897686 DOI: 10.1159/000084911] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2004] [Accepted: 12/12/2004] [Indexed: 11/19/2022]
Abstract
Refinement in procedures to assess skin surface water loss (SSWL) dynamics of the vulvar skin on a large sample of subjects (60) is described and compared to another semi-occluded skin site, the inner thigh. Vulvar SSWL significantly decreased over a 30-min period from 46.2 +/- 2.6 (SE) to 24.7 +/- 1.6 g m(-2) h (p < 0.001). The inner thigh, another semi-occluded region, showed no similar pattern for SSWL (6.2 +/- 0.3 to 6.6 +/- 0.5 g m(-2) h), and the values were significantly less than those for vulvar skin. There was no significant effect of age, body mass index or atopic status on vulvar SSWL.
Collapse
Affiliation(s)
- R Warren
- Winton Hill Technical Center Feminine Care, Procter and Gamble Company, Cincinnati, OH 45224, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Jones MB, Jani R, Ren D, Wood TK, Blaser MJ. Inhibition of Bacillus anthracis growth and virulence-gene expression by inhibitors of quorum-sensing. J Infect Dis 2005; 191:1881-8. [PMID: 15871122 DOI: 10.1086/429696] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 12/17/2004] [Indexed: 11/03/2022] Open
Abstract
Density-dependent gene expression, quorum sensing (QS), involves the synthesis and detection of low-molecular-weight molecules known as autoinducers. Inhibitors of bacterial QS systems offer potential treatment of infections with highly virulent or multidrug-resistant agents. We studied the effects on Bacillus anthracis growth and the virulence gene (pagA, lef, and cya) expression of the QS inhibitor (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone, which is naturally synthesized by the marine alga Delisea pulchra, as well as a related compound and synthetic derivatives. Growth of B. anthracis Sterne strain was substantially reduced in the presence of each furanone in a dose-dependent manner. When furanones were added to midlog-phase cultures of B. anthracis strains with LacZ reporters in pagA, lef, or cya, growth was inhibited, and expression of these virulence genes was inhibited to a proportionately greater extent. These data suggest that use of QS inhibitors could represent novel therapies for anthrax.
Collapse
Affiliation(s)
- Marcus B Jones
- Department of Microbiology, Sackler Institute, and Department of Medicine, New York University School of Medicine, New York, New York 10016, USA.
| | | | | | | | | |
Collapse
|
48
|
Abstract
The effect of temperature on the heart rate (fH) of Carcinus maenas exposed to a sublethal nominal concentration (0.5 mg l(-1)) of copper is reported. Adult, intermoult males (4 cm carapace width) were collected from Stavanger Fjord (Norway) in August (seawater TEMPERATURE=17 degrees C) and maintained in the laboratory (fed ad libitum) at 5, 15 and 25 degrees C for 7 days. Following this holding period, crabs were exposed to waterborne copper at the same temperature. After 3 days of exposure, individual fH was measured using the non-invasive Computer Aided Physiological MONitoring system (CAPMON) method. Copper-exposed individuals demonstrated significantly increased fH compared with controls at 5 and 25 degrees C (P<0.01). It is inferred that physiological function in C. maenas may be more vulnerable to copper contamination at seasonal temperature extremes (5 and 25 degrees C) than at the 'standard' test temperature (15 degrees C). Additionally, cardiac arrest observed at 5 degrees C is interpreted as a physiological response to limit copper uptake while the erratic fH in the 25 degrees C group reflected enhanced copper toxicity.
Collapse
Affiliation(s)
- L Camus
- School of Biological Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, UK.
| | | | | | | |
Collapse
|
49
|
Gold JA, Hoshino Y, Hoshino S, Jones MB, Nolan A, Weiden MD. Exogenous gamma and alpha/beta interferon rescues human macrophages from cell death induced by Bacillus anthracis. Infect Immun 2004; 72:1291-7. [PMID: 14977930 PMCID: PMC356021 DOI: 10.1128/iai.72.3.1291-1297.2004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
During the recent bioterrorism-related outbreaks, inhalational anthrax had a 45% mortality in spite of appropriate antimicrobial therapy, underscoring the need for better adjuvant therapies. The variable latency between exposure and development of disease suggests an important role for the host's innate immune response. Alveolar macrophages are likely the first immune cells exposed to inhalational anthrax, and the interferon (IFN) response of these cells comprises an important arm of the host innate immune response to intracellular infection with Bacillus anthracis. Furthermore, IFNs have been used as immunoadjuvants for treatment of another intracellular pathogen, Mycobacterium tuberculosis. We established a model of B. anthracis infection with the Sterne strain (34F(2)) which contains lethal toxin (LeTx). 34F(2) was lethal to murine and human macrophages. Treatment with IFNs significantly improved cell viability and reduced the number of germinated intracellular spores. Infection with 34F(2) failed to induce the latent transcription factors signal transducer and activators of transcription 1 (STAT1) and ISGF-3, which are central to the IFN response. Furthermore, 34F(2) reduced STAT1 activation in response to exogenous alpha/beta IFN, suggesting direct inhibition of IFN signaling. Even though 34F(2) has LeTx, there was no mitogen-activated protein kinase kinase 3 cleavage and p38 was normally induced, suggesting that these early effects of B. anthracis infection in macrophages are independent of LeTx. These data suggest an important role for both IFNs in the control of B. anthracis and the potential benefit of using exogenous IFN as an immunoadjuvant therapy.
Collapse
Affiliation(s)
- Jeffrey A Gold
- Division of Pulmonary and Critical Care Medicine, Sackler Institute of Biomedical Studies, New York University School of Medicine, New York, New York 10016, USA
| | | | | | | | | | | |
Collapse
|
50
|
Brown RJ, Galloway TS, Lowe D, Browne MA, Dissanayake A, Jones MB, Depledge MH. Differential sensitivity of three marine invertebrates to copper assessed using multiple biomarkers. Aquat Toxicol 2004; 66:267-278. [PMID: 15129769 DOI: 10.1016/j.aquatox.2003.10.001] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Understanding how biomarkers relate to each other on exposure to particular contaminants in different species is key to their widespread application in environmental management. However, few studies have systematically used multiple biomarkers in more than a single species to determine the variability of sublethal effects of a particular contaminant. In this study, three marine invertebrates, the shore crab Carcinus maenas, the common limpet Patella vulgata and the blue mussel Mytilus edulis, were exposed over 7 days in the laboratory to environmentally realistic concentrations of the priority pollutant copper. A combination of molecular, cellular and physiological biomarkers was measured in each organism to detect the toxic effects of copper. Biomarkers included lysosomal stability (neutral red retention), neurotoxicity (acetylcholinesterase activity), metabolic impairment (total haemolymph protein), physiological status (heart rate) and induction of protective metallothionein proteins. P. vulgata was the most sensitive to copper with significant effects measured in all biomarkers at concentrations of 6.1 microg Cu l(-1). In C. maenas, cellular and neurotoxic endpoints were affected significantly only at 68.1 microg Cu l(-1). Exposure to copper also induced metallothionein production in crabs. Over a 7-day exposure period, M. edulis was the most tolerant species to copper with significant effects being observed at the cellular level only at 68.1 microg Cu l(-1) . In all three species, cellular and neurotoxic pathways were more sensitive to disruption than physiological processes (protein and heart rate). Results illustrate how a suite of biomarkers applied to different sentinel species can provide a 'diagnosis of stress', whereby, effects at the molecular level can be used to interpret the level of physiological impairment of the organism.
Collapse
Affiliation(s)
- R J Brown
- School of Biological Sciences, Plymouth Environmental Research Centre, University of Plymouth, Drake Circus, Plymouth, Devon PL4 8AA, UK
| | | | | | | | | | | | | |
Collapse
|