Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.

Abstract:

:Pulmonary exacerbations are the leading cause of death in cystic fibrosis (CF) patients. To track microbial dynamics during acute exacerbations, a CF rapid response (CFRR) strategy was developed. The CFRR relies on viromics, metagenomics, metatranscriptomics, and metabolomics data to rapidly monitor active members of the viral and microbial community during acute CF exacerbations. To highlight CFRR, a case study of a CF patient is presented, in which an abrupt decline in lung function characterized a fatal exacerbation. The microbial community in the patient's lungs was closely monitored through the multi-omics strategy, which led to the identification of pathogenic shigatoxigenic Escherichia coli (STEC) expressing Shiga toxin. This case study illustrates the potential for the CFRR to deconstruct complicated disease dynamics and provide clinicians with alternative treatments to improve the outcomes of pulmonary exacerbations and expand the life spans of individuals with CF.IMPORTANCE Proper management of polymicrobial infections in patients with cystic fibrosis (CF) has extended their life span. Information about the composition and dynamics of each patient's microbial community aids in the selection of appropriate treatment of pulmonary exacerbations. We propose the cystic fibrosis rapid response (CFRR) as a fast approach to determine viral and microbial community composition and activity during CF pulmonary exacerbations. The CFRR potential is illustrated with a case study in which a cystic fibrosis fatal exacerbation was characterized by the presence of shigatoxigenic Escherichia coli The incorporation of the CFRR within the CF clinic could increase the life span and quality of life of CF patients.

journal_name

mBio

journal_title

mBio

authors

Cobián Güemes AG,Lim YW,Quinn RA,Conrad DJ,Benler S,Maughan H,Edwards R,Brettin T,Cantú VA,Cuevas D,Hamidi R,Dorrestein P,Rohwer F

doi

10.1128/mBio.00431-19

subject

Has Abstract

pub_date

2019-04-16 00:00:00

issue

2

issn

2150-7511

pii

mBio.00431-19

journal_volume

10

pub_type

杂志文章

相关文献

mBio文献大全
  • e-Biologics: Fabrication of Sustainable Electronics with "Green" Biological Materials.

    abstract::The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00695-17

    authors: Lovley DR

    更新日期:2017-06-27 00:00:00

  • Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus.

    abstract::Here, we investigate a monoclonal antibody, Z2B3, isolated from an H7N9-infected patient, that exhibited cross-reactivity to both N9 (group 2) and a broad range of seasonal and avian N1 (group 1) proteins but lost activity to the N1 with the substitution K432E. This substitution exists in 99.25% of seasonal influenza ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02315-20

    authors: Jiang H,Peng W,Qi J,Chai Y,Song H,Bi Y,Rijal P,Wang H,Oladejo BO,Liu J,Shi Y,Gao GF,Townsend AR,Wu Y

    更新日期:2020-10-06 00:00:00

  • Targeting Mannitol Metabolism as an Alternative Antimicrobial Strategy Based on the Structure-Function Study of Mannitol-1-Phosphate Dehydrogenase in Staphylococcus aureus.

    abstract::Mannitol-1-phosphate dehydrogenase (M1PDH) is a key enzyme in Staphylococcus aureus mannitol metabolism, but its roles in pathophysiological settings have not been established. We performed comprehensive structure-function analysis of M1PDH from S. aureus USA300, a strain of community-associated methicillin-resistant ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02660-18

    authors: Nguyen T,Kim T,Ta HM,Yeo WS,Choi J,Mizar P,Lee SS,Bae T,Chaurasia AK,Kim KK

    更新日期:2019-07-09 00:00:00

  • A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages.

    abstract::Mycoviruses infect fungi, and while most persist asymptomatically, there are examples of mycoviruses having both beneficial and detrimental effects on their host. Virus-infected Saccharomyces and Ustilago strains exhibit a killer phenotype conferring a growth advantage over uninfected strains and other competing yeast...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01534-20

    authors: Applen Clancey S,Ruchti F,LeibundGut-Landmann S,Heitman J,Ianiri G

    更新日期:2020-09-01 00:00:00

  • Convergent Evolution of HLA-C Downmodulation in HIV-1 and HIV-2.

    abstract::HLA-C-mediated antigen presentation induces the killing of human immunodeficiency virus (HIV)-infected CD4+ T cells by cytotoxic T lymphocytes (CTLs). To evade killing, many HIV-1 group M strains decrease HLA-C surface levels using their accessory protein Vpu. However, some HIV-1 group M isolates lack this activity, p...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00782-20

    authors: Hopfensperger K,Richard J,Stürzel CM,Bibollet-Ruche F,Apps R,Leoz M,Plantier JC,Hahn BH,Finzi A,Kirchhoff F,Sauter D

    更新日期:2020-07-14 00:00:00

  • The Yeast PCNA Unloader Elg1 RFC-Like Complex Plays a Role in Eliciting the DNA Damage Checkpoint.

    abstract::The PCNA (proliferating cell nuclear antigen) ring plays central roles during DNA replication and repair. The yeast Elg1 RFC-like complex (RLC) is the principal unloader of chromatin-bound PCNA and thus plays a central role in maintaining genome stability. Here we identify a role for Elg1 in the unloading of PCNA duri...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01159-19

    authors: Sau S,Liefshitz B,Kupiec M

    更新日期:2019-06-11 00:00:00

  • Petrobactin Protects against Oxidative Stress and Enhances Sporulation Efficiency in Bacillus anthracis Sterne.

    abstract::Bacillus anthracis is a Gram-positive bacillus that under conditions of environmental stress, such as low nutrients, can convert from a vegetative bacillus to a highly durable spore that enables long-term survival. The sporulation process is regulated by a sequential cascade of dedicated transcription factors but requ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02079-18

    authors: Hagan AK,Plotnick YM,Dingle RE,Mendel ZI,Cendrowski SR,Sherman DH,Tripathi A,Hanna PC

    更新日期:2018-11-06 00:00:00

  • Contribution of resistance-nodulation-cell division efflux systems to antibiotic resistance and biofilm formation in Acinetobacter baumannii.

    abstract:UNLABELLED:Acinetobacter baumannii is a nosocomial pathogen of increasing importance due to its multiple resistance to antibiotics and ability to survive in the hospital environment linked to its capacity to form biofilms. To fully characterize the contribution of AdeABC, AdeFGH, and AdeIJK resistance-nodulation-cell d...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00309-15

    authors: Yoon EJ,Chabane YN,Goussard S,Snesrud E,Courvalin P,Dé E,Grillot-Courvalin C

    更新日期:2015-03-24 00:00:00

  • Finding of Agr Phase Variants in Staphylococcus aureus.

    abstract::Staphylococcus aureus is an important human pathogen whose success is largely attributed to its vast arsenal of virulence factors that facilitate its invasion into, and survival within, the human host. The expression of these virulence factors is controlled by the quorum sensing accessory gene regulator (Agr) system. ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00796-19

    authors: Gor V,Takemura AJ,Nishitani M,Higashide M,Medrano Romero V,Ohniwa RL,Morikawa K

    更新日期:2019-08-06 00:00:00

  • Deep Sequencing Uncovers Caste-Associated Diversity of Symbionts in the Social Ant Camponotus japonicus.

    abstract::Symbiotic microorganisms can have a profound impact on the host physiology and behavior, and novel relationships between symbionts and their hosts are continually discovered. A colony of social ants consists of various castes that exhibit distinct lifestyles and is, thus, a unique model for investigating how symbionts...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00408-20

    authors: Koto A,Nobu MK,Miyazaki R

    更新日期:2020-04-21 00:00:00

  • Carboxylic Acid Transporters in Candida Pathogenesis.

    abstract::Opportunistic pathogens such as Candida species can use carboxylic acids, like acetate and lactate, to survive and successfully thrive in different environmental niches. These nonfermentable substrates are frequently the major carbon sources present in certain human body sites, and their efficient uptake by regulated ...

    journal_title:mBio

    pub_type: 杂志文章,评审

    doi:10.1128/mBio.00156-20

    authors: Alves R,Sousa-Silva M,Vieira D,Soares P,Chebaro Y,Lorenz MC,Casal M,Soares-Silva I,Paiva S

    更新日期:2020-05-12 00:00:00

  • Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo-Blood Group Antigen Binding Profiles.

    abstract::Emerging zoonotic viral diseases remain a challenge to global public health. Recent surveillance studies have implicated bats as potential reservoirs for a number of viral pathogens, including coronaviruses and Ebola viruses. Caliciviridae represent a major viral family contributing to emerging diseases in both human ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00869-18

    authors: Kocher JF,Lindesmith LC,Debbink K,Beall A,Mallory ML,Yount BL,Graham RL,Huynh J,Gates JE,Donaldson EF,Baric RS

    更新日期:2018-05-22 00:00:00

  • Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis.

    abstract:UNLABELLED:Glycoside hydrolases (GHs) are key enzymes in the depolymerization of plant-derived cellulose, a process central to the global carbon cycle and the conversion of plant biomass to fuels and chemicals. A limited number of GH families hydrolyze crystalline cellulose, often by a processive mechanism along the ce...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01106-16

    authors: Hiras J,Wu YW,Deng K,Nicora CD,Aldrich JT,Frey D,Kolinko S,Robinson EW,Jacobs JM,Adams PD,Northen TR,Simmons BA,Singer SW

    更新日期:2016-08-23 00:00:00

  • Dectin-1 is expressed in human lung and mediates the proinflammatory immune response to nontypeable Haemophilus influenzae.

    abstract:UNLABELLED:The C-type lectin receptor Dectin-1 is expressed mainly on myeloid cells mediating the immune response targeting respiratory pathogens such as Aspergillus fumigatus and Mycobacterium tuberculosis. The pulmonary epithelium serves as an important interface for interactions between these pathogens and the respi...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01492-14

    authors: Heyl KA,Klassert TE,Heinrich A,Müller MM,Klaile E,Dienemann H,Grünewald C,Bals R,Singer BB,Slevogt H

    更新日期:2014-08-26 00:00:00

  • Z-Ring-Associated Proteins Regulate Clustering of the Replication Terminus-Binding Protein ZapT in Caulobacter crescentus.

    abstract::Regulated organization of the chromosome is essential for faithful propagation of genetic information. In the model bacterium Caulobacter crescentus, the replication terminus of the chromosome is spatially arranged in close proximity to the cytokinetic Z-ring during the cell cycle. Although the Z-ring-associated prote...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02196-20

    authors: Ozaki S,Wakasugi Y,Katayama T

    更新日期:2021-01-26 00:00:00

  • A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack.

    abstract::Pseudomonas aeruginosa produces an extracellular biofilm matrix that consists of nucleic acids, exopolysaccharides, lipid vesicles, and proteins. In general, the protein component of the biofilm matrix is poorly defined and understudied relative to the other major matrix constituents. While matrix proteins have been s...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00543-18

    authors: Tseng BS,Reichhardt C,Merrihew GE,Araujo-Hernandez SA,Harrison JJ,MacCoss MJ,Parsek MR

    更新日期:2018-04-10 00:00:00

  • Viral Diversity of House Mice in New York City.

    abstract::The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manh...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01354-17

    authors: Williams SH,Che X,Garcia JA,Klena JD,Lee B,Muller D,Ulrich W,Corrigan RM,Nichol S,Jain K,Lipkin WI

    更新日期:2018-04-17 00:00:00

  • Shigella sonnei O-Antigen Inhibits Internalization, Vacuole Escape, and Inflammasome Activation.

    abstract::Two Shigella species, Shigella flexneri and Shigella sonnei, cause approximately 90% of bacterial dysentery worldwide. While S. flexneri is the dominant species in low-income countries, S. sonnei causes the majority of infections in middle- and high-income countries. S. flexneri is a prototypic cytosolic bacterium; on...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02654-19

    authors: Watson JL,Sanchez-Garrido J,Goddard PJ,Torraca V,Mostowy S,Shenoy AR,Clements A

    更新日期:2019-12-17 00:00:00

  • Aspergillus fumigatus Transcription Factors Involved in the Caspofungin Paradoxical Effect.

    abstract::Aspergillus fumigatus is the leading cause of pulmonary fungal diseases. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, in the last 10 years there have been several reports of azole resistance in A. fumigatus and new strategies are needed to com...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00816-20

    authors: Valero C,Colabardini AC,Chiaratto J,Pardeshi L,de Castro PA,Ferreira Filho JA,Silva LP,Rocha MC,Malavazi I,Costa JH,Fill T,Barros MH,Wong SSW,Aimanianda V,Wong KH,Goldman GH

    更新日期:2020-06-16 00:00:00

  • Nile red detection of bacterial hydrocarbons and ketones in a high-throughput format.

    abstract::A method for use in high-throughput screening of bacteria for the production of long-chain hydrocarbons and ketones by monitoring fluorescent light emission in the presence of Nile red is described. Nile red has previously been used to screen for polyhydroxybutyrate (PHB) and fatty acid esters, but this is the first r...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00109-11

    authors: Pinzon NM,Aukema KG,Gralnick JA,Wackett LP

    更新日期:2011-06-28 00:00:00

  • Noncanonical G-protein-dependent modulation of osteoclast differentiation and bone resorption mediated by Pasteurella multocida toxin.

    abstract:UNLABELLED:Pasteurella multocida toxin (PMT) induces atrophic rhinitis in animals, which is characterized by a degradation of nasal turbinate bones, indicating an effect of the toxin on bone cells such as osteoblasts and osteoclasts. The underlying molecular mechanism of PMT was defined as a persistent activation of he...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.02190-14

    authors: Strack J,Heni H,Gilsbach R,Hein L,Aktories K,Orth JH

    更新日期:2014-11-11 00:00:00

  • Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-β-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance.

    abstract::Production of metallo-β-lactamases (MBLs), which hydrolyze carbapenems, is a cause of carbapenem resistance in Enterobacteriaceae Development of effective inhibitors for MBLs is one approach to restore carbapenem efficacy in carbapenem-resistant Enterobacteriaceae (CRE). We report here that sulfamoyl heteroarylcarboxy...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.03144-19

    authors: Wachino JI,Jin W,Kimura K,Kurosaki H,Sato A,Arakawa Y

    更新日期:2020-03-17 00:00:00

  • Genomic avenue to avian colisepticemia.

    abstract:UNLABELLED:Here we present an extensive genomic and genetic analysis of Escherichia coli strains of serotype O78 that represent the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic Escherichia coli (APEC) strains. It is associated with high mortality and morbidity, resulting in sign...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01681-14

    authors: Huja S,Oren Y,Trost E,Brzuszkiewicz E,Biran D,Blom J,Goesmann A,Gottschalk G,Hacker J,Ron EZ,Dobrindt U

    更新日期:2015-01-13 00:00:00

  • Cyclic diguanylate signaling proteins control intracellular growth of Legionella pneumophila.

    abstract::Proteins that metabolize or bind the nucleotide second messenger cyclic diguanylate regulate a wide variety of important processes in bacteria. These processes include motility, biofilm formation, cell division, differentiation, and virulence. The role of cyclic diguanylate signaling in the lifestyle of Legionella pne...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00316-10

    authors: Levi A,Folcher M,Jenal U,Shuman HA

    更新日期:2011-01-11 00:00:00

  • Paracoccidioides Genomes Reflect High Levels of Species Divergence and Little Interspecific Gene Flow.

    abstract::The fungus Paracoccidioides is a prevalent human pathogen endemic to South America. The genus is composed of five species. In this report, we use 37 whole-genome sequences to study the allocation of genetic variation in Paracoccidioides We tested three genome-wide predictions of advanced speciation, namely, that all s...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01999-20

    authors: Mavengere H,Mattox K,Teixeira MM,Sepúlveda VE,Gomez OM,Hernandez O,McEwen J,Matute DR

    更新日期:2020-12-22 00:00:00

  • Exploring the parallel development of microbial systems in neonates with cystic fibrosis.

    abstract::Recent studies have greatly extended our understanding of the microbiota present in and on the human body. Here, advanced sequencing strategies have provided unprecedented analytical power. The important implications that the emerging data have for human health emphasize the need to intensify research in this area (D....

    journal_title:mBio

    pub_type: 评论,杂志文章

    doi:10.1128/mBio.00408-12

    authors: Rogers GB,Bruce KD

    更新日期:2012-11-06 00:00:00

  • Bacteriophages as pathogens and immune modulators?

    abstract::While Shiga toxins (Stx) are key determinants of enterohemorrhagic Escherichia coli (EHEC) pathophysiology in humans, their dissemination to target organs following gastrointestinal EHEC infection is still poorly understood. Most types of Stx target cells with globotriaosylceramide (Gb3) receptors, which are expressed...

    journal_title:mBio

    pub_type: 评论,杂志文章

    doi:10.1128/mBio.00868-13

    authors: Lengeling A,Mahajan A,Gally DL

    更新日期:2013-11-12 00:00:00

  • Kaposi's Sarcoma-Associated Herpesvirus Interleukin-6 Modulates Endothelial Cell Movement by Upregulating Cellular Genes Involved in Migration.

    abstract:UNLABELLED:Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of human Kaposi's sarcoma, a tumor that arises from endothelial cells, as well as two B cell lymphoproliferative diseases, primary effusion lymphoma and multicentric Castleman's disease. KSHV utilizes a variety of mechanisms to evade host ...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01499-15

    authors: Giffin L,West JA,Damania B

    更新日期:2015-12-08 00:00:00

  • Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress.

    abstract:UNLABELLED:Salmonella enterica serovar Typhimurium is one of the most common S. enterica serovars associated with U.S. foodborne outbreaks. S. Typhimurium bacteria isolated from humans exhibit wide-ranging virulence phenotypes in inbred mice, leading to speculation that some strains are more virulent in nature. However...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.00154-16

    authors: Hayden HS,Matamouros S,Hager KR,Brittnacher MJ,Rohmer L,Radey MC,Weiss EJ,Kim KB,Jacobs MA,Sims-Day EH,Yue M,Zaidi MB,Schifferli DM,Manning SD,Walson JL,Miller SI

    更新日期:2016-03-08 00:00:00

  • Escherichia coli ZipA Organizes FtsZ Polymers into Dynamic Ring-Like Protofilament Structures.

    abstract::ZipA is an essential cell division protein in Escherichia coli Together with FtsA, ZipA tethers dynamic polymers of FtsZ to the cytoplasmic membrane, and these polymers are required to guide synthesis of the cell division septum. This dynamic behavior of FtsZ has been reconstituted on planar lipid surfaces in vitro, v...

    journal_title:mBio

    pub_type: 杂志文章

    doi:10.1128/mBio.01008-18

    authors: Krupka M,Sobrinos-Sanguino M,Jiménez M,Rivas G,Margolin W

    更新日期:2018-06-19 00:00:00