Kinome Expansion in theFusarium oxysporumSpecies Complex Driven by Accessory Chromosomes

ABSTRACTTheFusarium oxysporumspecies complex (FOSC) is a group of soilborne pathogens causing severe disease in more than 100 plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host-specific pathogenicity. However, little is known about the functional importance of genes encoded in these LS chromosomes. Focusing on signaling transduction, this study compared the kinomes of 12F. oxysporumisolates, including both plant and human pathogens and 1 nonpathogenic biocontrol strain, with 7 additional publicly available ascomycete genomes. Overall,F. oxysporumkinomes are the largest, facilitated in part by the acquisitions of the LS chromosomes. The comparative study identified 99 kinases that are present in almost all examined fungal genomes, forming the core signaling network of ascomycete fungi. Compared to the conserved ascomycete kinome, the expansion of theF. oxysporumkinome occurs in several kinase families such as histidine kinases that are involved in environmental signal sensing and target of rapamycin (TOR) kinase that mediates cellular responses. Comparative kinome analysis suggests a convergent evolution that shapes individualF. oxysporumisolates with an enhanced and unique capacity for environmental perception and associated downstream responses.IMPORTANCEIsolates ofFusarium oxysporumare adapted to survive a wide range of host and nonhost conditions. In addition,F. oxysporumwas recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12F. oxysporumisolates and highlighted kinase families that distinguishF. oxysporumfrom other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly setsFusariumapart from otherAscomycetes. Although the functions of many of these kinases are still unclear, their specific proliferation highlights them as a result of the evolutionary forces that have shaped this species complex and clearly marks them as targets for exploitation in order to combat disease.

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Kinome expansion in theFusarium oxysporumspecies complex driven by accessary chromosomes

10.1101/308064 ◽

2018 ◽

Author(s):

Gregory A. DeIulio ◽

Li Guo ◽

Yong Zhang ◽

Jonathan Goldberg ◽

H. Corby Kistler ◽

...

Keyword(s):

Species Complex ◽

Severe Disease ◽

Cellular Responses ◽

Human Pathogens ◽

Evolutionary Forces ◽

Environmental Signal ◽

Wide Range ◽

Tor Kinase ◽

Opportunistic Fungal Pathogen ◽

Almost All

ABSTRACTTheFusarium oxysporumspecies complex (FOSC) is a group of soil-borne pathogens causing severe disease in over one hundred plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host specific pathogenicity. However, little is known about the functional importance of genes encoded in these LS chromosomes. Focusing on signaling transduction, this study compared kinomes of 12F. oxysporumisolates, including both plant and human pathogens and one non-pathogenic biocontrol strain, with seven additional publicly available ascomycete genomes. Overall,F. oxysporumkinomes are the largest, facilitated in part by the acquisitions of the LS chromosomes. The comparative study identified 99 kinases that are present in almost all examined fungal genomes, forming the core signaling network of ascomycete fungi. Compared to the conserved ascomycete kinome, the expansion of theF. oxysporumkinome occurs in several kinases families such as Histidine kinases that are involved in environmental signal sensing and TOR kinase that mediates cellular responses. Comparative kinome analysis suggests a convergent evolution that shapes individualF. oxysporumisolates with an enhanced and unique capacity for environmental perception and associated downstream responses.IMPORTANCEIsolates ofF. oxysporumare adapted to survive a wide range of host and non-host conditions. In addition,F. oxysporumwas recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptability of this group. We have examined the kinomes of 12F. oxysporumisolates and highlighted kinase families that distinguishF. oxysporumfrom other fungi, as well as different isolates from one another. The amplification of kinases involved in environmental signal relay and regulating downstream cellular responses clearly setsFusariumapart from other Ascomycetes. Though the function of many of these kinases is still unclear, their specific proliferation highlights them as a result of the evolutionary forces which have shaped this species complex, and clearly marks them as targets for exploitation in order to combat disease.

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Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment

Applied and Environmental Microbiology ◽

10.1128/aem.02939-19 ◽

2020 ◽

Vol 86 (10) ◽

Author(s):

Dewa A. P. Rasmika Dewi ◽

Barbara Götz ◽

Torsten Thomas

Keyword(s):

Aquatic Environment ◽

Carbapenem Resistance ◽

Clinical Samples ◽

Resistant Bacteria ◽

Clinical Environment ◽

Human Pathogens ◽

Environmental Distribution ◽

Content Type ◽

Pseudomonas Monteilii ◽

Wide Range

ABSTRACT Resistance to the “last-resort” antibiotics, such as carbapenems, has led to very few antibiotics being left to treat infections by multidrug-resistant bacteria. Spread of carbapenem resistance (CR) has been well characterized for the clinical environment. However, there is a lack of information about its environmental distribution. Our study reveals that CR is present in a wide range of Gram-negative bacteria in the coastal seawater environment, including four phyla, eight classes, and 30 genera. These bacteria were likely introduced into seawater via stormwater flows. Some CR isolates found here, such as Acinetobacter junii, Acinetobacter johnsonii, Brevundimonas vesicularis, Enterococcus durans, Pseudomonas monteilii, Pseudomonas fulva, and Stenotrophomonas maltophilia, are further relevant to human health. We also describe a novel metallo-β-lactamase (MBL) for marine Rheinheimera isolates with CR, which has likely been horizontally transferred to Citrobacter freundii or Enterobacter cloacae. In contrast, another MBL of the New Delhi type was likely acquired by environmental Variovorax isolates from Escherichia coli, Klebsiella pneumoniae, or Acinetobacter baumannii utilizing a plasmid. Our findings add to the growing body of evidence that the aquatic environment is both a reservoir and a vector for novel CR genes. IMPORTANCE Resistance against the “last-resort” antibiotics of the carbapenem family is often based on the production of carbapenemases, and this has been frequently observed in clinical samples. However, the dissemination of carbapenem resistance (CR) in the environment has been less well explored. Our study shows that CR is commonly found in a range of bacterial taxa in the coastal aquatic environment and can involve the exchange of novel metallo-β-lactamases from typical environmental bacteria to potential human pathogens or vice versa. The outcomes of this study contribute to a better understanding of how aquatic and marine bacteria can act as reservoirs and vectors for CR outside the clinical setting.

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The ecnA Antitoxin Is Important Not Only for Human Pathogens: Evidence of Its Role in the Plant Pathogen Xanthomonas citri subsp. citri

Journal of Bacteriology ◽

10.1128/jb.00796-18 ◽

2019 ◽

Vol 201 (20) ◽

Cited By ~ 2

Author(s):

Laís Moreira Granato ◽

Simone Cristina Picchi ◽

Maxuel de Oliveira Andrade ◽

Paula Maria Moreira Martins ◽

Marco Aurélio Takita ◽

...

Keyword(s):

Biofilm Formation ◽

Host Plants ◽

Citrus Canker ◽

Human Pathogens ◽

Xanthomonas Citri ◽

Content Type ◽

Canker Disease ◽

Bacterial Pathogenicity ◽

Wide Range ◽

Host Infection

ABSTRACT Xanthomonas citri subsp. citri causes citrus canker disease worldwide in most commercial varieties of citrus. Its transmission occurs mainly by wind-driven rain. Once X. citri reaches a leaf, it can epiphytically survive by forming a biofilm, which enhances the persistence of the bacteria under different environmental stresses and plays an important role in the early stages of host infection. Therefore, the study of genes involved in biofilm formation has been an important step toward understanding the bacterial strategy for survival in and infection of host plants. In this work, we show that the ecnAB toxin-antitoxin (TA) system, which was previously identified only in human bacterial pathogens, is conserved in many Xanthomonas spp. We further show that in X. citri, ecnA is involved in important processes, such as biofilm formation, exopolysaccharide (EPS) production, and motility. In addition, we show that ecnA plays a role in X. citri survival and virulence in host plants. Thus, this mechanism represents an important bacterial strategy for survival under stress conditions. IMPORTANCE Very little is known about TA systems in phytopathogenic bacteria. ecnAB, in particular, has only been studied in bacterial human pathogens. Here, we showed that it is present in a wide range of Xanthomonas sp. phytopathogens; moreover, this is the first work to investigate the functional role of this TA system in Xanthomonas citri biology, suggesting an important new role in adaptation and survival with implications for bacterial pathogenicity.

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Antibiofilm activity in the culture supernatant of a marine Pseudomonas sp. bacterium

Microbiology ◽

10.1099/mic.0.000878 ◽

2020 ◽

Vol 166 (3) ◽

pp. 239-252 ◽

Cited By ~ 1

Author(s):

Ibtissem Doghri ◽

Florence Brian-Jaisson ◽

Marianne Graber ◽

Alexis Bazire ◽

Alain Dufour ◽

...

Keyword(s):

Marine Bacteria ◽

Type Species ◽

Culture Supernatant ◽

Heterotrophic Bacteria ◽

Bioactive Metabolites ◽

Antibiofilm Activity ◽

Human Pathogens ◽

Content Type ◽

Link Type ◽

Wide Range

In the marine environment, most solid surfaces are covered by microbial biofilms, mainly composed of bacteria and diatoms. The negative effects of biofilms on materials and equipment are numerous and pose a major problem for industry and human activities. Since marine micro-organisms are an important source of bioactive metabolites, it is possible that they synthesize natural ecofriendly molecules that inhibit the adhesion of organisms. In this work, the antibiofilm potential of marine bacteria was investigated using Flavobacterium sp. II2003 as a target. This strain is potentially a pioneer strain of bacteria that was previously selected from marine biofilms for its strong biofilm-forming ability. The culture supernatants of 86 marine heterotrophic bacteria were tested for their ability to inhibit Flavobacterium sp. II2003 biofilm formation and the Pseudomonas sp. IV2006 strain was identified as producing a strong antibiofilm activity. The Pseudomonas sp. IV2006 culture supernatant (SNIV2006) inhibited Flavobacterium sp. II2003 adhesion without killing the bacteria or inhibiting its growth. Moreover, SNIV2006 had no effect on the Flavobacterium sp. II2003 cell surface hydrophilic/hydrophobic and general Lewis acid–base characteristics, but modified the surface properties of glass, making it on the whole more hydrophilic and more alkaline and significantly reducing bacterial cell adhesion. The glass-coating molecules produced by Pseudomonas sp. IV2006 were found to probably be polysaccharides, whereas the antibiofilm molecules contained in SNIV2006 and acting during the 2 h adhesion step on glass and polystyrene surfaces would be proteinaceous. Finally, SNIV2006 exhibited a broad spectrum of antibiofilm activity on other marine bacteria such as Flavobacterium species that are pathogenic for fish, and human pathogens in both the medical environment, such as Staphylococcus aureus and Pseudomonas aeruginosa , and in the food industry, such as Yersinia enterocolitica . Thus, a wide range of applications could be envisaged for the SNIV2006 compounds, both in aquaculture and human health.

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High-Throughput Analysis of Gene Function in the Bacterial PredatorBdellovibrio bacteriovorus

mBio ◽

10.1128/mbio.01040-19 ◽

2019 ◽

Vol 10 (3) ◽

Cited By ~ 11

Author(s):

Miles C. Duncan ◽

Rebecca K. Gillette ◽

Micah A. Maglasang ◽

Elizabeth A. Corn ◽

Albert K. Tai ◽

...

Keyword(s):

High Throughput ◽

Gram Negative Bacteria ◽

Human Pathogens ◽

High Throughput Analysis ◽

Bdellovibrio Bacteriovorus ◽

Gram Negative ◽

Content Type ◽

Genetically Engineer ◽

Wide Range ◽

Specific Species

ABSTRACTBdellovibrio bacteriovorusis a bacterial predator capable of killing and replicating inside most Gram-negative bacteria, including antibiotic-resistant pathogens. Despite growing interest in this organism as a potential therapeutic, many of its genes remain uncharacterized. Here, we perform a high-throughput genetic screen withB. bacteriovorususing transposon sequencing (Tn-seq) to explore the genetic requirements of predation. Two hundred one genes were deemed essential for growth in the absence of prey, whereas over 100 genes were found to be specifically required for predative growth on the human pathogensVibrio choleraeandEscherichia coliin both planktonic and biofilm states. To further this work, we created an ordered-knockout library inB. bacteriovorusand developed new high-throughput techniques to characterize the mutants by their stage of deficiency in the predator life cycle. Using microscopy and flow cytometry, we confirmed 10 mutants defective in prey attachment and eight mutants defective in prey rounding. The majority of these genes are hypothetical and previously uncharacterized. Finally, we propose new nomenclature to groupB. bacteriovorusmutants into classes based on their stage of predation defect. These results contribute to our basic understanding of bacterial predation and may be useful for harnessingB. bacteriovorusto kill harmful pathogens in the clinical setting.IMPORTANCEBdellovibrio bacteriovorusis a predatory bacterium that can kill a wide range of Gram-negative bacteria, including many human pathogens. Given the global rise of antibiotic resistance and dearth of new antibiotics discovered in the past 30 years, this predator has potential as an alternative to traditional antibiotics. For many years,B. bacteriovorusresearch was hampered by a lack of genetic tools, and the genetic mechanisms of predation have only recently begun to be established. Here, we comprehensively identify and characterize predator genes required for killing bacterial prey, as well as genes that interfere in this process, which may allow us to design better therapeutic predators. Based on our study, we and other researchers may ultimately be able to genetically engineer strains that have improved killing rates, target specific species of prey, or preferentially target prey in the planktonic or biofilm state.

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Draft Genome Sequences of 12 Isolates from 3 Fusarium Species Recovered from Moldy Peanuts

Microbiology Resource Announcements ◽

10.1128/mra.01642-18 ◽

2019 ◽

Vol 8 (15) ◽

Cited By ~ 2

Author(s):

Solomon T. Gebru ◽

Mark K. Mammel ◽

Jayanthi Gangiredla ◽

Vasiliki H. Tournas ◽

Keith A. Lampel ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Species Complex ◽

Fusarium Species ◽

Draft Genome ◽

Fusarium Proliferatum ◽

Washington Dc ◽

Genome Sequences ◽

Fusarium Equiseti ◽

Content Type

In this report, we announce the sequences of six genomes of Fusarium proliferatum (isolates MOD1-FUNGI8, -12, -13, -14, -15, and -19), four genomes of Fusarium oxysporum (MOD1-FUNGI9, -10, -11, and -16), and two genomes of the Fusarium incarnatum-Fusarium equiseti species complex (MOD1-FUNGI17 and MOD1-FUNGI18) isolated from moldy peanuts from the Washington, DC, area.

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Susceptibility of Mycobacterium abscessus to Antimycobacterial Drugs in Preclinical Models

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00459-15 ◽

2015 ◽

Vol 59 (11) ◽

pp. 6904-6912 ◽

Cited By ~ 53

Author(s):

Andrés Obregón-Henao ◽

Kimberly A. Arnett ◽

Marcela Henao-Tamayo ◽

Lisa Massoudi ◽

Elizabeth Creissen ◽

...

Keyword(s):

Severe Combined Immunodeficiency ◽

Antimycobacterial Activity ◽

Multidrug Resistant ◽

Mycobacterium Abscessus ◽

Prolonged Treatment ◽

Human Pathogens ◽

Content Type ◽

Infection Models ◽

Wide Range ◽

Compound Screening

ABSTRACTOver the last 10 years,Mycobacterium abscessusgroup strains have emerged as important human pathogens, which are associated with significantly higher fatality rates than any other rapidly growing mycobacteria. These opportunistic pathogens are widespread in the environment and can cause a wide range of clinical diseases, including skin, soft tissue, central nervous system, and disseminated infections; by far, the most difficult to treat is the pulmonary form. Infections withM. abscessusare often multidrug-resistant (MDR) and require prolonged treatment with various regimens and, many times, result in high mortality despite maximal therapy. We report here the evaluation of diverse mouse infection models for their ability to produce a progressive high level of infection withM. abscessus. The nude (nu/nu), SCID (severe combined immunodeficiency), gamma interferon knockout (GKO), and granulocyte-macrophage colony-stimulating factor (GMCSF) knockout mice fulfilled the criteria for an optimal model for compound screening. Thus, we set out to assess the antimycobacterial activity of clarithromycin, clofazimine, bedaquiline, and clofazimine-bedaquiline combinations againstM. abscessus-infected GKO and SCID murine infection models. Treatment of GKO and SCID mice with a combination of clofazimine and bedaquiline was the most effective in decreasing theM. abscessusorgan burden.

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Phylogenetic Evidence for the Existence of Multiple Strains ofRickettsia parkeriin the New World

Applied and Environmental Microbiology ◽

10.1128/aem.02872-17 ◽

2018 ◽

Vol 84 (8) ◽

pp. e02872-17 ◽

Cited By ~ 22

Author(s):

Fernanda A. Nieri-Bastos ◽

Arlei Marcili ◽

Rita De Sousa ◽

Christopher D. Paddock ◽

Marcelo B. Labruna

Keyword(s):

South America ◽

Species Complex ◽

New World ◽

Sensu Stricto ◽

Species Group ◽

Atlantic Rainforest ◽

South American ◽

Human Pathogens ◽

Amblyomma Maculatum ◽

Content Type

ABSTRACTThe bacteriumRickettsia parkerihas been reported to infect ticks of the “Amblyomma maculatumspecies complex” in the New World, where it causes spotted fever illness in humans. In South America, three additional rickettsial strains, namely, Atlantic rainforest, NOD, and Parvitarsum, have been isolated from the ticksAmblyomma ovale,Amblyomma nodosum, andAmblyomma parvitarsum, respectively. These three strains are phylogenetically closely related toR. parkeri,Rickettsia africae, andRickettsia sibirica. Herein, we performed a robust phylogenetic analysis encompassing 5 genes (gltA,ompA,virB4,dnaA, anddnaK) and 3 intergenic spacers (mppE-pur,rrl-rrf-ITS, andrpmE-tRNAfMet) from 41 rickettsial isolates, including different isolates ofR. parkeri,R. africae,R. sibirica,Rickettsia conorii, and strains Atlantic rainforest, NOD, and Parvitarsum. In our phylogenetic analyses, all New World isolates grouped in a major clade distinct from the Old WorldRickettsiaspecies (R. conorii,R. sibirica, andR. africae). This New World clade was subdivided into the following 4 clades: theR. parkerisensu strictoclade, comprising the type strain Maculatum 20 and all other isolates ofR. parkerifrom North and South America, associated with ticks of theA. maculatumspecies complex; the strain NOD clade, comprising two South American isolates fromA. nodosumticks; the Parvitarsum clade, comprising two South American isolates fromA. parvitarsumticks; and the strain Atlantic rainforest clade, comprising six South American isolates from theA. ovalespecies complex (A. ovaleorAmblyomma aureolatum). Under such evidences, we propose that strains Atlantic rainforest, NOD, and Parvitarsum are South American strains ofR. parkeri.IMPORTANCESince the description ofRickettsia parkeriinfecting ticks of the “Amblyomma maculatumspecies complex” and humans in the New World, three novel phylogenetic close-related rickettsial isolates were reported in South America. Herein, we provide genetic evidence that these novel isolates, namely, strains Atlantic rainforest, NOD, and Parvitarsum, are South American strains ofR. parkeri.Interestingly, each of theseR. parkeristrains seems to be primarily associated with a tick species group, namely,R. parkerisensu strictowith the “Amblyomma maculatumspecies group,”R. parkeristrain NOD withAmblyomma nodosum,R. parkeristrain Parvitarsum withAmblyomma parvitarsum, andR. parkeristrain Atlantic rainforest with the “Amblyomma ovalespecies group.” Such rickettsial strain-tick species specificity suggests a coevolution of each tick-strain association. Finally, becauseR. parkerisensu strictoandR. parkeristrain Atlantic rainforest are human pathogens, the potential ofR. parkeristrains NOD and Parvitarsum to be human pathogens cannot be discarded.

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Lipid A Structural Divergence in Rickettsia Pathogens

mSphere ◽

10.1128/msphere.00184-21 ◽

2021 ◽

Vol 6 (3) ◽

Author(s):

Mark L. Guillotte ◽

Courtney E. Chandler ◽

Victoria I. Verhoeve ◽

Joseph J. Gillespie ◽

Timothy P. Driscoll ◽

...

Keyword(s):

Lipid A ◽

Spotted Fever ◽

Membrane Dynamics ◽

Spotted Fever Group ◽

Human Pathogens ◽

Rocky Mountain Spotted Fever ◽

Content Type ◽

O Antigen ◽

Wide Range ◽

Acyl Chains

ABSTRACT Species of Rickettsia (Alphaproteobacteria: Rickettsiales) are obligate intracellular parasites of a wide range of eukaryotes, with recognized arthropod-borne human pathogens belonging to the transitional group (TRG), typhus group (TG), and spotted fever group (SFG) rickettsiae. Growing in the host cytosol, rickettsiae pilfer numerous metabolites to make a typical Gram-negative bacterial cell envelope. The O-antigen of rickettsial lipopolysaccharide (LPS) is immunogenic and has been shown to tether the S-layer to the rickettsial surface; however, little is known about the structure and immunogenicity of the Rickettsia lipid A moiety. The structure of lipid A, the membrane anchor of LPS, affects the ability of this molecule to interact with components of the host innate immune system, specifically the MD-2/TLR4 receptor complex. To dissect the host responses that can occur during Rickettsia in vitro and in vivo infection, structural analysis of Rickettsia lipid A is needed. Lipid A was extracted from four Rickettsia species and structurally analyzed. R. akari (TRG), R. typhi (TG), and R. montanensis (SFG) produced a similar structure, whereas R. rickettsii (SFG) altered the length of a secondary acyl group. While all structures have longer acyl chains than known highly inflammatory hexa-acylated lipid A structures, the R. rickettsii modification should differentially alter interactions with the hydrophobic internal pocket in MD2. The significance of these characteristics toward inflammatory potential as well as membrane dynamics between arthropod and vertebrate cellular environments warrants further investigation. Our work adds lipid A to the secretome and O-antigen as variable factors possibly correlating with phenotypically diverse rickettsioses. IMPORTANCE Spikes in rickettsioses occur as deforestation, urbanization, and homelessness increase human exposure to blood-feeding arthropods. Still, effective Rickettsia vaccines remain elusive. Recent studies have determined that Rickettsia lipopolysaccharide anchors the protective S-layer to the bacterial surface and elicits bactericidal antibodies. Furthermore, growing immunological evidence suggests vertebrate sensors (MD-2/TLR4 and noncanonical inflammasome) typically triggered by the lipid A portion of lipopolysaccharide are activated during Rickettsia infection. However, the immunopotency of Rickettsia lipid A is unknown due to poor appreciation for its structure. We determined lipid A structures for four distinct rickettsiae, revealing longer acyl chains relative to highly inflammatory bacterial lipid A. Surprisingly, lipid A of the Rocky Mountain spotted fever agent deviates in structure from other rickettsiae. Thus, lipid A divergence may contribute to variable disease phenotypes, sounding an alarm for determining its immunopotency and possible utility (i.e., as an adjuvant or anti-inflammatory) for development of more prudent rickettsiacidal therapies.

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