1
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Bhowmik BK, Kumar A, Gangaiah D. Transcriptome Analyses of Chicken Primary Macrophages Infected With Attenuated Salmonella Typhimurium Mutants. Front Microbiol 2022; 13:857378. [PMID: 35591991 PMCID: PMC9111174 DOI: 10.3389/fmicb.2022.857378] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is one of the most common foodborne illnesses in the United States and worldwide, with nearly one-third of the cases attributed to contaminated eggs and poultry products. Vaccination has proven to be an effective strategy to reduce Salmonella load in poultry. The Salmonella Typhimurium Δcrp-cya (MeganVac1) strain is the most commonly used vaccine in the United States; however, the mechanisms of virulence attenuation and host response to this vaccine strain are poorly understood. Here, we profiled the invasion and intracellular survival phenotypes of Δcrp-cya and its derivatives (lacking key genes required for intra-macrophage survival) in HD11 macrophages and the transcriptome response in primary chicken macrophages using RNA-seq. Compared to the parent strain UK1, all the mutant strains were highly defective in metabolizing carbon sources related to the TCA cycle and had greater doubling times in macrophage-simulating conditions. Compared to UK1, the majority of the mutants were attenuated for invasion and intra-macrophage survival. Compared to Δcrp-cya, while derivatives lacking phoPQ, ompR-envZ, feoABC and sifA were highly attenuated for invasion and intracellular survival within macrophages, derivatives lacking ssrAB, SPI13, SPI2, mgtRBC, sitABCD, sopF, sseJ and sspH2 showed increased ability to invade and survive within macrophages. Transcriptome analyses of macrophages infected with UK1, Δcrp-cya and its derivatives lacking phoPQ, sifA and sopF demonstrated that, compared to uninfected macrophages, 138, 148, 153, 155 and 142 genes were differentially expressed in these strains, respectively. Similar changes in gene expression were observed in macrophages infected with these strains; the upregulated genes belonged to innate immune response and host defense and the downregulated genes belonged to various metabolic pathways. Together, these data provide novel insights on the relative phenotypes and early response of macrophages to the vaccine strain and its derivatives. The Δcrp-cya derivatives could facilitate development of next-generation vaccines with improved safety.
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Affiliation(s)
- Bijit K Bhowmik
- Discovery Bacteriology and Microbiome, Elanco Animal Health Inc., Greenfield, IN, United States
| | - Arvind Kumar
- Discovery Bacteriology and Microbiome, Elanco Animal Health Inc., Greenfield, IN, United States
| | - Dharanesh Gangaiah
- Discovery Bacteriology and Microbiome, Elanco Animal Health Inc., Greenfield, IN, United States
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2
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Gangaiah D, Ryan V, Van Hoesel D, Mane SP, Mckinley ET, Lakshmanan N, Reddy ND, Dolk E, Kumar A. Recombinant
Limosilactobacillus
(
Lactobacillus
) delivering nanobodies against
Clostridium perfringens
NetB and alpha toxin confers potential protection from necrotic enteritis. Microbiologyopen 2022; 11:e1270. [PMID: 35478283 PMCID: PMC8924699 DOI: 10.1002/mbo3.1270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/08/2022] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Dharanesh Gangaiah
- Division of Bacteriology and Microbiome Elanco Animal Health Greenfield Indiana USA
| | - Valerie Ryan
- Division of Bacteriology and Microbiome Elanco Animal Health Greenfield Indiana USA
| | - Daphne Van Hoesel
- Division of Nanobody Discovery and Development QVQ Holding BV Utrecht The Netherlands
| | - Shrinivasrao P. Mane
- Division of Bacteriology and Microbiome Elanco Animal Health Greenfield Indiana USA
| | - Enid T. Mckinley
- Division of Bacteriology and Microbiome Elanco Animal Health Greenfield Indiana USA
| | | | - Nandakumar D. Reddy
- Division of Bacteriology and Microbiome Elanco Animal Health Greenfield Indiana USA
| | - Edward Dolk
- Division of Nanobody Discovery and Development QVQ Holding BV Utrecht The Netherlands
| | - Arvind Kumar
- Division of Bacteriology and Microbiome Elanco Animal Health Greenfield Indiana USA
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3
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Susanti D, Volland A, Tawari N, Baxter N, Gangaiah D, Plata G, Nagireddy A, Hawkins T, Mane SP, Kumar A. Multi-Omics Characterization of Host-Derived Bacillus spp. Probiotics for Improved Growth Performance in Poultry. Front Microbiol 2021; 12:747845. [PMID: 34745051 PMCID: PMC8563996 DOI: 10.3389/fmicb.2021.747845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/26/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
Microbial feed ingredients or probiotics have been used widely in the poultry industry to improve production efficiency. Spore-forming Bacillus spp. offer advantages over traditional probiotic strains as Bacillus spores are resilient to high temperature, acidic pH, and desiccation. This results in increased strain viability during manufacturing and feed-pelleting processes, extended product shelf-life, and increased stability within the animal’s gastrointestinal tract. Despite numerous reports on the use of Bacillus spores as feed additives, detailed characterizations of Bacillus probiotic strains are typically not published. Insufficient characterizations can lead to misidentification of probiotic strains in product labels, and the potential application of strains carrying virulence factors, toxins, antibiotic resistance, or toxic metabolites. Hence, it is critical to characterize in detail the genomic and phenotypic properties of these strains to screen out undesirable properties and to tie individual traits to clinical outcomes and possible mechanisms. Here, we report a screening workflow and comprehensive multi-omics characterization of Bacillus spp. for use in broiler chickens. Host-derived Bacillus strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two Bacillus amyloliquefaciens (Ba ATCC PTA126784 and ATCC PTA126785), and a Bacillus subtilis (Bs ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of Ba ATCC PTA12684 (Ba-PTA84) in the feed of broiler chickens resulted in improved growth performance, as shown by a significantly improved feed conversion ratio (3.3%), increased of European Broiler Index (6.2%), and increased average daily gain (ADG) (3.5%). Comparison of the cecal microbiomes from Ba PTA84-treated and control animals suggested minimal differences in microbiome structure, indicating that the observed growth promotion presumably was not mediated by modulation of cecal microbiome.
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Affiliation(s)
- Dwi Susanti
- Division of Discovery Biology, Bacteriology and Microbiome, Elanco Animal Health, Greenfield, IN, United States
| | - Alyssa Volland
- Division of Discovery Biology, Bacteriology and Microbiome, Elanco Animal Health, Greenfield, IN, United States
| | - Nilesh Tawari
- Division of Global Computational Sciences, Elanco Animal Health, Greenfield, IN, United States
| | - Nielson Baxter
- Division of Nutritional Health, Elanco Animal Health, Greenfield, IN, United States
| | - Dharanesh Gangaiah
- Division of Discovery Biology, Bacteriology and Microbiome, Elanco Animal Health, Greenfield, IN, United States
| | - Germán Plata
- Division of Global Computational Sciences, Elanco Animal Health, Greenfield, IN, United States
| | - Akshitha Nagireddy
- Division of Global Computational Sciences, Elanco Animal Health, Greenfield, IN, United States
| | - Troy Hawkins
- Division of Global Computational Sciences, Elanco Animal Health, Greenfield, IN, United States
| | - Shrinivasrao P Mane
- Division of Global Computational Sciences, Elanco Animal Health, Greenfield, IN, United States
| | - Arvind Kumar
- Division of Discovery Biology, Bacteriology and Microbiome, Elanco Animal Health, Greenfield, IN, United States
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4
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Grant JC, González-Beiras C, Amick KM, Fortney KR, Gangaiah D, Humphreys TL, Mitjà O, Abecasis A, Spinola SM. Multiple Class I and Class II Haemophilus ducreyi Strains Cause Cutaneous Ulcers in Children on an Endemic Island. Clin Infect Dis 2019; 67:1768-1774. [PMID: 29897409 DOI: 10.1093/cid/ciy343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/18/2018] [Indexed: 12/14/2022] Open
Abstract
Background Together with Treponema pallidum subspecies pertenue, Haemophilus ducreyi is a major cause of exudative cutaneous ulcers (CUs) in children. For H. ducreyi, both class I and class II strains, asymptomatic colonization, and environmental reservoirs have been found in endemic regions, but the epidemiology of this infection is unknown. Methods Based on published whole-genome sequences of H. ducreyi CU strains, a single-locus typing system was developed and applied to H. ducreyi-positive CU samples obtained prior to, 1 year after, and 2 years after the initiation of a mass drug administration campaign to eradicate CU on Lihir Island in Papua New Guinea. DNA from the CU samples was amplified with class I and class II dsrA-specific primers and sequenced; the samples were classified into dsrA types, which were geospatially mapped. Selection pressure analysis was performed on the dsrA sequences. Results Thirty-seven samples contained class I sequences, 27 contained class II sequences, and 13 contained both. There were 5 class I and 4 class II types circulating on the island; 3 types accounted for approximately 87% of the strains. The composition and geospatial distribution of the types varied little over time and there was no evidence of selection pressure. Conclusions Multiple strains of H. ducreyi cause CU on an endemic island and coinfections are common. In contrast to recent findings with T. pallidum pertenue, strain composition is not affected by antibiotic pressure, consistent with environmental reservoirs of H. ducreyi. Such reservoirs must be addressed to achieve eradication of H. ducreyi.
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Affiliation(s)
- Jacob C Grant
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis
| | | | - Kristen M Amick
- Department of Biology, Allegheny College, Meadville, Pennsylvania
| | - Kate R Fortney
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis
| | - Dharanesh Gangaiah
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis
| | | | - Oriol Mitjà
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea.,Barcelona Institute for Global Health, Hospital Clinic, University of Barcelona, Spain.,School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby
| | - Ana Abecasis
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Lisbon, Portugal
| | - Stanley M Spinola
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis.,Department of Medicine, Indiana University School of Medicine, Indianapolis.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis
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5
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Toh E, Gangaiah D, Batteiger BE, Williams JA, Arno JN, Tai A, Batteiger TA, Nelson DE. Neisseria meningitidis ST11 Complex Isolates Associated with Nongonococcal Urethritis, Indiana, USA, 2015-2016. Emerg Infect Dis 2018; 23:336-339. [PMID: 28098538 PMCID: PMC5324800 DOI: 10.3201/eid2302.161434] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
At a clinic in Indianapolis, Indiana, USA, we observed an increase in Neisseria gonorrhoeae–negative men with suspected gonococcal urethritis who had urethral cultures positive for N. meningitidis. We describe genomes of 2 of these N. meningitidis sequence type 11 complex urethritis isolates. Clinical evidence suggests these isolates may represent an emerging urethrotropic clade.
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6
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Gangaiah D, Raterman EL, Wu H, Fortney KR, Gao H, Liu Y, Jerse AE, Spinola SM. Both MisR (CpxR) and MisS (CpxA) Are Required for Neisseria gonorrhoeae Infection in a Murine Model of Lower Genital Tract Infection. Infect Immun 2017; 85:e00307-17. [PMID: 28652307 PMCID: PMC5563589 DOI: 10.1128/iai.00307-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 04/29/2017] [Accepted: 06/17/2017] [Indexed: 12/29/2022] Open
Abstract
During infection, Neisseria gonorrhoeae senses and responds to stress; such responses may be modulated by MisRS (NGO0177 and NGO0176), a two-component system that is a homolog of CpxRA. In Escherichia coli, CpxRA senses and responds to envelope stress; CpxA is a sensor kinase/phosphatase for CpxR, a response regulator. When a cpxA mutant is grown in medium containing glucose, CpxR is phosphorylated by acetyl phosphate but cannot be dephosphorylated, resulting in constitutive activation. Kandler and coworkers (J. L. Kandler, C. L. Holley, J. L. Reimche, V. Dhulipala, J. T. Balthazar, A. Muszyński, R. W. Carlson, and W. M. Shafer, Antimicrob Agents Chemother 60:4690-4700, 2016, https://doi.org/10.1128/AAC.00823-16) showed that MisR (CpxR) is required for the maintenance of membrane integrity and resistance to antimicrobial peptides, suggesting a role in gonococcal survival in vivo Here, we evaluated the contributions of MisR and MisS (CpxA) to gonococcal infection in a murine model of cervicovaginal colonization and identified MisR-regulated genes using RNA sequencing (RNA-Seq). The deletion of misR or misS severely reduced the capacity of N. gonorrhoeae to colonize mice or maintain infection over a 7-day period and reduced microbial fitness after exposure to heat shock. Compared to the wild type (WT), the inactivation of misR identified 157 differentially regulated genes, most of which encoded putative envelope proteins. The inactivation of misS identified 17 differentially regulated genes compared to the WT and 139 differentially regulated genes compared to the misR mutant, 111 of which overlapped those differentially expressed in the comparison of the WT versus the misR mutant. These data indicate that an intact MisRS system is required for gonococcal infection of mice. Provided the MisR is constitutively phosphorylated in the misS mutant, the data suggest that controlled but not constitutive activation is required for gonococcal infection in mice.
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Affiliation(s)
- Dharanesh Gangaiah
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erica L Raterman
- Department of Microbiology and Immunology, F. Edward Herbert School of Medicine, Uniformed Services University, Bethesda, Maryland, USA
| | - Hong Wu
- Department of Microbiology and Immunology, F. Edward Herbert School of Medicine, Uniformed Services University, Bethesda, Maryland, USA
| | - Kate R Fortney
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ann E Jerse
- Department of Microbiology and Immunology, F. Edward Herbert School of Medicine, Uniformed Services University, Bethesda, Maryland, USA
| | - Stanley M Spinola
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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7
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Gangaiah D, Spinola SM. Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies. PLoS Negl Trop Dis 2016; 10:e0005259. [PMID: 28027326 PMCID: PMC5222509 DOI: 10.1371/journal.pntd.0005259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 09/30/2016] [Revised: 01/09/2017] [Accepted: 12/14/2016] [Indexed: 01/15/2023] Open
Abstract
Background Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. Methodology/Principal Findings We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. Conclusions/Significance CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities. Cutaneous ulcers (CU) in children in yaws-endemic regions have long been attributed to Treponema pallidum subsp. pertenue; however, recent studies show that Haemophilus ducreyi is an important cause of CU in these regions. H. ducreyi was once thought to cause only the genital ulcer (GU) disease chancroid; phylogenetically, GU strains belong to two distinct classes called class I and class II. We previously showed that CU strains obtained from Samoa, Vanuatu and Papua New Guinea are genetically almost identical to class 1 GU strains. In this study, using published genomes from 11 additional CU strains from Ghana and Vanuatu, we show that CU strains diverged from both class I and class II GU strains and that multiple CU clones may circulate in endemic areas. These findings have implications for epidemiological typing and recovery of H. ducreyi strains from both CU and GU clinical samples.
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Affiliation(s)
- Dharanesh Gangaiah
- Departments of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Stanley M. Spinola
- Departments of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Departments of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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8
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Dbeibo L, Rensburg JV, Gangaiah D, Fortney K, Gao H, Liu Y, Spinola S. The CpxRA System in Uropathogenic Escherichia coli Regulates Major Virulence Genes. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.1758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lana Dbeibo
- Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Julia Van Rensburg
- Department of Microbiology and Immunology, Indiana University, Indianapolis, Indiana
| | - Dharanesh Gangaiah
- Department of Microbiology and Immunology, Indiana University, Indianapolis, Indiana
| | - Kate Fortney
- Department of Microbiology and Immunology, Indiana University, Indianapolis, Indiana
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana
| | - Stanley Spinola
- Department of Microbiology and Immunology, Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, Indiana
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9
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Kumar A, Gangaiah D, Torrelles JB, Rajashekara G. Polyphosphate and associated enzymes as global regulators of stress response and virulence in Campylobacter jejuni. World J Gastroenterol 2016; 22:7402-7414. [PMID: 27672264 PMCID: PMC5011657 DOI: 10.3748/wjg.v22.i33.7402] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/03/2016] [Accepted: 07/21/2016] [Indexed: 02/06/2023] Open
Abstract
Campylobacter jejuni (C. jejuni), a Gram-negative microaerophilic bacterium, is a predominant cause of bacterial foodborne gastroenteritis in humans worldwide. Despite its importance as a major foodborne pathogen, our understanding of the molecular mechanisms underlying C. jejuni stress survival and pathogenesis is limited. Inorganic polyphosphate (poly P) has been shown to play significant roles in bacterial resistance to stress and virulence in many pathogenic bacteria. C. jejuni contains the complete repertoire of enzymes required for poly P metabolism. Recent work in our laboratory and others have demonstrated that poly P controls a plethora of C. jejuni properties that impact its ability to survive in the environment as well as to colonize/infect mammalian hosts. This review article summarizes the current literature on the role of poly P in C. jejuni stress survival and virulence and discusses on how poly P-related enzymes can be exploited for therapeutic/prevention purposes. Additionally, the review article identifies potential areas for future investigation that would enhance our understanding of the role of poly P in C. jejuni and other bacteria, which ultimately would facilitate design of effective therapeutic/preventive strategies to reduce not only the burden of C. jejuni-caused foodborne infections but also of other bacterial infections in humans.
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10
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Chandrashekhar K, Kassem II, Nislow C, Gangaiah D, Candelero-Rueda RA, Rajashekara G. Transcriptome analysis of Campylobacter jejuni polyphosphate kinase (ppk1 and ppk2) mutants. Virulence 2015; 6:814-8. [PMID: 26537695 DOI: 10.1080/21505594.2015.1104449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Kshipra Chandrashekhar
- a Food Animal Health Research Program; Ohio Agricultural Research and Development Center; Department of Veterinary Preventive Medicine ; The Ohio State University ; Wooster , OH , USA
| | - Issmat I Kassem
- a Food Animal Health Research Program; Ohio Agricultural Research and Development Center; Department of Veterinary Preventive Medicine ; The Ohio State University ; Wooster , OH , USA
| | - Corey Nislow
- b Department of Pharmaceutical Sciences ; University of British Columbia ; Vancouver , BC Canada
| | - Dharanesh Gangaiah
- a Food Animal Health Research Program; Ohio Agricultural Research and Development Center; Department of Veterinary Preventive Medicine ; The Ohio State University ; Wooster , OH , USA
| | - Rosario A Candelero-Rueda
- a Food Animal Health Research Program; Ohio Agricultural Research and Development Center; Department of Veterinary Preventive Medicine ; The Ohio State University ; Wooster , OH , USA
| | - Gireesh Rajashekara
- a Food Animal Health Research Program; Ohio Agricultural Research and Development Center; Department of Veterinary Preventive Medicine ; The Ohio State University ; Wooster , OH , USA
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11
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Chandrashekhar K, Gangaiah D, Pina-Mimbela R, Kassem II, Jeon BH, Rajashekara G. Transducer like proteins of Campylobacter jejuni 81-176: role in chemotaxis and colonization of the chicken gastrointestinal tract. Front Cell Infect Microbiol 2015; 5:46. [PMID: 26075188 PMCID: PMC4444964 DOI: 10.3389/fcimb.2015.00046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 10/08/2014] [Accepted: 05/11/2015] [Indexed: 01/06/2023] Open
Abstract
Transducer Like Proteins (Tlps), also known as methyl accepting chemotaxis proteins (MCP), enable enteric pathogens to respond to changing nutrient levels in the environment by mediating taxis toward or away from specific chemoeffector molecules. Despite recent advances in the characterization of chemotaxis responses in Campylobacter jejuni, the impact of Tlps on the adaptation of this pathogen to disparate niches and hosts is not fully characterized. The latter is particularly evident in the case of C. jejuni 81-176, a strain that is known to be highly invasive. Furthermore, the cytoplasmic group C Tlps (Tlp5, 6, and 8) were not extensively evaluated. Here, we investigated the role of C. jejuni 81-176 Tlps in chemotaxis toward various substrates, biofilm formation, in vitro interaction with human intestinal cells, and chicken colonization. We found that the Δtlp6 and Δtlp10 mutants exhibited decreased chemotaxis toward aspartate, whereas the Δtlp6 mutant displayed a decreased chemotaxis toward Tri-Carboxylic Acid (TCA) cycle intermediates such as pyruvate, isocitrate, and succinate. Our findings also corroborated that more than one Tlp is involved in mediating chemotaxis toward the same nutrient. The deletion of tlps affected important phenotypes such as motility, biofilm formation, and invasion of human intestinal epithelial cells (INT-407). The Δtlp8 mutant displayed increased motility in soft agar and showed decreased biofilm formation. The Δtlp8 and Δtlp9 mutants were significantly defective in invasion in INT-407 cells. The Δtlp10 mutant was defective in colonization of the chicken proximal and distal gastrointestinal tract, while the Δtlp6 and Δtlp8 mutants showed reduced colonization of the duodenum and jejunum. Our results highlight the importance of Tlps in C. jejuni's adaptation and pathobiology.
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Affiliation(s)
- Kshipra Chandrashekhar
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research Development Center, The Ohio State University Wooster, OH, USA
| | - Dharanesh Gangaiah
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research Development Center, The Ohio State University Wooster, OH, USA
| | - Ruby Pina-Mimbela
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research Development Center, The Ohio State University Wooster, OH, USA
| | - Issmat I Kassem
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research Development Center, The Ohio State University Wooster, OH, USA
| | - Byeong H Jeon
- Department of Environmental Health Sciences, School of Public Health, University of Alberta Edmonton, AB, Canada
| | - Gireesh Rajashekara
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research Development Center, The Ohio State University Wooster, OH, USA
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12
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Zhang X, Gangaiah D, Munson RS, Spinola SM, Liu Y. Correcting imbalanced reads coverage in bacterial transcriptome sequencing with extreme deep coverage. ACTA ACUST UNITED AC 2014; 7:195-213. [PMID: 24878730 DOI: 10.1504/ijcbdd.2014.061646] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High throughput bacterial RNA-Seq experiments can generate extremely high and imbalanced sequencing coverage. Over- or under-estimation of gene expression levels will hinder accurate gene differential expression analysis. Here we evaluated strategies to identify expression differences of genes with high coverage in bacterial transcriptome data using either raw sequence reads or unique reads with duplicate fragments removed. In addition, we proposed a generalised linear model (GLM) based approach to identify imbalance in read coverage based on sequence compositions. Our results show that analysis using raw reads identifies more differentially expressed genes with more accurate fold change than using unique reads. We also demonstrate the presence of sequence composition related biases that are independent of gene expression levels and experimental conditions. Finally, genes that still show strong coverage imbalance after correction were tagged using statistical approach.
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Affiliation(s)
- Xinjun Zhang
- Center for Computational Biology and Bioinformatics, School of Informatics and Computing, Indiana University Bloomington, Bloomington, IN 47408, USA
| | - Dharanesh Gangaiah
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Robert S Munson
- The Center for Microbial Pathogenesis in the Research Institute at Nationwide Children's Hospital, Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Stanley M Spinola
- Department of Microbiology and Immunology, Department of Medicine, Department of Pathology and Laboratory Medicine, Center for Immunobiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Center for Medical Genomics, Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Malde A, Gangaiah D, Chandrashekhar K, Pina-Mimbela R, Torrelles JB, Rajashekara G. Functional characterization of exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) of Campylobacter jejuni. Virulence 2014; 5:521-33. [PMID: 24569519 DOI: 10.4161/viru.28311] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The inorganic polyphosphate (poly-P) is a key regulator of stress responses and virulence in many bacterial pathogens including Campylobacter jejuni. The role of exopolyphosphatases/guanosine pentaphosphate (pppGpp) phosphohydrolases (PPX/GPPA) in poly-P homeostasis and C. jejuni pathobiology remains unexplored. Here, we analyzed deletion mutants (∆ppx1, ∆ppx2) and the double knockout mutant (dkppx), all ∆ppx mutants exhibited increased capacity to accumulate poly-P; however only ∆ppx1 and dkppx mutants showed decreased accumulation of ppGpp, an alarmone molecule that regulates stringent response in bacteria, suggesting potential dual role for PPX1/GPPA. Nutrient survival defect of ∆ppx mutants was rescued by the supplementation of specific amino acids implying that survival defect may be associated with decreased ppGpp and/ or increased poly-P in ∆ppx mutants. The ppk1 and spoT were upregulated in both ∆ppx1 and ∆ppx2 suggesting a compensatory role for SpoT and Ppk1 in poly-P and ppGpp homeostasis. The lack of ppx genes resulted in defects in motility, biofilm formation, nutrient stress survival, invasion and intracellular survival indicating that maintaining a certain level of poly-P is critical for ppx genes in C. jejuni pathophysiology. Both ppx1 and ppx2 mutants were resistant to human complement-mediated killing; however, the dkppx mutant was sensitive. The serum susceptibility did not occur in the presence of MgCl 2 and EGTA suggesting an involvement of the classical or lectin pathway of complement mediated killing. Interestingly, the chicken serum did not have any effect on the ∆ppx mutants' survival. The observed serum susceptibility was not related to C. jejuni surface capsule and lipooligosaccharide structures. Our study underscores the importance of PPX/GPPA proteins in poly-P and ppGpp homeostasis, two critical molecules that modulate environmental stress responses and virulence in C. jejuni.
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Affiliation(s)
- Anandkumar Malde
- Food Animal Health Research Program; Department of Veterinary Preventive Medicine; College of Veterinary Medicine; The Ohio State University; Wooster, OH USA
| | - Dharanesh Gangaiah
- Food Animal Health Research Program; Department of Veterinary Preventive Medicine; College of Veterinary Medicine; The Ohio State University; Wooster, OH USA
| | - Kshipra Chandrashekhar
- Food Animal Health Research Program; Department of Veterinary Preventive Medicine; College of Veterinary Medicine; The Ohio State University; Wooster, OH USA
| | - Ruby Pina-Mimbela
- Food Animal Health Research Program; Department of Veterinary Preventive Medicine; College of Veterinary Medicine; The Ohio State University; Wooster, OH USA
| | - Jordi B Torrelles
- Department of Microbial Infection and Immunity; Center for Microbial Interface Biology; The Ohio State University; Columbus, OH USA
| | - Gireesh Rajashekara
- Food Animal Health Research Program; Department of Veterinary Preventive Medicine; College of Veterinary Medicine; The Ohio State University; Wooster, OH USA
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14
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Drozd M, Gangaiah D, Liu Z, Rajashekara G. Contribution of TAT system translocated PhoX to Campylobacter jejuni phosphate metabolism and resilience to environmental stresses. PLoS One 2011; 6:e26336. [PMID: 22028859 PMCID: PMC3197622 DOI: 10.1371/journal.pone.0026336] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 09/25/2011] [Indexed: 12/12/2022] Open
Abstract
Campylobacter jejuni is a common gastrointestinal pathogen that colonizes food animals; it is transmitted via fecal contamination of food, and infections in immune-compromised people are more likely to result in serious long-term illness. Environmental phosphate is likely an important sensor of environmental fitness and the ability to obtain extracellular phosphate is central to the bacteria's core metabolic responses. PhoX is the sole alkaline phosphatase in C. jejuni, a substrate of the TAT transport system. Alkaline phosphatases mediate the hydrolytic removal of inorganic phosphate (Pi) from phospho-organic compounds and thereby contribute significantly to the polyphosphate kinase 1 (ppk1) mediated formation of poly P, a molecule that regulates bacterial response to stresses and virulence. Similarly, deletion of the tatC gene, a key component of the TAT system, results in diverse phenotypes in C. jejuni including reduced stress tolerance and in vivo colonization. Therefore, here we investigated the contribution of phoX in poly P synthesis and in TAT-system mediated responses. The phoX deletion mutant showed significant decrease (P<0.05) in poly P accumulation in stationary phase compared to the wild-type, suggesting that PhoX is a major contributor to the inorganic phosphate pool in the cell which is essential for poly P synthesis. The phoX deletion is sufficient for a nutrient stress defect similar to the defect previously described for the ΔtatC mutant. Additionally, the phoX deletion mutant has increased resistance to certain antimicrobials. The ΔphoX mutant was also moderately defective in invasion and intracellular survival within human intestinal epithelial cells as well as in chicken colonization. Further, the ΔphoX mutant produced increased biofilm that can be rescued with 1 mM inorganic phosphate. The qRT-PCR of the ΔphoX mutant revealed transcriptional changes that suggest potential mechanisms for the increased biofilm phenotype.
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Affiliation(s)
- Mary Drozd
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Dharanesh Gangaiah
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Zhe Liu
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
| | - Gireesh Rajashekara
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, United States of America
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15
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Kassem II, Sanad Y, Gangaiah D, Lilburn M, Lejeune J, Rajashekara G. Use of bioluminescence imaging to monitor Campylobacter survival in chicken litter. J Appl Microbiol 2011; 109:1988-97. [PMID: 20722878 DOI: 10.1111/j.1365-2672.2010.04828.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [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
AIM The aim of this study was to develop a novel approach for characterizing the growth and persistence of Campylobacter in different poultry-rearing environments. Specifically, we constructed bioluminescent Campylobacter strains and used them to monitor the survival of these pathogens in litter (bedding) material. METHODS AND RESULTS We inserted shuttle plasmids carrying the luminescence genes (luxCDABE) into C. jejuni and C. coli to construct bioluminescent strains of these pathogens. The strains were spiked into microcosms containing samples of litter-washings and dry litter collected from different enclosures that housed broiler chickens. Our results show that C. jejuni and C. coli survived for at least 20 days in reused (old) litter while the growth of these pathogens was inhibited in clean (new) litter. Furthermore, our results suggest that the availability of nutrients and the condition of the litter (reused vs new) are important factors in the persistence of these pathogens. CONCLUSIONS Reused litter can potentially predispose chickens to Campylobacter contamination and maintaining clean litter might reduce the incidences of colonization with these pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY Bioluminescence provided a simple, sensitive, and rapid approach for analysing the growth dynamics of Campylobacter. Using this technology, we highlighted the potential role of litter material in maintaining these pathogens in the chicken environment.
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Affiliation(s)
- I I Kassem
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA
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16
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Gangaiah D, Liu Z, Arcos J, Kassem II, Sanad Y, Torrelles JB, Rajashekara G. Polyphosphate kinase 2: a novel determinant of stress responses and pathogenesis in Campylobacter jejuni. PLoS One 2010; 5:e12142. [PMID: 20808906 PMCID: PMC2923150 DOI: 10.1371/journal.pone.0012142] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Inorganic polyphosphate (poly P) plays an important role in stress tolerance and virulence in many bacteria. PPK1 is the principal enzyme involved in poly P synthesis, while PPK2 uses poly P to generate GTP, a signaling molecule that serves as an alternative energy source and a precursor for various physiological processes. Campylobacter jejuni, an important cause of foodborne gastroenteritis in humans, possesses homologs of both ppk1 and ppk2. ppk1 has been previously shown to impact the pathobiology of C. jejuni. METHODOLOGY/PRINCIPAL FINDINGS Here, we demonstrate for the first time that the deletion of ppk2 in C. jejuni resulted in a significant decrease in poly P-dependent GTP synthesis, while displaying an increased intracellular ATP:GTP ratio. The Deltappk2 mutant exhibited a significant survival defect under osmotic, nutrient, aerobic, and antimicrobial stresses and displayed an enhanced ability to form static biofilms. However, the Deltappk2 mutant was not defective in poly P and ppGpp synthesis suggesting that PPK2-mediated stress tolerance is not ppGpp-mediated. Importantly, the Deltappk2 mutant was significantly attenuated in invasion and intracellular survival within human intestinal epithelial cells as well as in chicken colonization. CONCLUSIONS/SIGNIFICANCE Taken together, we have highlighted the role of PPK2 as a novel pathogenicity determinant that is critical for C. jejuni survival, adaptation, and persistence in the host environments. PPK2 is absent in humans and animals; therefore, can serve as a novel target for therapeutic intervention of C. jejuni infections.
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Affiliation(s)
- Dharanesh Gangaiah
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, United States of America
| | - Zhe Liu
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, United States of America
| | - Jesús Arcos
- Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Issmat I. Kassem
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, United States of America
| | - Yasser Sanad
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, United States of America
| | - Jordi B. Torrelles
- Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Gireesh Rajashekara
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, United States of America
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Rajashekara G, Drozd M, Gangaiah D, Jeon B, Liu Z, Zhang Q. Functional characterization of the twin-arginine translocation system in Campylobacter jejuni. Foodborne Pathog Dis 2010; 6:935-45. [PMID: 19799526 DOI: 10.1089/fpd.2009.0298] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human campylobacterosis is one of the most commonly occurring types of bacterial food poisoning in the United States and other developed countries. Most human cases are due to Campylobacter jejuni that is commonly found in the gastrointestinal tract of chickens. The twin-arginine translocase (TAT) secretion system uses N-terminal peptide tags with a distinct twin-arginine-containing motif to identify partially or fully folded proteins and directs them across the cytoplasmic membrane. In other bacteria, the TAT system contributes to diverse phenotypes, including virulence, but the role of this secretion system in Campylobacter pathophysiology is still not well defined. Genome sequence of C. jejuni revealed TAT pathway genes as well as several proteins that contain TAT pathway targeting motifs. The predicted Tat substrates are highly conserved among all sequenced C. jejuni strains. Phenotypic analyses revealed that the tatC knockout has defects in biofilm formation, motility, and flagellation, as well as an increased susceptibility to antimicrobials. Additionally, the tatC mutant was defective in survival under osmotic shock, oxidative, and nutrient stresses. Our results also indicated that tatC is essential for C. jejuni to sustain colonization in chickens. These findings suggest that the TAT pathway affects Campylobacter physiology and contributes to stress responses, allowing this fastidious pathogen to adapt to various environmental conditions.
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Affiliation(s)
- Gireesh Rajashekara
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio 44691, USA.
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