1
|
Díaz-Formoso L, Contente D, Feito J, Hernández PE, Borrero J, Muñoz-Atienza E, Cintas LM. Genomic Sequence of Streptococcus salivarius MDI13 and Latilactobacillus sakei MEI5: Two Promising Probiotic Strains Isolated from European Hakes ( Merluccius merluccius, L.). Vet Sci 2024; 11:365. [PMID: 39195819 PMCID: PMC11359882 DOI: 10.3390/vetsci11080365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Frequently, diseases in aquaculture have been fought indiscriminately with the use of antibiotics, which has led to the development and dissemination of (multiple) antibiotic resistances in bacteria. Consequently, it is necessary to look for alternative and complementary approaches to chemotheraphy that are safe for humans, animals, and the environment, such as the use of probiotics in fish farming. The objective of this work was the Whole-Genome Sequencing (WGS) and bioinformatic and functional analyses of S. salivarius MDI13 and L. sakei MEI5, two LAB strains isolated from the gut of commercial European hakes (M. merluccius, L.) caught in the Northeast Atlantic Ocean. The WGS and bioinformatic and functional analyses confirmed the lack of transferable antibiotic resistance genes, the lack of virulence and pathogenicity issues, and their potentially probiotic characteristics. Specifically, genes involved in adhesion and aggregation, vitamin biosynthesis, and amino acid metabolism were detected in both strains. In addition, genes related to lactic acid production, active metabolism, and/or adaptation to stress and adverse conditions in the host gastrointestinal tract were detected in L. sakei MEI5. Moreover, a gene cluster encoding three bacteriocins (SlvV, BlpK, and BlpE) was identified in the genome of S. salivarius MDI13. The in vitro-synthesized bacteriocin BlpK showed antimicrobial activity against the ichthyopathogens Lc. garvieae and S. parauberis. Altogether, our results suggest that S. salivarius MDI13 and L. sakei MEI5 have a strong potential as probiotics to prevent fish diseases in aquaculture as an appropriate alternative/complementary strategy to the use of antibiotics.
Collapse
Affiliation(s)
| | | | - Javier Feito
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (Grupo SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos (Nutrición, Bromatología, Higiene y Seguridad Alimentaria), Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain; (L.D.-F.); (D.C.); (P.E.H.); (J.B.); (L.M.C.)
| | | | | | - Estefanía Muñoz-Atienza
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (Grupo SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos (Nutrición, Bromatología, Higiene y Seguridad Alimentaria), Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro, s/n, 28040 Madrid, Spain; (L.D.-F.); (D.C.); (P.E.H.); (J.B.); (L.M.C.)
| | | |
Collapse
|
2
|
Kobayashi J, Ohkusu M, Matsumoto T, Kubota N, Ishiwada N. Bacteriological and molecular characterization of temperature- and CO 2-dependent Streptococcus pneumoniae serotype 24F ST162 isolated from Japanese children. Microbiol Spectr 2023; 11:e0216523. [PMID: 37823633 PMCID: PMC10714769 DOI: 10.1128/spectrum.02165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE We characterized Streptococcus pneumoniae serotype 24F sequence type (ST) 162 isolated from Japanese children with invasive pneumococcal disease (IPD). Owing to its highly invasive nature, serotype 24F is expected to be isolated from clinically significant cases. Serotype 24F ST162 isolates tested in the present study did not grow at 35°C in ambient air. Therefore, antimicrobial susceptibility testing using the broth microdilution method, which is usually conducted in ambient air, cannot be performed, posing a clinical challenge. Clinical practitioners and laboratory personnel should be aware of the epidemiological, bacteriological, and molecular characteristics of serotype 24F ST162. We believe that our findings can help diagnose and treat IPD caused by serotype 24F ST162, a serotype expected to become problematic in the post-13 valent pneumococcal conjugate vaccine era.
Collapse
Affiliation(s)
- Jun Kobayashi
- Department of Laboratory Medicine, Nagano Children’s Hospital, Azumino, Japan
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, Japan
| | - Noriko Kubota
- Department of Laboratory Medicine, Nagano Children’s Hospital, Azumino, Japan
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, Chiba, Japan
| |
Collapse
|
3
|
Sabra W, Wang W, Goepfert C, Zeng AP. Food-web and metabolic interactions of the lung inhabitants Streptococcus pneumoniae and Pseudomonas aeruginosa. Environ Microbiol 2022; 24:4885-4898. [PMID: 35706134 DOI: 10.1111/1462-2920.16105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022]
Abstract
Bacteria that successfully adapt to different substrates and environmental niches within the lung and overcome the immune defence can cause serious lung infections. Such infections are generally complex, and recognised as polymicrobial in nature. Both Pseudomonas aeruginosa and Streptococcus pneumoniae can cause chronic lung infections and were both detected in cystic fibrosis (CF) lung at different stages. In this study, single and dual species cultures of Pseudomonas aeruginosa and Streptococcus pneumoniae were studied under well controlled planktonic growth conditions. Under pH-controlled conditions, both species apparently benefited from the presence of the other. In co-culture with P. aeruginosa, S. pneumoniae grew efficiently under aerobic conditions, whereas in pure S. pneumoniae culture, growth inhibition occurred in bioreactors with dissolved oxygen concentrations above the microaerobic range. Lactic acid and acetoin that are produced by S. pneumoniae was efficiently utilised by P. aeruginosa. In pH-uncontrolled co-cultures, the low pH triggered by S. pneumoniae assimilation of glucose and lactic acid production negatively affected the growth of both strains. Nevertheless, ammonia production improved significantly, and P. aeruginosa growth dominated at later growth stages. This study revealed unreported metabolic interactions of two important pathogenic microorganisms and shed new lights into pathophysiology of bacterial lung infection. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Wael Sabra
- Faculty of life science, Rheine-Waal University of applied sciences, Marie-Curie-Straße 1, Kleve.,Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, Hamburg, Germany
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, Hamburg, Germany
| | - Christiane Goepfert
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, Hamburg, Germany.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering
| |
Collapse
|
4
|
Pang X, Wu Y, Liu X, Wu Y, Shu Q, Niu J, Chen Q, Zhang X. The Lipoteichoic Acid-Related Proteins YqgS and LafA Contribute to the Resistance of Listeria monocytogenes to Nisin. Microbiol Spectr 2022; 10:e0209521. [PMID: 35196823 PMCID: PMC8865564 DOI: 10.1128/spectrum.02095-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a major pathogen contributing to foodborne outbreaks with high mortality. Nisin, a natural antimicrobial, has been widely used as a food preservative. However, the mechanisms of L. monocytogenes involved in nisin resistance have not yet to be fully defined. A mariner transposon library was constructed in L. monocytogenes, leading to the identification of 99 genes associated with the innate resistance to nisin via Transposon sequencing (Tn-seq) analysis. To validate the accuracy of the Tn-seq results, we constructed five mutants (ΔyqgS, ΔlafA, ΔvirR, ΔgtcA, and Δlmo1464) in L. monocytogenes. The results revealed that yqgS and lafA, the lipoteichoic acid-related genes, were essential for resistance to nisin, while the gtcA and lmo1464 mutants showed substantially enhanced nisin resistance. Densely wrinkled, collapsed surface and membrane breakdown were shown on ΔyqgS and ΔlafA mutants under nisin treatment. Deletion of yqgS and lafA altered the surface charge, and decreased the resistance to general stress conditions and cell envelope-acting antimicrobials. Furthermore, YqgS and LafA are required for biofilm formation and cell invasion of L. monocytogenes. Collectively, these results reveal novel mechanisms of nisin resistance in L. monocytogenes and may provide unique targets for the development of food-grade inhibitors for nisin-resistant foodborne pathogens. IMPORTANCE Listeria monocytogenes is an opportunistic Gram-positive pathogen responsible for listeriosis, and is widely present in a variety of foods including ready-to-eat foods, meat, and dairy products. Nisin is the only licensed lantibiotic by the FDA for use as a food-grade inhibitor in over 50 countries. A prior study suggests that L. monocytogenes are more resistant than other Gram-positive pathogens in nisin-mediated bactericidal effects. However, the mechanisms of L. monocytogenes involved in nisin resistance have not yet to be fully defined. Here, we used a mariner transposon library to identify nisin-resistance-related genes on a genome-wide scale via transposon sequencing. We found, for the first time, that YqgS and LafA (Lipoteichoic acid-related proteins) are required for resistance to nisin. Subsequently, we investigated the roles of YqgS and LafA in L. monocytogenes stress resistance, antimicrobial resistance, biofilm formation, and virulence in mammalian cells.
Collapse
Affiliation(s)
- Xinxin Pang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Yansha Wu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Xiayu Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Yajing Wu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Qin Shu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Jianrui Niu
- College of Agriculture and Forestry, Linyi University, Linyi, China
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Xinglin Zhang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
- College of Agriculture and Forestry, Linyi University, Linyi, China
| |
Collapse
|
5
|
Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. Front Genet 2020; 11:116. [PMID: 32194617 PMCID: PMC7063969 DOI: 10.3389/fgene.2020.00116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/31/2020] [Indexed: 11/22/2022] Open
Abstract
The mitis group of streptococci (MGS) is a member of the healthy human microbiome in the oral cavity and upper respiratory tract. Troublingly, some MGS are able to escape this niche and cause infective endocarditis, a severe and devastating disease. Genome-scale models have been shown to be valuable in investigating metabolism of bacteria. Here we present the first genome-scale model, iCJ415, for Streptococcus oralis SK141. We validated the model using gene essentiality and amino acid auxotrophy data from closely related species. iCJ415 has 71-76% accuracy in predicting gene essentiality and 85% accuracy in predicting amino acid auxotrophy. Further, the phenotype of S. oralis was tested using the Biolog Phenotype microarrays, giving iCJ415 a 82% accuracy in predicting carbon sources. iCJ415 can be used to explore the metabolic differences within the MGS, and to explore the complicated metabolic interactions between different species in the human oral cavity.
Collapse
Affiliation(s)
- Christian S Jensen
- The Regional Department of Clinical Microbiology, Region Zealand, Slagelse, Denmark
| | - Charles J Norsigian
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Xin Fang
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Xiaohui C Nielsen
- The Regional Department of Clinical Microbiology, Region Zealand, Slagelse, Denmark
| | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Slagelse, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| |
Collapse
|
6
|
Matsumoto Y, Miyake K, Ozawa K, Baba Y, Kusube T. Bicarbonate and unsaturated fatty acids enhance capsular polysaccharide synthesis gene expression in oral streptococci, Streptococcus anginosus. J Biosci Bioeng 2019; 128:511-517. [PMID: 31130336 DOI: 10.1016/j.jbiosc.2019.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 11/15/2022]
Abstract
We recently reported on the capsular polysaccharide (CP) synthesis (cps) genes of the oral streptococci, Streptococcus anginosus. In this study, we investigate the effects of carbon dioxide (CO2), bicarbonate (HCO3-) and unsaturated fatty acids (UFAs) on CP synthesis of S. anginosus. We found that CP production increased when bacteria were exposed to high concentrations of CO2. This increase was similarly observed in the presence of sodium bicarbonate (NaHCO3) under atmospheric condition. Since ectopic expression of carbonic anhydrase, which converts CO2 to HCO3-, eliminated the requirement for CO2 in CP production and growth of S. anginosus lacking this enzyme, it seemed that HCO3- is an essential factor for CP production. Furthermore, UFAs also stimulated the CP production. Promoter-reporter assay and quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis confirmed that stimulation of CP production occurs at the transcription level. The results of the promoter assays suggest that the expression and stimulation of cps genes by HCO3- or UFAs require the cpsA gene, which is located in the first position of the cps operon. With respect to the relationship between HCO3-and UFAs, HCO3- may stimulate UFA synthesis pathway at transcription level. Therefore, it is possible that UFAs are definitive signals for the CP production in S. anginosus.
Collapse
Affiliation(s)
- Yuko Matsumoto
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Katsuhide Miyake
- Department of Environmental Science and Technology, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tenpaku, Nagoya, Aichi 468-8502, Japan.
| | - Kento Ozawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasunori Baba
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Takasei Kusube
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| |
Collapse
|
7
|
Zhang X, de Maat V, Guzmán Prieto AM, Prajsnar TK, Bayjanov JR, de Been M, Rogers MRC, Bonten MJM, Mesnage S, Willems RJL, van Schaik W. RNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum. BMC Genomics 2017; 18:893. [PMID: 29162049 PMCID: PMC5699109 DOI: 10.1186/s12864-017-4299-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/13/2017] [Indexed: 12/30/2022] Open
Abstract
Background The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can survive and grow in blood during an infection have not yet been characterized. Here, we identify genes that contribute to growth of E. faecium in human serum through transcriptome profiling (RNA-seq) and a high-throughput transposon mutant library sequencing approach (Tn-seq). Results We first sequenced the genome of E. faecium E745, a vancomycin-resistant clinical isolate, using a combination of short- and long read sequencing, revealing a 2,765,010 nt chromosome and 6 plasmids, with sizes ranging between 9.3 kbp and 223.7 kbp. We then compared the transcriptome of E. faecium E745 during exponential growth in rich medium and in human serum by RNA-seq. This analysis revealed that 27.8% of genes on the E. faecium E745 genome were differentially expressed in these two conditions. A gene cluster with a role in purine biosynthesis was among the most upregulated genes in E. faecium E745 upon growth in serum. The E. faecium E745 transposon mutant library was then used to identify genes that were specifically required for growth of E. faecium in serum. Genes involved in de novo nucleotide biosynthesis (including pyrK_2, pyrF, purD, purH) and a gene encoding a phosphotransferase system subunit (manY_2) were thus identified to be contributing to E. faecium growth in human serum. Transposon mutants in pyrK_2, pyrF, purD, purH and manY_2 were isolated from the library and their impaired growth in human serum was confirmed. In addition, the pyrK_2 and manY_2 mutants were tested for their virulence in an intravenous zebrafish infection model and exhibited significantly attenuated virulence compared to E. faecium E745. Conclusions Genes involved in carbohydrate metabolism and nucleotide biosynthesis of E. faecium are essential for growth in human serum and contribute to the pathogenesis of this organism. These genes may serve as targets for the development of novel anti-infectives for the treatment of E. faecium bloodstream infections. Electronic supplementary material The online version of this article (10.1186/s12864-017-4299-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xinglin Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.,Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Vincent de Maat
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Ana M Guzmán Prieto
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Tomasz K Prajsnar
- Krebs Institute, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Mark de Been
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Marc J M Bonten
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Stéphane Mesnage
- Krebs Institute, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands. .,Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, United Kingdom.
| |
Collapse
|
8
|
Zhao L, Anderson MT, Wu W, T Mobley HL, Bachman MA. TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. BMC Bioinformatics 2017; 18:326. [PMID: 28683752 PMCID: PMC5500955 DOI: 10.1186/s12859-017-1745-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that multiple mutants in a gene provides independent evidence to prioritize that gene as being essential. The existing methods do not account for this feature or rely on a high-density transposon library. Moreover, these methods are unable to accommodate complex designs. RESULTS The method proposed here is specifically designed for the analysis of Tn-Seq data. It utilizes two steps to estimate the conditional essentiality for each gene in the genome. First, it collects evidence of conditional essentiality for each insertion by comparing read counts of that insertion between conditions. Second, it combines insertion-level evidence for the corresponding gene. It deals with data from both low- and high-density transposon libraries and accommodates complex designs. Moreover, it is very fast to implement. The performance of the proposed method was tested on simulated data and experimental Tn-Seq data from Serratia marcescens transposon mutant library used to identify genes that contribute to fitness in a murine model of infection. CONCLUSION We describe a new, efficient method for identifying conditionally essential genes in Tn-Seq experiments with high detection sensitivity and specificity. It is implemented as TnseqDiff function in R package Tnseq and can be installed from the Comprehensive R Archive Network, CRAN.
Collapse
Affiliation(s)
- Lili Zhao
- Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, USA.
| | - Mark T Anderson
- Department of Microbiology and Immunology, School of medicine, University of Michigan, Ann Arbor, USA
| | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, School of medicine, University of Michigan, Ann Arbor, USA
| | - Michael A Bachman
- Department of Pathology, School of medicine, University of Michigan, Ann Arbor, USA
| |
Collapse
|
9
|
Liu X, Gallay C, Kjos M, Domenech A, Slager J, van Kessel SP, Knoops K, Sorg RA, Zhang JR, Veening JW. High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae. Mol Syst Biol 2017; 13:931. [PMID: 28490437 PMCID: PMC5448163 DOI: 10.15252/msb.20167449] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genome‐wide screens have discovered a large set of essential genes in the opportunistic human pathogen Streptococcus pneumoniae. However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn‐seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high‐content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi‐based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp‐proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP‐dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets.
Collapse
Affiliation(s)
- Xue Liu
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands.,Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Clement Gallay
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Morten Kjos
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Arnau Domenech
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Sebastiaan P van Kessel
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Kèvin Knoops
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Robin A Sorg
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands .,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
10
|
de Vries SP, Gupta S, Baig A, Wright E, Wedley A, Jensen AN, Lora LL, Humphrey S, Skovgård H, Macleod K, Pont E, Wolanska DP, L'Heureux J, Mobegi FM, Smith DGE, Everest P, Zomer A, Williams N, Wigley P, Humphrey T, Maskell DJ, Grant AJ. Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models. Sci Rep 2017; 7:1251. [PMID: 28455506 PMCID: PMC5430854 DOI: 10.1038/s41598-017-01133-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/27/2017] [Indexed: 01/22/2023] Open
Abstract
Campylobacter is the most common cause of foodborne bacterial illness worldwide. Faecal contamination of meat, especially chicken, during processing represents a key route of transmission to humans. There is a lack of insight into the mechanisms driving C. jejuni growth and survival within hosts and the environment. Here, we report a detailed analysis of C. jejuni fitness across models reflecting stages in its life cycle. Transposon (Tn) gene-inactivation libraries were generated in three C. jejuni strains and the impact on fitness during chicken colonisation, survival in houseflies and under nutrient-rich and -poor conditions at 4 °C and infection of human gut epithelial cells was assessed by Tn-insertion site sequencing (Tn-seq). A total of 331 homologous gene clusters were essential for fitness during in vitro growth in three C. jejuni strains, revealing that a large part of its genome is dedicated to growth. We report novel C. jejuni factors essential throughout its life cycle. Importantly, we identified genes that fulfil important roles across multiple conditions. Our comprehensive screens showed which flagella elements are essential for growth and which are vital to the interaction with host organisms. Future efforts should focus on how to exploit this knowledge to effectively control infections caused by C. jejuni.
Collapse
Affiliation(s)
- Stefan P de Vries
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Srishti Gupta
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Abiyad Baig
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonnington, Leicestershire, United Kingdom
| | - Elli Wright
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Amy Wedley
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | | | - Lizeth LaCharme Lora
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Suzanne Humphrey
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Henrik Skovgård
- Department of Agroecology, University of Aarhus, Slagelse, Denmark
| | - Kareen Macleod
- University of Glasgow, Veterinary School, Glasgow, United Kingdom
| | - Elsa Pont
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Dominika P Wolanska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Joanna L'Heureux
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fredrick M Mobegi
- Department of Paediatric Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - David G E Smith
- Heriot-Watt University, School of Life Sciences, Edinburgh, Scotland, United Kingdom
| | - Paul Everest
- University of Glasgow, Veterinary School, Glasgow, United Kingdom
| | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nicola Williams
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Paul Wigley
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Thomas Humphrey
- School of Medicine, Institute of Life Sciences, Swansea University, Swansea, United Kingdom
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
11
|
Analysis of Campylobacter jejuni infection in the gnotobiotic piglet and genome-wide identification of bacterial factors required for infection. Sci Rep 2017; 7:44283. [PMID: 28281647 PMCID: PMC5345035 DOI: 10.1038/srep44283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 12/30/2022] Open
Abstract
To investigate how Campylobacter jejuni causes the clinical symptoms of diarrhoeal disease in humans, use of a relevant animal model is essential. Such a model should mimic the human disease closely in terms of host physiology, incubation period before onset of disease, clinical signs and a comparable outcome of disease. In this study, we used a gnotobiotic piglet model to study determinants of pathogenicity of C. jejuni. In this model, C. jejuni successfully established infection and piglets developed an increased temperature with watery diarrhoea, which was caused by a leaky epithelium and reduced bile re-absorption in the intestines. Further, we assessed the C. jejuni genes required for infection of the porcine gastrointestinal tract utilising a transposon (Tn) mutant library screen. A total of 123 genes of which Tn mutants showed attenuated piglet infection were identified. Our screen highlighted a crucial role for motility and chemotaxis, as well as central metabolism. In addition, Tn mutants of 14 genes displayed enhanced piglet infection. This study gives a unique insight into the mechanisms of C. jejuni disease in terms of host physiology and contributing bacterial factors.
Collapse
|
12
|
Identification of Bicarbonate as a Trigger and Genes Involved with Extracellular DNA Export in Mycobacterial Biofilms. mBio 2016; 7:mBio.01597-16. [PMID: 27923918 PMCID: PMC5142616 DOI: 10.1128/mbio.01597-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Extracellular DNA (eDNA) is an integral biofilm matrix component of numerous pathogens, including nontuberculous mycobacteria (NTM). Cell lysis is the source of eDNA in certain bacteria, but the source of eDNA remains unidentified for NTM, as well as for other eDNA-containing bacterial species. In this study, conditions affecting eDNA export were examined, and genes involved with the eDNA export mechanism were identified. After a method for monitoring eDNA in real time in undisturbed biofilms was established, different conditions affecting eDNA were investigated. Bicarbonate positively influenced eDNA export in a pH-independent manner in Mycobacterium avium, M. abscessus, and M. chelonae The surface-exposed proteome of M. avium in eDNA-containing biofilms revealed abundant carbonic anhydrases. Chemical inhibition of carbonic anhydrases with ethoxzolamide significantly reduced eDNA export. An unbiased transposon mutant library screen for eDNA export in M. avium identified many severely eDNA-attenuated mutants, including one not expressing a unique FtsK/SpoIIIE-like DNA-transporting pore, two with inactivation of carbonic anhydrases, and nine with inactivation of genes belonging to a unique genomic region, as well as numerous mutants involved in metabolism and energy production. Complementation of nine mutants that included the FtsK/SpoIIIE and carbonic anhydrase significantly restored eDNA export. Interestingly, several attenuated eDNA mutants have mutations in genes encoding proteins that were found with the surface proteomics, and many more mutations are localized in operons potentially encoding surface proteins. Collectively, our data strengthen the evidence of eDNA export being an active mechanism that is activated by the bacterium responding to bicarbonate. IMPORTANCE Many bacteria contain extracellular DNA (eDNA) in their biofilm matrix, as it has various biological and physical functions. We recently reported that nontuberculous mycobacteria (NTM) can contain significant quantities of eDNA in their biofilms. In some bacteria, eDNA is derived from dead cells, but that does not appear to be the case for all eDNA-containing organisms, including NTM. In this study, we found that eDNA export in NTM is conditionally dependent on the molecules to which the bacteria are exposed and that bicarbonate positively influences eDNA export. We also identified genes and proteins important for eDNA export, which begins to piece together a description of a mechanism for eDNA. Better understanding of eDNA export can give new targets for the development of antivirulence drugs, which are attractive because resistance to classical antibiotics is currently a significant problem.
Collapse
|
13
|
Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances. Sci Rep 2016; 6:34668. [PMID: 27876765 PMCID: PMC5120286 DOI: 10.1038/srep34668] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/16/2016] [Indexed: 01/14/2023] Open
Abstract
Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.
Collapse
|
14
|
Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing. Appl Environ Microbiol 2016; 82:6664-6671. [PMID: 27590816 PMCID: PMC5086560 DOI: 10.1128/aem.02281-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/31/2016] [Indexed: 01/04/2023] Open
Abstract
The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. IMPORTANCE A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.
Collapse
|
15
|
Kwon YM, Ricke SC, Mandal RK. Transposon sequencing: methods and expanding applications. Appl Microbiol Biotechnol 2015; 100:31-43. [DOI: 10.1007/s00253-015-7037-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/15/2015] [Accepted: 09/20/2015] [Indexed: 12/26/2022]
|
16
|
Ramirez M. Streptococcus pneumoniae. MOLECULAR MEDICAL MICROBIOLOGY 2015:1529-1546. [DOI: 10.1016/b978-0-12-397169-2.00086-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
17
|
Mobegi FM, van Hijum SAFT, Burghout P, Bootsma HJ, de Vries SPW, van der Gaast-de Jongh CE, Simonetti E, Langereis JD, Hermans PWM, de Jonge MI, Zomer A. From microbial gene essentiality to novel antimicrobial drug targets. BMC Genomics 2014; 15:958. [PMID: 25373505 PMCID: PMC4233050 DOI: 10.1186/1471-2164-15-958] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/23/2014] [Indexed: 01/12/2023] Open
Abstract
Background Bacterial respiratory tract infections, mainly caused by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are among the leading causes of global mortality and morbidity. Increased resistance of these pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials. Result Here, we report a proof of concept study for the reliable identification of potential drug targets in these human respiratory pathogens by combining high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics. Approximately 20% of all genes in these three species were essential for growth and viability, including 128 essential and conserved genes, part of 47 metabolic pathways. By comparing these essential genes to the human genome, and a database of genes from commensal human gut microbiota, we identified and excluded potential drug targets in respiratory tract pathogens that will have off-target effects in the host, or disrupt the natural host microbiota. We propose 249 potential drug targets, 67 of which are targets for 75 FDA-approved antimicrobials and 35 other researched small molecule inhibitors. Two out of four selected novel targets were experimentally validated, proofing the concept. Conclusion Here we have pioneered an attempt in systematically combining the power of high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics to discover potential drug targets at genome-scale. By circumventing the time-consuming and expensive laboratory screens traditionally used to select potential drug targets, our approach provides an attractive alternative that could accelerate the much needed discovery of novel antimicrobials. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-958) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Sacha A F T van Hijum
- Radboud Institute for Molecular Life Sciences, Laboratory of Paediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Verhagen LM, de Jonge MI, Burghout P, Schraa K, Spagnuolo L, Mennens S, Eleveld MJ, van der Gaast-de Jongh CE, Zomer A, Hermans PWM, Bootsma HJ. Genome-wide identification of genes essential for the survival of Streptococcus pneumoniae in human saliva. PLoS One 2014; 9:e89541. [PMID: 24586856 PMCID: PMC3934895 DOI: 10.1371/journal.pone.0089541] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Since Streptococcus pneumoniae transmits through droplet spread, this respiratory tract pathogen may be able to survive in saliva. Here, we show that saliva supports survival of clinically relevant S. pneumoniae strains for more than 24 h in a capsule-independent manner. Moreover, saliva induced growth of S. pneumoniae in growth-permissive conditions, suggesting that S. pneumoniae is well adapted for uptake of nutrients from this bodily fluid. By using Tn-seq, a method for genome-wide negative selection screening, we identified 147 genes potentially required for growth and survival of S. pneumoniae in saliva, among which genes predicted to be involved in cell envelope biosynthesis, cell transport, amino acid metabolism, and stress response predominated. The Tn-seq findings were validated by testing a panel of directed gene deletion mutants for their ability to survive in saliva under two testing conditions: at room temperature without CO2, representing transmission, and at 37°C with CO2, representing in-host carriage. These validation experiments confirmed that the plsX gene and the amiACDEF and aroDEBC operons, involved in respectively fatty acid metabolism, oligopeptide transport, and biosynthesis of aromatic amino acids play an important role in the growth and survival of S. pneumoniae in saliva at 37°C. In conclusion, this study shows that S. pneumoniae is well-adapted for growth and survival in human saliva and provides a genome-wide list of genes potentially involved in adaptation. This notion supports earlier evidence that S. pneumoniae can use human saliva as a vector for transmission.
Collapse
Affiliation(s)
- Lilly M. Verhagen
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marien I. de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Peter Burghout
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Kiki Schraa
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Lorenza Spagnuolo
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Svenja Mennens
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marc J. Eleveld
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - Aldert Zomer
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Peter W. M. Hermans
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Hester J. Bootsma
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
- * E-mail:
| |
Collapse
|
19
|
de Vries SPW, Rademakers RJA, van der Gaast-de Jongh CE, Eleveld MJ, Hermans PWM, Bootsma HJ. Deciphering the genetic basis ofMoraxella catarrhaliscomplement resistance: a critical role for the disulphide bond formation system. Mol Microbiol 2013; 91:522-37. [DOI: 10.1111/mmi.12475] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Stefan P. W. de Vries
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Rob J. A. Rademakers
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | | | - Marc J. Eleveld
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Peter W. M. Hermans
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Hester J. Bootsma
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| |
Collapse
|
20
|
de Vries SPW, Eleveld MJ, Hermans PWM, Bootsma HJ. Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells. PLoS One 2013; 8:e72193. [PMID: 23936538 PMCID: PMC3735583 DOI: 10.1371/journal.pone.0072193] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/05/2013] [Indexed: 12/31/2022] Open
Abstract
Moraxella catarrhalis is a mucosal pathogen that causes childhood otitis media and exacerbations of chronic obstructive pulmonary disease in adults. During the course of infection, M. catarrhalis needs to adhere to epithelial cells of different host niches such as the nasopharynx and lungs, and consequently, efficient adhesion to epithelial cells is considered an important virulence trait of M. catarrhalis. By using Tn-seq, a genome-wide negative selection screenings technology, we identified 15 genes potentially required for adherence of M. catarrhalis BBH18 to pharyngeal epithelial Detroit 562 and lung epithelial A549 cells. Validation with directed deletion mutants confirmed the importance of aroA (3-phosphoshikimate 1-carboxyvinyl-transferase), ecnAB (entericidin EcnAB), lgt1 (glucosyltransferase), and MCR_1483 (outer membrane lipoprotein) for cellular adherence, with ΔMCR_1483 being most severely attenuated in adherence to both cell lines. Expression profiling of M. catarrhalis BBH18 during adherence to Detroit 562 cells showed increased expression of 34 genes in cell-attached versus planktonic bacteria, among which ABC transporters for molybdate and sulfate, while reduced expression of 16 genes was observed. Notably, neither the newly identified genes affecting adhesion nor known adhesion genes were differentially expressed during adhesion, but appeared to be constitutively expressed at a high level. Profiling of the transcriptional response of Detroit 562 cells upon adherence of M. catarrhalis BBH18 showed induction of a panel of pro-inflammatory genes as well as genes involved in the prevention of damage of the epithelial barrier. In conclusion, this study provides new insight into the molecular interplay between M. catarrhalis and host epithelial cells during the process of adherence.
Collapse
Affiliation(s)
- Stefan P. W. de Vries
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Marc J. Eleveld
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter W. M. Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hester J. Bootsma
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
- * E-mail:
| |
Collapse
|
21
|
Burghout P, Quintero B, Bos L, Beilharz K, Veening JW, de Jonge MI, van der Linden M, van der Ende A, Hermans PWM. A single amino acid substitution in the MurF UDP-MurNAc-pentapeptide synthetase renders Streptococcus pneumoniae dependent on CO2 and temperature. Mol Microbiol 2013; 89:494-506. [PMID: 23750975 DOI: 10.1111/mmi.12292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2013] [Indexed: 11/30/2022]
Abstract
The respiratory tract pathogen Streptococcus pneumoniae encounters different levels of environmental CO2 during transmission, host colonization and disease. About 8% of all pneumococcal isolates are capnophiles that require CO2 -enriched growth conditions. The underlying molecular mechanism for caphnophilic behaviour, as well as its biological function is unknown. Here, we found that capnophilic S. pneumoniae isolates from clonal complex (CC) 156 (i.e. Spain(9V) -3 ancestry) and CC344 (i.e. Norway(NT) -42 ancestry) have a valine at position 179 in the MurF UDP-MurNAc-pentapeptide synthetase. At ≤ 30°C, the growth characteristics of capnophilic and non-capnophilic CC156 strains were equal, but at > 30°C growth and survival of MurF(V) (179) strains was dependent on > 0.1% CO2 -enriched conditions. Expression of MurF(V) (179) in S. pneumoniae R6 and G54 rendered these, otherwise non-capnophilic strains, capnophilic. Time-lapse microscopy revealed that a capnophilic CC156 strain undergoes rapid autolysis upon exposure to CO2 -poor conditions at 37°C, and staining with fluorescently labelled vancomycin showed a defect in de novo cell wall synthesis. In summary, in capnophilic S. pneumoniae strains from CC156 and CC344 cell wall synthesis is placed under control of environmental CO2 levels and temperature. This mechanism might represent a novel strategy of the pneumococcus to rapidly adapt and colonize its host under changing environmental conditions.
Collapse
Affiliation(s)
- Peter Burghout
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|