1
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Ma X, Chen J, Zwietering MH, Abee T, Den Besten HMW. Stress resistant rpsU variants of Listeria monocytogenes can become underrepresented due to enrichment bias. Int J Food Microbiol 2024; 416:110680. [PMID: 38522149 DOI: 10.1016/j.ijfoodmicro.2024.110680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/21/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
Population heterogeneity is an important component of the survival mechanism of Listeria monocytogenes, leading to cells in a population with diverse stress resistance levels. We previously demonstrated that several ribosomal gene rpsU mutations enhanced the stress resistance of L. monocytogenes and lowered the growth rate at 30 °C and lower temperatures. This study investigated whether these switches in phenotypes could result in a bias in strain detection when standard enrichment-based procedures are applied to a variety of strains. Detailed growth kinetics analysis of L. monocytogenes strains were performed, including the LO28 wild type (WT) and rpsU variants V14 and V15, during two commonly used enrichment-based procedures described in the ISO 11290-1:2017 and the U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM). WT had a higher growth rate than the variants during the enrichment processes. Co-culture growth kinetics predictions for WT and rpsU variants showed that the detection chances of the rpsU mutants were reduced from ∼52 % to less than ∼13 % and ∼ 3 % during ISO and BAM enrichment, respectively, which were further validated through subsequent qPCR experiments. Higher heat stress resistance of rpsU variants did not lead to faster recovery during enrichment after heat treatment, and different pre-culturing temperatures before heat treatment did not significantly affect the growth kinetics of the WT and rpsU variants. Additionally, post-enrichment isolation procedures involving streaking on selective agar plates did not show preferences for isolating WT or rpsU variants nor affect the detection chance of rpsU variants. The difference in detection chance suggests that the selective enrichment procedures inadequately represent the genotypic diversity present in a sample. Hence, the enrichment bias during the L. monocytogenes isolation procedure may contribute to the observed underrepresentation of the rpsU mutation among L. monocytogenes isolates deposited in publicly available genome databases. The underrepresentation of rpsU mutants in our findings suggests that biases introduced by standard isolation and enrichment procedures could inadvertently skew our understanding of genetic diversity when relying on public databases.
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Affiliation(s)
- Xuchuan Ma
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jingjie Chen
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Marcel H Zwietering
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Heidy M W Den Besten
- Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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2
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Koomen J, Ma X, Bombelli A, Tempelaars MH, Boeren S, Zwietering MH, den Besten HMW, Abee T. Ribosomal mutations enable a switch between high fitness and high stress resistance in Listeria monocytogenes. Front Microbiol 2024; 15:1355268. [PMID: 38605704 PMCID: PMC11006974 DOI: 10.3389/fmicb.2024.1355268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
Multiple stress resistant variants of Listeria monocytogenes with mutations in rpsU encoding ribosomal protein RpsU have previously been isolated after a single exposure to acid stress. These variants, including L. monocytogenes LO28 variant V14 with a complete deletion of the rpsU gene, showed upregulation of the general stress sigma factor Sigma B-mediated stress resistance genes and had a lower maximum specific growth rate than the LO28 WT, signifying a trade-off between stress resistance and fitness. In the current work V14 has been subjected to an experimental evolution regime, selecting for higher fitness in two parallel evolving cultures. This resulted in two evolved variants with WT-like fitness: 14EV1 and 14EV2. Comparative analysis of growth performance, acid and heat stress resistance, in combination with proteomics and RNA-sequencing, indicated that in both lines reversion to WT-like fitness also resulted in WT-like stress sensitivity, due to lack of Sigma B-activated stress defense. Notably, genotyping of 14EV1 and 14EV2 provided evidence for unique point-mutations in the ribosomal rpsB gene causing amino acid substitutions at the same position in RpsB, resulting in RpsB22Arg-His and RpsB22Arg-Ser, respectively. Combined with data obtained with constructed RpsB22Arg-His and RpsB22Arg-Ser mutants in the V14 background, we provide evidence that loss of function of RpsU resulting in the multiple stress resistant and reduced fitness phenotype, can be reversed by single point mutations in rpsB leading to arginine substitutions in RpsB at position 22 into histidine or serine, resulting in a WT-like high fitness and low stress resistance phenotype. This demonstrates the impact of genetic changes in L. monocytogenes' ribosomes on fitness and stress resistance.
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Affiliation(s)
- Jeroen Koomen
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Xuchuan Ma
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alberto Bombelli
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | | | | | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
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3
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Kohiyama M, Herrick J, Norris V. Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle. Life (Basel) 2023; 13:1890. [PMID: 37763294 PMCID: PMC10532879 DOI: 10.3390/life13091890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.
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Affiliation(s)
- Masamichi Kohiyama
- Institut Jacques Monod, Université Paris Cité, CNRS, 75013 Paris, France;
| | - John Herrick
- Independent Researcher, 3 rue des Jeûneurs, 75002 Paris, France;
| | - Vic Norris
- CBSA UR 4312, University of Rouen Normandy, University of Caen Normandy, Normandy University, 76000 Rouen, France
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4
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McNutt ZA, Roy B, Gemler BT, Shatoff EA, Moon KM, Foster L, Bundschuh R, Fredrick K. Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae. Nucleic Acids Res 2023; 51:1927-1942. [PMID: 36727479 PMCID: PMC9976891 DOI: 10.1093/nar/gkad047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) of 16S rRNA. Inhibition of SD-ASD pairing is due to sequestration of the 3' tail of 16S rRNA in a pocket formed by bS21, bS18, and bS6 on the 30S platform. Interestingly, in many Flavobacteriales, the gene encoding bS21, rpsU, contains an extended SD sequence. In this work, we present genetic and biochemical evidence that bS21 synthesis in Flavobacterium johnsoniae is autoregulated via a subpopulation of ribosomes that specifically lack bS21. Mutation or depletion of bS21 in the cell increases translation of reporters with strong SD sequences, such as rpsU'-gfp, but has no effect on other reporters. Purified ribosomes lacking bS21 (or its C-terminal region) exhibit higher rates of initiation on rpsU mRNA and lower rates of initiation on other (SD-less) mRNAs than control ribosomes. The mechanism of autoregulation depends on extensive pairing between mRNA and 16S rRNA, and exceptionally strong SD sequences, with predicted pairing free energies of < -13 kcal/mol, are characteristic of rpsU across the Bacteroidota. This work uncovers a clear example of specialized ribosomes in bacteria.
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Affiliation(s)
- Zakkary A McNutt
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Bappaditya Roy
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Bryan T Gemler
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V3T1Z4, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V3T1Z4, Canada
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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5
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Trautmann HS, Ramsey KM. A Ribosomal Protein Homolog Governs Gene Expression and Virulence in a Bacterial Pathogen. J Bacteriol 2022; 204:e0026822. [PMID: 36121290 PMCID: PMC9578407 DOI: 10.1128/jb.00268-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
The molecular machine necessary for protein synthesis, the ribosome, is generally considered constitutively functioning and lacking any inherent regulatory capacity. Yet ribosomes are commonly heterogeneous in composition and the impact of ribosome heterogeneity on translation is not well understood. Here, we determined that changes in ribosome protein composition govern gene expression in the intracellular bacterial pathogen Francisella tularensis. F. tularensis encodes three distinct homologs for bS21, a ribosomal protein involved in translation initiation, and analysis of purified F. tularensis ribosomes revealed they are heterogeneous with respect to bS21. The loss of one homolog, bS21-2, resulted in significant changes to the cellular proteome unlinked to changes in the transcriptome. Among the reduced proteins were components of the type VI secretion system (T6SS), an essential virulence factor encoded by the Francisella Pathogenicity Island. Furthermore, loss of bS21-2 led to an intramacrophage growth defect. Although multiple bS21 homologs complemented the loss of bS21-2 with respect to T6SS protein abundance, bS21-2 was uniquely necessary for robust intramacrophage growth, suggesting bS21-2 modulates additional virulence gene(s) distinct from the T6SS. Our results indicate that ribosome composition in F. tularensis, either directly or indirectly, posttranscriptionally modulates gene expression and virulence. Our findings are consistent with a model in which bS21 homologs function as posttranscriptional regulators, allowing preferential translation of specific subsets of mRNAs, likely at the stage of translation initiation. This work also raises the possibility that bS21 in other organisms may function similarly and that ribosome heterogeneity may permit many bacteria to posttranscriptionally regulate gene expression. IMPORTANCE While bacterial ribosomes are commonly heterogeneous in composition (e.g., incorporating different homologs for a ribosomal protein), how heterogeneity impacts translation is unclear. We found that the intracellular human pathogen Francisella tularensis has heterogeneous ribosomes, incorporating one of three homologs for ribosomal protein bS21. Furthermore, one bS21 homolog posttranscriptionally governs the expression of the F. tularensis type VI secretion system, an essential virulence factor. This bS21 homolog is also uniquely important for robust intracellular growth. Our data support a model in which bS21 heterogeneity leads to modulation of translation, providing another source of posttranscriptional gene regulation. Regulation of translation by bS21, or other sources of ribosomal heterogeneity, may be a conserved mechanism to control gene expression across the bacterial phylogeny.
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Affiliation(s)
- Hannah S. Trautmann
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Kathryn M. Ramsey
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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6
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Liu X, Pang X, Wu Y, Wu Y, Shi Y, Zhang X, Chen Q. Synergistic Antibacterial Mechanism of Mannosylerythritol Lipid-A and Lactic Acid on Listeria monocytogenes Based on Transcriptomic Analysis. Foods 2022; 11:foods11172660. [PMID: 36076848 PMCID: PMC9455235 DOI: 10.3390/foods11172660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 11/21/2022] Open
Abstract
Mannosylerythritol lipids-A (MEL-A) is a novel biosurfactant with multiple biological effects. The synergistic antibacterial activity and mechanism of MEL-A and lactic acid (LA) against Listeria monocytogenes were investigated. The synergistic effect resulted in a significant increase in the antibacterial rate compared to LA treatment alone. Genome-wide transcriptomic analysis was applied to deeply investigate the synergistic antibacterial mechanism. Gene Ontology (GO) enrichment analysis showed that the synergy between MEL-A and LA affected many potential cellular responses, including the sugar phosphotransferase system, carbohydrate transport, and ribosomes. KEGG enrichment analysis showed that the PTS system and ribosome-related pathways were significantly enriched. In addition, synergistic treatment affected locomotion and membrane-related cellular responses in GO enrichment analysis and carbohydrate metabolism and amino acid metabolism pathways in KEGG enrichment analysis compared to LA treatment alone. The accuracy of the transcriptome analysis results was verified by qPCR (R2 = 0.9903). This study will provide new insights for the prevention and control of L. monocytogenes.
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Affiliation(s)
- Xiayu Liu
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
| | - Xinxin Pang
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
| | - Yansha Wu
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
| | - Yajing Wu
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
| | - Ying Shi
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
| | - Xinglin Zhang
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
- College of Agriculture and Forestry, Linyi University, Linyi 276005, China
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Yuhangtang Rd. 866, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-571-86984316
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7
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Quereda JJ, Morón-García A, Palacios-Gorba C, Dessaux C, García-del Portillo F, Pucciarelli MG, Ortega AD. Pathogenicity and virulence of Listeria monocytogenes: A trip from environmental to medical microbiology. Virulence 2021; 12:2509-2545. [PMID: 34612177 PMCID: PMC8496543 DOI: 10.1080/21505594.2021.1975526] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
Listeria monocytogenes is a saprophytic gram-positive bacterium, and an opportunistic foodborne pathogen that can produce listeriosis in humans and animals. It has evolved an exceptional ability to adapt to stress conditions encountered in different environments, resulting in a ubiquitous distribution. Because some food preservation methods and disinfection protocols in food-processing environments cannot efficiently prevent contaminations, L. monocytogenes constitutes a threat to human health and a challenge to food safety. In the host, Listeria colonizes the gastrointestinal tract, crosses the intestinal barrier, and disseminates through the blood to target organs. In immunocompromised individuals, the elderly, and pregnant women, the pathogen can cross the blood-brain and placental barriers, leading to neurolisteriosis and materno-fetal listeriosis. Molecular and cell biology studies of infection have proven L. monocytogenes to be a versatile pathogen that deploys unique strategies to invade different cell types, survive and move inside the eukaryotic host cell, and spread from cell to cell. Here, we present the multifaceted Listeria life cycle from a comprehensive perspective. We discuss genetic features of pathogenic Listeria species, analyze factors involved in food contamination, and review bacterial strategies to tolerate stresses encountered both during food processing and along the host's gastrointestinal tract. Then we dissect host-pathogen interactions underlying listerial pathogenesis in mammals from a cell biology and systemic point of view. Finally, we summarize the epidemiology, pathophysiology, and clinical features of listeriosis in humans and animals. This work aims to gather information from different fields crucial for a comprehensive understanding of the pathogenesis of L. monocytogenes.
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Affiliation(s)
- Juan J. Quereda
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities. Valencia, Spain
| | - Alvaro Morón-García
- Departamento de Biología Celular. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid. Madrid, Spain
| | - Carla Palacios-Gorba
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities. Valencia, Spain
| | - Charlotte Dessaux
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
| | - Francisco García-del Portillo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
| | - M. Graciela Pucciarelli
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Biología Molecular ‘Severo Ochoa’. Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid. Madrid, Spain
| | - Alvaro D. Ortega
- Departamento de Biología Celular. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid. Madrid, Spain
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
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8
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Koomen J, Huijboom L, Ma X, Tempelaars MH, Boeren S, Zwietering MH, den Besten HMW, Abee T. Amino acid substitutions in ribosomal protein RpsU enable switching between high fitness and multiple-stress resistance in Listeria monocytogenes. Int J Food Microbiol 2021; 351:109269. [PMID: 34102570 DOI: 10.1016/j.ijfoodmicro.2021.109269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Microbial population heterogeneity contributes to differences in stress response between individual cells in a population, and can lead to the selection of genetically stable variants with increased stress resistance. We previously provided evidence that the multiple-stress resistant Listeria monocytogenes LO28 variant 15, carries a point mutation in the rpsU gene, resulting in an arginine-proline substitution in ribosomal protein RpsU (RpsU17Arg-Pro). Here, we investigated the trade-off between general stress sigma factor SigB-mediated stress resistance and fitness in variant 15 using experimental evolution. By selecting for higher fitness in two parallel evolving cultures, we identified two evolved variants: 15EV1 and 15EV2. Whole genome sequencing and SNP analysis showed that both parallel lines mutated in the same codon in rpsU as the original mutation resulting in RpsU17Pro-His (15EV1) and RpsU17Pro-Thr (15EV2). Using a combined phenotyping and proteomics approach, we assessed the resistance of the evolved variants to both heat and acid stress, and found that in both lines reversion to WT-like fitness also resulted in WT-like stress sensitivity. Proteome analysis of L. monocytogenes LO28 WT, variant 15, 15EV1, and 15EV2 revealed high level expression of SigB regulon members only in variant 15, whereas protein profiles of both evolved variants were highly similar to that of the LO28 WT. Experiments with constructed RpsU17Arg-Pro mutants in L. monocytogenes LO28 and EGDe, and RpsU17Arg-His and RpsU17Arg-Thr in LO28, confirmed that single amino acid substitutions in RpsU enable switching between multiple-stress resistant and high fitness states in L. monocytogenes.
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Affiliation(s)
- Jeroen Koomen
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Linda Huijboom
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Xuchuan Ma
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Marcel H Tempelaars
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, the Netherlands
| | - Marcel H Zwietering
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Heidy M W den Besten
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, the Netherlands, P.O. Box 17, 6700 AA Wageningen, the Netherlands.
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9
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Yang X, Wei Y, Shi Y, Han X, Chen S, Yang L, Li H, Sun B, Shi Y. Cucumber Ribosomal Protein CsRPS21 Interacts With P22 Protein of Cucurbit Chlorotic Yellows Virus. Front Microbiol 2021; 12:654697. [PMID: 33995313 PMCID: PMC8116660 DOI: 10.3389/fmicb.2021.654697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
Cucurbit chlorotic yellows virus (CCYV) is a cucurbit-infecting crinivirus. RNA silencing can be initiated as a plant defense against viruses. Viruses encode various RNA silencing suppressors to counteract antiviral silencing. P22 protein encoded by RNA1 of CCYV is a silencing suppressor, but its mechanism of action remains unclear. In this study, the cucumber ribosomal-like protein CsRPS21 was found to interact with P22 protein in vitro and in vivo. A conserved CsRPS21 domain was indispensable for its nuclear localization and interaction with P22. Transient expression of CsRPS21 in Nicotiana benthamiana leaves interfered with P22 accumulation and inhibited P22 silencing suppressor activity. CsRPS21 expression in N. benthamiana protoplasts inhibited CCYV accumulation. Increasing numbers of ribosomal proteins are being found to be involved in viral infections of plants. We identified a P22-interacting ribosomal protein, CsRPS21, and uncovered its role in early viral replication and silencing suppressor activity. Our study increases knowledge of the function of ribosomal proteins during viral infection.
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Affiliation(s)
- Xue Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ying Wei
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yajuan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xiaoyu Han
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Siyu Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Lingling Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Bingjian Sun
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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10
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Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning. Sci Rep 2021; 11:7736. [PMID: 33833319 PMCID: PMC8032699 DOI: 10.1038/s41598-021-87300-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/26/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus uberis is one of the leading pathogens causing mastitis worldwide. Identification of S. uberis strains that fail to respond to treatment with antibiotics is essential for better decision making and treatment selection. We demonstrate that the combination of supervised machine learning and matrix-assisted laser desorption ionization/time of flight (MALDI-TOF) mass spectrometry can discriminate strains of S. uberis causing clinical mastitis that are likely to be responsive or unresponsive to treatment. Diagnostics prediction systems trained on 90 individuals from 26 different farms achieved up to 86.2% and 71.5% in terms of accuracy and Cohen’s kappa. The performance was further increased by adding metadata (parity, somatic cell count of previous lactation and count of positive mastitis cases) to encoded MALDI-TOF spectra, which increased accuracy and Cohen’s kappa to 92.2% and 84.1% respectively. A computational framework integrating protein–protein networks and structural protein information to the machine learning results unveiled the molecular determinants underlying the responsive and unresponsive phenotypes.
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11
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Jha V, Roy B, Jahagirdar D, McNutt ZA, Shatoff EA, Boleratz BL, Watkins DE, Bundschuh R, Basu K, Ortega J, Fredrick K. Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Nucleic Acids Res 2021; 49:547-567. [PMID: 33330920 PMCID: PMC7797042 DOI: 10.1093/nar/gkaa1195] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein—bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.
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Affiliation(s)
- Vikash Jha
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Zakkary A McNutt
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Elan A Shatoff
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Bethany L Boleratz
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Dean E Watkins
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry & Biochemistry, Division of Hematology, The Ohio State University, Columbus, OH 43210, USA
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.,Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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12
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Njage PMK, Leekitcharoenphon P, Hansen LT, Hendriksen RS, Faes C, Aerts M, Hald T. Quantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data: Case of Listeria monocytogenes. Microorganisms 2020; 8:microorganisms8111772. [PMID: 33187247 PMCID: PMC7698238 DOI: 10.3390/microorganisms8111772] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 01/02/2023] Open
Abstract
The application of high-throughput DNA sequencing technologies (WGS) data remain an increasingly discussed but vastly unexplored resource in the public health domain of quantitative microbial risk assessment (QMRA). This is due to challenges including high dimensionality of WGS data and heterogeneity of microbial growth phenotype data. This study provides an innovative approach for modeling the impact of population heterogeneity in microbial phenotypic stress response and integrates this into predictive models inputting a high-dimensional WGS data for increased precision exposure assessment using an example of Listeria monocytogenes. Finite mixture models were used to distinguish the number of sub-populations for each of the stress phenotypes, acid, cold, salt and desiccation. Machine learning predictive models were selected from six algorithms by inputting WGS data to predict the sub-population membership of new strains with unknown stress response data. An example QMRA was conducted for cultured milk products using the strains of unknown stress phenotype to illustrate the significance of the findings of this study. Increased resistance to stress conditions leads to increased growth, the likelihood of higher exposure and probability of illness. Neglecting within-species genetic and phenotypic heterogeneity in microbial stress response may over or underestimate microbial exposure and eventual risk during QMRA.
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Affiliation(s)
- Patrick Murigu Kamau Njage
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (P.L.); (R.S.H.); (T.H.)
- Correspondence: ; Tel.: +45-35-88-75-31
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (P.L.); (R.S.H.); (T.H.)
| | - Lisbeth Truelstrup Hansen
- Research Group for Microbiology and Hygiene, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Rene S. Hendriksen
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (P.L.); (R.S.H.); (T.H.)
| | - Christel Faes
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University Katholieke Universiteit Leuven, 3590 Diepenbeek, Belgium; (C.F.); (M.A.)
| | - Marc Aerts
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University Katholieke Universiteit Leuven, 3590 Diepenbeek, Belgium; (C.F.); (M.A.)
| | - Tine Hald
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark; (P.L.); (R.S.H.); (T.H.)
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13
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Jayeola V, McClelland M, Porwollik S, Chu W, Farber J, Kathariou S. Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis. Front Microbiol 2020; 11:726. [PMID: 32499760 PMCID: PMC7242855 DOI: 10.3389/fmicb.2020.00726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 01/11/2023] Open
Abstract
Salmonella enterica is the leading foodborne pathogen associated with outbreaks involving low-moisture foods (LMFs). However, the genes involved in Salmonella's long-term survival on LMFs remain poorly characterized. In this study, in-shell pistachios were inoculated with Tn5-based mutant libraries of S. Enteritidis P125109, S. Typhimurium 14028s, and S. Newport C4.2 at approximate 108 CFU/g and stored at 25°C. Transposon sequencing analysis (Tn-seq) was then employed to determine the relative abundance of each Tn5 insertion site immediately after inoculation (T0), after drying (T1), and at 120 days (T120). In S. Enteritidis, S. Typhimurium, and S. Newport mutant libraries, the relative abundance of 51, 80, and 101 Tn5 insertion sites, respectively, was significantly lower at T1 compared to T0, while in libraries of S. Enteritidis and S. Typhimurium the relative abundance of 42 and 68 Tn5 insertion sites, respectively, was significantly lower at T120 compared to T1. Tn5 insertion sites with reduced relative abundance in this competition assay were localized in DNA repair, lipopolysaccharide biosynthesis and stringent response genes. Twelve genes among those under strong negative selection in the competition assay were selected for further study. Whole gene deletion mutants in ten of these genes, sspA, barA, uvrB, damX, rfbD, uvrY, lrhA, yifE, rbsR, and ompR, were impaired for individual survival on pistachios. The findings highlight the value of combined mutagenesis and sequencing to identify novel genes important for the survival of Salmonella in low-moisture foods.
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Affiliation(s)
- Victor Jayeola
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Jeffrey Farber
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Sophia Kathariou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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14
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Different carbon sources result in differential activation of sigma B and stress resistance in Listeria monocytogenes. Int J Food Microbiol 2020; 320:108504. [DOI: 10.1016/j.ijfoodmicro.2019.108504] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/23/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
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15
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Alves Â, Magalhães R, Brandão TR, Pimentel L, Rodríguez-Alcalá LM, Teixeira P, Ferreira V. Impact of exposure to cold and cold-osmotic stresses on virulence-associated characteristics of Listeria monocytogenes strains. Food Microbiol 2020; 87:103351. [DOI: 10.1016/j.fm.2019.103351] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/08/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
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16
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Stratakos AC, Ijaz UZ, Ward P, Linton M, Kelly C, Pinkerton L, Scates P, McBride J, Pet I, Criste A, Stef D, Couto JM, Sloan WT, Dorrell N, Wren BW, Stef L, Gundogdu O, Corcionivoschi N. In vitro and in vivo characterisation of Listeria monocytogenes outbreak isolates. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Zeng Z, Smid EJ, Boeren S, Notebaart RA, Abee T. Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization Stimulates Anaerobic Growth of Listeria monocytogenes EGDe. Front Microbiol 2019; 10:2660. [PMID: 31803170 PMCID: PMC6873790 DOI: 10.3389/fmicb.2019.02660] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles that optimize specific metabolic pathways referred to as metabolosomes involving transient production of toxic volatile metabolites such as aldehydes. Previous bioinformatics analysis predicted the presence of BMCs in 23 bacterial phyla including foodborne pathogens and a link with gene clusters for the utilization of host-derived substrates such as 1,2-propanediol utilization, i.e., the Pdu cluster. Although, transcriptional regulation of the Pdu cluster and its role in Listeria monocytogenes virulence in animal models have recently been reported, the experimental identification and the physiological role of BMCs in L. monocytogenes is still unexplored. Here, we ask whether BMCs could enable utilization of 1,2-propanediol (Pd) in L. monocytogenes under anaerobic conditions. Using L. monocytogenes EGDe as a model strain, we could demonstrate efficient utilization of Pd with concomitant production of 1-propanol and propionate after 24 h of anaerobic growth, while the utilization was significantly reduced in aerobic conditions. In line with this, expression of genes encoding predicted shell proteins and the signature enzyme propanediol dehydratase is upregulated more than 20-fold in cells anaerobically grown in Pdu-induced versus non-induced control conditions. Additional proteomics analysis confirmed the presence of BMC shell proteins and Pdu enzymes in cells that show active degradation of Pd. Furthermore, using transmission electron microscopy, BMC structures have been detected in these cells linking gene expression, protein composition, and BMCs to activation of the Pdu cluster in anaerobic growth of L. monocytogenes. Studies in defined minimal medium with Pd as an energy source showed a significant increase in cell numbers, indicating that Pdu and the predicted generation of ATP in the conversion of propionyl-phosphate to the end product propionate can support anaerobic growth of L. monocytogenes. Our findings may suggest a role for BMC-dependent utilization of Pd in L. monocytogenes growth, transmission, and interaction with the human host.
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Affiliation(s)
- Zhe Zeng
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Richard A Notebaart
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
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18
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Survival of acid stress adapted cells of Listeria monocytogenes serotypes 1/2a and 4b in commonly used disinfectants in broth and water models. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Peng G, Hou X, Zhang W, Song M, Yin M, Wang J, Li J, Liu Y, Zhang Y, Zhou W, Li X, Li G. Alkyl rhamnosides, a series of amphiphilic materials exerting broad-spectrum anti-biofilm activity against pathogenic bacteria via multiple mechanisms. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 46:S217-S232. [PMID: 30618296 DOI: 10.1080/21691401.2018.1491474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As novel amphiphilic materials, six uncharged alkyl rhamnosides incorporating various alkyl chain and one rhamnose amine quaternary ammonium salt were successfully synthesized in this study. Their amphiphilic properties (HLB and CMC), antimicrobial and anti-biofilm activity against S. aureus and P. aeruginosa were investigated. Differentially regulated proteins and pathways were identified by comparative proteomics research to first give a sight on how alkyl rhamnosides performed the anti-biofilm activity at protein and pathway levels. Among the uncharged alkyl rhamnosides, dodecyl rhamnoside and octyl rhamnoside showed the best antimicrobial and anti-biofilm ability against S. aureus and against P. aeruginosa, respectively. Interestingly, the relationships between amphiphilic properties or MIC with anti-biofilm activity were first established. Uncharged alkyl rhamnoside with an optimized HLB value of 5.0 had both the strongest antibacterial and anti-biofilm activity against S. aureus, and MIC was the maximum biofilm inhibitory concentration for all alkyl rhamnosides. Alkyl rhamnosides have a significant overall regulatory effect on the proteomics and pathways of bacterial biofilms, including energy production, substrates transportation, signal transduction, key molecules balance, and so on. These amphiphilic materials have a great potential to be used as additives in pharmaceutic, cosmetic, food industry, hospital and in other non-medical fields.
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Affiliation(s)
- Guanghua Peng
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Xucheng Hou
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Wenxi Zhang
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Maoyuan Song
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Mengya Yin
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Jiaxing Wang
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Jiajia Li
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Yajie Liu
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Yuanyuan Zhang
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Wenkai Zhou
- b Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College , Beijing , China
| | - Xinru Li
- a Beijing Key Laboratory of Molecular Pharmaceutics and New Drug System, School of Pharmaceutical Sciences , Peking University Health Science Center , Beijing , China
| | - Guiling Li
- b Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College , Beijing , China
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20
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den Besten HM, Amézquita A, Bover-Cid S, Dagnas S, Ellouze M, Guillou S, Nychas G, O'Mahony C, Pérez-Rodriguez F, Membré JM. Next generation of microbiological risk assessment: Potential of omics data for exposure assessment. Int J Food Microbiol 2018; 287:18-27. [DOI: 10.1016/j.ijfoodmicro.2017.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/15/2017] [Accepted: 10/03/2017] [Indexed: 12/30/2022]
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21
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Koomen J, den Besten HM, Metselaar KI, Tempelaars MH, Wijnands LM, Zwietering MH, Abee T. Gene profiling-based phenotyping for identification of cellular parameters that contribute to fitness, stress-tolerance and virulence of Listeria monocytogenes variants. Int J Food Microbiol 2018; 283:14-21. [DOI: 10.1016/j.ijfoodmicro.2018.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 10/14/2022]
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22
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Wu H, Zhao Y, Du Y, Miao S, Liu J, Li Y, Caiyin Q, Qiao J. Quantitative proteomics of Lactococcus lactis F44 under cross-stress of low pH and lactate. J Dairy Sci 2018; 101:6872-6884. [DOI: 10.3168/jds.2018-14594] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
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23
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Crespo Tapia N, den Besten HM, Abee T. Glycerol metabolism induces Listeria monocytogenes biofilm formation at the air-liquid interface. Int J Food Microbiol 2018; 273:20-27. [DOI: 10.1016/j.ijfoodmicro.2018.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 11/26/2022]
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24
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Castro H, Ruusunen M, Lindström M. Occurrence and growth of Listeria monocytogenes in packaged raw milk. Int J Food Microbiol 2017; 261:1-10. [PMID: 28850852 DOI: 10.1016/j.ijfoodmicro.2017.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 06/30/2017] [Accepted: 08/20/2017] [Indexed: 10/19/2022]
Abstract
The increased availability of packaged raw drinking milk necessitates the investigation of the occurrence and growth of Listeria monocytogenes in raw milk during distribution and storage. The occurrence of L. monocytogenes in 105 retailed raw milk bottles, 115 bulk tank milk samples, 23 in-line milk filter socks and in 50 environmental samples collected from an on-farm dairy establishment were investigated. Growth of inoculated low-level L. monocytogenes contamination was also investigated in two types of raw milk packaging, namely in 1-litre plastic bottles and 3-litre bag-in-boxes, both stored at three different storage temperatures of 6, 8 and 10°C. The occurrence of L. monocytogenes was higher (4.8%) in bottled raw milk stored until the use-by-date of the package compared to fresh bulk tank milk (1.7%). L. monocytogenes counts were ≤13CFU/ml in bottled raw milk and ≤1CFU/ml in bulk tank milk. L. monocytogenes was not detected in the packaging facility, but occurred very frequently (39%) in the milk filter socks. Subtyping of L. monocytogenes isolates using pulsed-field gel-electrophoresis revealed seven pulsotypes, of which two occurred in multiple samples. Targeted inoculum levels of 1-2CFU/ml yielded L. monocytogenes counts≥100CFU/ml within seven days of storage in 22% of the raw milk packages stored at 6°C, and in all of the raw milk packages stored at 8°C. The frequent occurrence of L. monocytogenes in raw milk and the ability of a low-level L. monocytogenes contamination to grow at refrigeration temperatures highlight the importance of consumer education regarding the appropriate raw milk storage and handling.
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Affiliation(s)
- Hanna Castro
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marjo Ruusunen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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25
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Hingston P, Chen J, Dhillon BK, Laing C, Bertelli C, Gannon V, Tasara T, Allen K, Brinkman FSL, Truelstrup Hansen L, Wang S. Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress. Front Microbiol 2017; 8:369. [PMID: 28337186 PMCID: PMC5340757 DOI: 10.3389/fmicb.2017.00369] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 01/11/2023] Open
Abstract
The human pathogen Listeria monocytogenes is a large concern in the food industry where its continuous detection in food products has caused a string of recalls in North America and Europe. Most recognized for its ability to grow in foods during refrigerated storage, L. monocytogenes can also tolerate several other food-related stresses with some strains possessing higher levels of tolerances than others. The objective of this study was to use a combination of phenotypic analyses and whole genome sequencing to elucidate potential relationships between L. monocytogenes genotypes and food-related stress tolerance phenotypes. To accomplish this, 166 L. monocytogenes isolates were sequenced and evaluated for their ability to grow in cold (4°C), salt (6% NaCl, 25°C), and acid (pH 5, 25°C) stress conditions as well as survive desiccation (33% RH, 20°C). The results revealed that the stress tolerance of L. monocytogenes is associated with serotype, clonal complex (CC), full length inlA profiles, and the presence of a plasmid which was identified in 55% of isolates. Isolates with full length inlA exhibited significantly (p < 0.001) enhanced cold tolerance relative to those harboring a premature stop codon (PMSC) in this gene. Similarly, isolates possessing a plasmid demonstrated significantly (p = 0.013) enhanced acid tolerance. We also identified nine new L. monocytogenes sequence types, a new inlA PMSC, and several connections between CCs and the presence/absence or variations of specific genetic elements. A whole genome single-nucleotide-variants phylogeny revealed sporadic distribution of tolerant isolates and closely related sensitive and tolerant isolates, highlighting that minor genetic differences can influence the stress tolerance of L. monocytogenes. Specifically, a number of cold and desiccation sensitive isolates contained PMSCs in σB regulator genes (rsbS, rsbU, rsbV). Collectively, the results suggest that knowing the sequence type of an isolate in addition to screening for the presence of full-length inlA and a plasmid, could help food processors and food agency investigators determine why certain isolates might be persisting in a food processing environment. Additionally, increased sequencing of L. monocytogenes isolates in combination with stress tolerance profiling, will enhance the ability to identify genetic elements associated with higher risk strains.
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Affiliation(s)
- Patricia Hingston
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
| | - Jessica Chen
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
| | - Bhavjinder K. Dhillon
- Department of Molecular Biology and Biochemistry, Simon Fraser UniversityBurnaby, BC, Canada
| | - Chad Laing
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaLethbridge, AB, Canada
| | - Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser UniversityBurnaby, BC, Canada
| | - Victor Gannon
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaLethbridge, AB, Canada
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Kevin Allen
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser UniversityBurnaby, BC, Canada
| | - Lisbeth Truelstrup Hansen
- Division for Microbiology and Production, National Food Institute, Technical University of DenmarkKongens Lyngby, Denmark
| | - Siyun Wang
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
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26
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den Besten HM, Aryani DC, Metselaar KI, Zwietering MH. Microbial variability in growth and heat resistance of a pathogen and a spoiler: All variabilities are equal but some are more equal than others. Int J Food Microbiol 2017; 240:24-31. [DOI: 10.1016/j.ijfoodmicro.2016.04.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/14/2016] [Accepted: 04/22/2016] [Indexed: 11/25/2022]
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27
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Metselaar KI, Abee T, Zwietering MH, den Besten HMW. Modeling and Validation of the Ecological Behavior of Wild-Type Listeria monocytogenes and Stress-Resistant Variants. Appl Environ Microbiol 2016; 82:5389-401. [PMID: 27342563 PMCID: PMC4988195 DOI: 10.1128/aem.00442-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/21/2016] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Listeria monocytogenes exhibits a heterogeneous response upon stress exposure which can be partially attributed to the presence of stable stress-resistant variants. This study aimed to evaluate the impact of the presence of stress-resistant variants of Listeria monocytogenes and their corresponding trade-offs on population composition under different environmental conditions. A set of stress robustness and growth parameters of the wild type (WT) and an rpsU deletion variant was obtained and used to model their growth behavior under combined mild stress conditions and to model their kinetics under single- and mixed-strain conditions in a simulated food chain. Growth predictions for the WT and the rpsU deletion variant matched the experimental data generally well, although some deviations from the predictions were observed. The data highlighted the influence of the environmental conditions on the ratio between the WT and variant. Prediction of performance in the simulated food chain proved to be challenging. The trend of faster growth and lower stress robustness for the WT than for the rpsU variant in the different steps of the chain was confirmed, but especially for the inactivation steps and the time needed to resume growth after an inactivation step, the experimental data deviated from the model predictions. This report provides insights into the conditions which can select for stress-resistant variants in industrial settings and discusses their potential persistence in food processing environments. IMPORTANCE Listeria monocytogenes exhibits a heterogeneous stress response which can partially be attributed to the presence of genetic variants. These stress-resistant variants survive better under severe conditions but have, on the other hand, a reduced growth rate. To date, the ecological behavior and potential impact of the presence of stress-resistant variants is not fully understood. In this study, we quantitatively assessed growth and inactivation behavior of wild-type L. monocytogenes and its stress-resistant variants. Predictions were validated under different conditions, as well as along a model food chain. This work illustrates the effects of environmental factors on population dynamics of L. monocytogenes and is a first step in evaluating the impact of population diversity on food safety.
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Affiliation(s)
- Karin I Metselaar
- Top Institute Food and Nutrition, Wageningen, the Netherlands Laboratory of Food Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition, Wageningen, the Netherlands Laboratory of Food Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Marcel H Zwietering
- Top Institute Food and Nutrition, Wageningen, the Netherlands Laboratory of Food Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Heidy M W den Besten
- Laboratory of Food Microbiology, Wageningen University, Wageningen, the Netherlands
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Cordero N, Maza F, Navea-Perez H, Aravena A, Marquez-Fontt B, Navarrete P, Figueroa G, González M, Latorre M, Reyes-Jara A. Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature. Front Microbiol 2016; 7:229. [PMID: 26973610 PMCID: PMC4772535 DOI: 10.3389/fmicb.2016.00229] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 02/12/2016] [Indexed: 01/12/2023] Open
Abstract
Listeria monocytogenes has become one of the principal foodborne pathogens worldwide. The capacity of this bacterium to grow at low temperatures has opened an interesting field of study in terms of the identification and classification of new strains of L. monocytogenes with different growth capacities at low temperatures. We determined the growth rate at 8°C of 110 strains of L. monocytogenes isolated from different food matrices. We identified a group of slow and fast strains according to their growth rate at 8°C and performed a global transcriptomic assay in strains previously adapted to low temperature. We then identified shared and specific transcriptional mechanisms, metabolic and cellular processes of both groups; bacterial motility was the principal process capable of differentiating the adaptation capacity of L. monocytogenes strains with different ranges of tolerance to low temperatures. Strains belonging to the fast group were less motile, which may allow these strains to achieve a greater rate of proliferation at low temperature.
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Affiliation(s)
- Ninoska Cordero
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Felipe Maza
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Helen Navea-Perez
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Istanbul University Istanbul, Turkey
| | - Bárbara Marquez-Fontt
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Paola Navarrete
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Guillermo Figueroa
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de ChileSantiago, Chile
| | - Mauricio Latorre
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de ChileSantiago, Chile; Mathomics, Center for Mathematical Modeling, Universidad de ChileSantiago, Chile
| | - Angélica Reyes-Jara
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
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Ostermann MF, Neubauer H, Frickmann H, Hagen RM. Correlation of rpsU Gene Sequence Clusters and Biochemical Properties, Gc-Ms Spectra and Resistance Profiles of Clinical Burkholderia Spp. Isolates. Eur J Microbiol Immunol (Bp) 2016; 6:25-39. [PMID: 27141312 PMCID: PMC4838983 DOI: 10.1556/1886.2016.00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 01/23/2023] Open
Abstract
This study assessed the variation of phenotypic features of clinical isolates of Burkholderia spp. from common rpsU gene sequence clusters. A total of 41 clinical Burkholderia spp. isolates from German mucoviscidosis patients was subjected to rpsU gene sequencing. Biochemical assessment included the API systems 20 NE and 50 CHE as well as the Micronaut NF system. Fatty acid patterns were assessed using gas chromatography-mass spectrometry (GC-MS). Broth microdilution was used to identify minimum inhibitory concentrations. Five rpsU gene sequence clusters comprised more than one clinical isolate. Altogether, assignments to three species and seven clusters comprising more than one Burkholderia species were performed. Inhomogeneity of biochemical reactions within the clusters ranged from 0/28 to 45/50 reactions. The standard deviation for fatty acid distributions ranged from 0% to 11.5%. Minimum inhibitory concentrations within the clusters showed a wide variation but only minor differences between the clusters. Broad variations within identified rpsU gene sequence clusters regarding biochemical reactions, fatty acid patterns, and resistance patterns of clinical Burkholderia spp. isolates make the application of rpsU gene sequence analysis as a stand-alone procedure for discriminations within the Burkholderia cepacia complex unreliable.
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Affiliation(s)
| | | | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Germany; Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Germany
| | - Ralf Matthias Hagen
- Deployment Health Surveillance Capability, NATO Center of Excellence for Military Medicine , Munich, Germany
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Metselaar KI, Saá Ibusquiza P, Ortiz Camargo AR, Krieg M, Zwietering MH, den Besten HMW, Abee T. Performance of stress resistant variants of Listeria monocytogenes in mixed species biofilms with Lactobacillus plantarum. Int J Food Microbiol 2015; 213:24-30. [PMID: 25935090 DOI: 10.1016/j.ijfoodmicro.2015.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 11/25/2022]
Abstract
Population diversity and the ability to adapt to changing environments allow Listeria monocytogenes to grow and survive under a wide range of environmental conditions. In this study, we aimed to evaluate the performance of a set of acid resistant L. monocytogenes variants in mixed-species biofilms with Lactobacillus plantarum as well as their benzalkonium chloride (BAC) resistance in these biofilms. L. monocytogenes LO28 wild type and acid resistant variants were capable of forming mixed biofilms with L. plantarum at 20°C and 30°C in BHI supplemented with manganese and glucose. Homolactic fermentation of glucose by L. plantarum created an acidic environment with pH values below the growth boundary of L. monocytogenes. Some of the variants were able to withstand the low pH in the mixed biofilms for a longer time than the WT and there were clear differences in survival between the variants which could not be correlated to (lactic) acid resistance alone. Adaptation to mild pH of liquid cultures during growth to stationary phase increased the acid resistance of some variants to a greater extent than of others, indicating differences in adaptive behaviour between the variants. Two variants that showed a high level of acid adaptation when grown in liquid cultures, showed also better performance in mixed species biofilms. There were no clear differences in BAC resistance between the wild type and variants in mixed biofilms. It can be concluded that acid resistant variants of L. monocytogenes show diversity in their adaptation to acidic conditions and their capacity to survive in mixed cultures and biofilms with L. plantarum.
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Affiliation(s)
- Karin I Metselaar
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Paula Saá Ibusquiza
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Angela R Ortiz Camargo
- Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Myriam Krieg
- Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Marcel H Zwietering
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Heidy M W den Besten
- Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Tjakko Abee
- Top Institute Food and Nutrition, P.O. Box 557, 6700 AN Wageningen, The Netherlands; Laboratory of Food Microbiology, Wageningen University, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
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