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Detert K, Währer J, Nieselt K, Schmidt H. Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:582-596. [PMID: 37644642 PMCID: PMC10667640 DOI: 10.1111/1758-2229.13198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.
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Affiliation(s)
- Katharina Detert
- Department of Food Microbiology and Hygiene, Institute of Food Science and BiotechnologyUniversity of HohenheimStuttgartGermany
| | - Jonathan Währer
- Institute for Bioinformatics and Medical InformaticsUniversity of TübingenTübingenGermany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical InformaticsUniversity of TübingenTübingenGermany
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and BiotechnologyUniversity of HohenheimStuttgartGermany
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Huang YH, Yu KY, Huang SP, Chuang HW, Lin WZ, Cherng JH, Hung YW, Yeh MK, Hong PD, Liu CC. Development of a Nucleic Acid Lateral Flow Immunoassay for the Detection of Human Polyomavirus BK. Diagnostics (Basel) 2020; 10:E403. [PMID: 32545649 PMCID: PMC7345645 DOI: 10.3390/diagnostics10060403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 01/20/2023] Open
Abstract
The BK virus (BKV) is an emerging pathogen in immunocompromised individuals and widespread in the human population. Polymerase chain reaction is a simple and highly sensitive method for detecting BKV, but it is time consuming and requires expensive instruments and expert judgment. The lateral flow assay, a rapid, low-cost, minimal-labor, and easy-to-use diagnostic method, was successfully applied for pathogen detection. In this study, we used oligonucleotide probes to develop a simple and rapid sandwich-type lateral flow immunoassay for detecting BKV DNA within 45 minutes. The detection limit for the synthetic single-stranded DNA was 5 nM. The specificity study showed no cross-reactivity with other polyomaviruses, such as JC virus and simian virus 40. For the Escherichia coli containing BKV plasmid cultured samples, the sensitivity was determined to be 107 copies/mL. The approach offers great potential for BKV detection of various target analytes in point-of-care settings.
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Affiliation(s)
- Yi-Huei Huang
- Biomedical Engineering Program, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan;
| | - Kuan-Yi Yu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan; (K.-Y.Y.); (H.-W.C.); (M.-K.Y.)
| | - Shou-Ping Huang
- Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Hui-Wen Chuang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan; (K.-Y.Y.); (H.-W.C.); (M.-K.Y.)
| | - Wen-Zhi Lin
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 11490, Taiwan; (W.-Z.L.); (Y.-W.H.)
| | - Juin-Hong Cherng
- Department and Graduate Institute of Biology and Anatomy, National Defense Medical Center, Taipei 11490, Taiwan;
- Department of Gerontological Health Care, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan
| | - Yao-Wen Hung
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 11490, Taiwan; (W.-Z.L.); (Y.-W.H.)
| | - Ming-Kung Yeh
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11490, Taiwan; (K.-Y.Y.); (H.-W.C.); (M.-K.Y.)
| | - Po-Da Hong
- Biomedical Engineering Program, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan;
| | - Cheng-Che Liu
- Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taipei 11490, Taiwan;
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 11490, Taiwan; (W.-Z.L.); (Y.-W.H.)
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Somorin Y, Bouchard G, Gallagher J, Abram F, Brennan F, O’Byrne C. Roles for RpoS in survival of Escherichia coli during protozoan predation and in reduced moisture conditions highlight its importance in soil environments. FEMS Microbiol Lett 2017; 364:4159366. [DOI: 10.1093/femsle/fnx198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/13/2017] [Indexed: 11/13/2022] Open
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