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Tan L, Guo Z, Shao Y, Ye L, Wang M, Deng X, Chen S, Li R. Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing. Nucleic Acids Res 2024; 52:8746-8762. [PMID: 39011882 PMCID: PMC11347139 DOI: 10.1093/nar/gkae601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
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Affiliation(s)
- Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhihao Guo
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yanwen Shao
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Miaomiao Wang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Xin Deng
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong, China
| | - Runsheng Li
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, 518057, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
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An L, Wu Y, Zhang B, Xu Q, Liao L, Wu S, Xu X, He Q, Pei X, Chen J. Transmission chains and molecular characterizations of extended-spectrum β-lactamase producing Enterobacteriaceae at a veterinary hospital in Chengdu, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 124:105658. [PMID: 39168275 DOI: 10.1016/j.meegid.2024.105658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/15/2024] [Accepted: 08/17/2024] [Indexed: 08/23/2024]
Abstract
The rapid emergence of Extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E) is a major global public health concern. Previous studies have identified that intensive medical care of dogs and cats in veterinary hospitals have accelerated the infections and spread of ESBL-E. To investigate the spread of ESBL-E in a veterinary hospital, a total of 202 samples including hospitalized animals, veterinary healthcare workers and environment were collected from a veterinary hospital in Chengdu, China. ESBL-E were identified by antimicrobial susceptibility testing and 16 s rRNA sequencing and were further conducted on ESBL gene detection and multilocus sequence typing (MLST). At last, strains with transmission potential were analyzed by whole genome sequencing (WGS). Our results showed that the overall prevalence of ESBL-positive isolates was 34.7% (70/202), with 55.3% (26/47) in animals, 29.3% (12/41) in healthcare workers and 28.1% (32/114) in environment swabs. Twenty diverse MLST types were detected, with ST744, ST231 as the most prevalent ones. Transmission chains of two ESBL-E.coli (ST744 blaCTX-M-18, blaTEM-1) from cat_21 to cat_14, and two ESBL-Kp (ST231 blaCTX-M-27, blaTEM-1, blaSHV-1) from cat_20 to cat_37 were further confirmed by WGS. Furthermore, interdisciplinary investigation and cooperation of AMR are needed to better limit the transmissions of high-risk strains and to implement effective public health interventions.
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Affiliation(s)
- Longyi An
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Yating Wu
- Beijing Tongzhou District Center for Disease Control and Prevention, Luhe Middle School, 1 North Street, Tongzhou District, Beijing, China
| | - Baochao Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Qiuhong Xu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Linxuan Liao
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Shanshan Wu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Xin Xu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Qiurong He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China
| | - Xiaofang Pei
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China; Non-Communicable Diseases Research Center, West China-PUMC C. C. Chen Institute of Health, Sichuan University, Chengdu 610041, China
| | - Jiayi Chen
- West China School of Public Health and West China Fourth Hospital, Sichuan University, 16#, Section 3, Renmin Road South, Chengdu 610041, Sichuan, China.
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Giles-Gómez M, Morales Huerta X, Pastelin-Palacios R, López-Macías C, Flores Montesinos MS, Astudillo-Melgar F, Escalante A. Analysis of the Probiotic Potential of Lactiplantibacillus plantarum LB1_P46 Isolated from the Mexican Fermented Pulque Beverage: A Functional and Genomic Analysis. Microorganisms 2024; 12:1652. [PMID: 39203494 PMCID: PMC11356911 DOI: 10.3390/microorganisms12081652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The traditional Mexican fermented beverage pulque has been considered a healthy product for treating gastrointestinal disorders. Lactic acid bacteria (LAB) have been identified as one of the most abundant microbial groups during pulque fermentation. As traditional pulque is consumed directly from the fermentation vessel, the naturally associated LABs are ingested, reaching the consumer's small intestine alive, suggesting their potential probiotic capability. In this contribution, we assayed the probiotic potential of the strain of Lactiplantibacillus plantarum LB1_P46 isolated from pulque produced in Huitzilac, Morelos State, Mexico. The characterization included resistance to acid pH (3.5) and exposure to bile salts at 37 °C; the assay of the hemolytic activity and antibiotic resistance profiling; the functional traits of cholesterol reduction and β-galactosidase activity; and several cell surface properties, indicating that this LAB possesses probiotic properties comparable to other LAB. Additionally, this L. plantarum showed significance in in vitro antimicrobial activity against several Gram-negative and Gram-positive bacteria and in vivo preventive anti-infective capability against Salmonella in a BALB/c mouse model. Several functional traits and probiotic activities assayed were correlated with the corresponding enzymes encoded in the complete genome of the strain. The genome mining for bacteriocins led to the identification of several bacteriocins and a ribosomally synthesized and post-translationally modified peptide encoding for the plantaricin EF. Results indicated that L. plantarum LB1_P46 is a promising probiotic LAB for preparing functional non-dairy and dairy beverages.
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Affiliation(s)
- Martha Giles-Gómez
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.G.-G.); (X.M.H.)
| | - Ximena Morales Huerta
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.G.-G.); (X.M.H.)
| | - Rodolfo Pastelin-Palacios
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (M.G.-G.); (X.M.H.)
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social (IMSS), Cuauhtémoc, Ciudad de México 06720, Mexico
| | - Mayrene Sarai Flores Montesinos
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (M.S.F.M.)
| | - Fernando Astudillo-Melgar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (M.S.F.M.)
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (M.S.F.M.)
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Yang J, Xu L, Zhou Y, Cui M, Liu D, Wang J, Wang Y, Deng X. Repurposing harmaline as a novel approach to reverse tmexCD1-toprJ1-mediated tigecycline resistance against klebsiella pneumoniae infections. Microb Cell Fact 2024; 23:152. [PMID: 38790017 PMCID: PMC11127330 DOI: 10.1186/s12934-024-02410-4] [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: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND A novel plasmid-mediated resistance-nodulation-division (RND) efflux pump gene cluster tmexCD1-toprJ1 in Klebsiella pneumoniae tremendously threatens the use of convenient therapeutic options in the post-antibiotic era, including the "last-resort" antibiotic tigecycline. RESULTS In this work, the natural alkaloid harmaline was found to potentiate tigecycline efficacy (4- to 32-fold) against tmexCD1-toprJ1-positive K. pneumoniae, which also thwarted the evolution of tigecycline resistance. Galleria mellonella and mouse infection models in vivo further revealed that harmaline is a promising candidate to reverse tigecycline resistance. Inspiringly, harmaline works synergistically with tigecycline by undermining tmexCD1-toprJ1-mediated multidrug resistance efflux pump function via interactions with TMexCD1-TOprJ1 active residues and dissipation of the proton motive force (PMF), and triggers a vicious cycle of disrupting cell membrane integrity and metabolic homeostasis imbalance. CONCLUSION These results reveal the potential of harmaline as a novel tigecycline adjuvant to combat hypervirulent K. pneumoniae infections.
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Affiliation(s)
- Jindian Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lei Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yonglin Zhou
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan, China
| | - Minhe Cui
- Jilin Province Mushuo Livestock Farming Co., Ltd., Jilin, China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianfeng Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Xuming Deng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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Wang X, Cui Y, Wang Z, Jiang H, Ma L, Li W, Yang X, Zhang J, Zhao Y, Li G. NhaA: A promising adjuvant target for colistin against resistant Escherichia coli. Int J Biol Macromol 2024; 268:131833. [PMID: 38663703 DOI: 10.1016/j.ijbiomac.2024.131833] [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: 03/03/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
The emergence and widespread of multidrug-resistant Gram-negative bacteria have posed a severe threat to human health and environmental safety, escalating into a global medical crisis. Utilization of antibiotic adjuvants is a rapid approach to combat bacterial resistance effectively since the development of new antimicrobial agents is a formidable challenge. NhaA, driven by proton motive force, is a crucial secondary transporter on the cytoplasmic membrane of Escherichia coli. We found that 2-Aminoperimidine (2-AP), which is a specific inhibitor of NhaA, could enhance the activity of colistin against sensitive E. coli and reverse the resistance in mcr-1 positive E. coli. Mechanistic studies indicated that 2-AP induced dysfunction in cytoplasmic membrane through the suppression of NhaA, leading to metabolic inhibition and ultimately enhancing the sensitivity of E. coli to colistin. Moreover, 2-AP restored the efficacy of colistin against resistant E. coli in two animal infection models. Our findings reveal the potential of NhaA as a novel target for colistin adjuvants, providing new possibilities for the clinical application of colistin.
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Affiliation(s)
- Xuelin Wang
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Yong Cui
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhaohui Wang
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Huilin Jiang
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Lei Ma
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Wenwen Li
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinghai Zhang
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Yongshan Zhao
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China.
| | - Guoqing Li
- Beijing Key Laboratory of Antimicrobial Agents, Laboratory of Pharmacology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Division for Medicinal Microorganisms Related Strains, CAMS Collection Center of Pathogenic Microorganisms, Beijing 100050, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [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] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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Huang Y, Wipat A, Bacardit J. Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains. Biotechnol Bioeng 2024; 121:355-365. [PMID: 37807718 PMCID: PMC10953381 DOI: 10.1002/bit.28567] [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: 05/09/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
Abstract
Foreign proteins are produced by introducing synthetic constructs into host bacteria for biotechnology applications. This process can cause resource competition between synthetic circuits and host cells, placing a metabolic burden on the host cells which may result in load stress and detrimental physiological changes. Consequently, the host bacteria can experience slow growth, and the synthetic system may suffer from suboptimal function. To help in the detection of bacterial load stress, we developed machine-learning strategies to select a minimal number of genes that could serve as biomarkers for the design of load stress reporters. We identified pairs of biomarkers that showed discriminative capacity to detect the load stress states induced in 41 engineered Escherichia coli strains.
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Affiliation(s)
- Yiming Huang
- Interdisciplinary Computing and Complex BioSystems GroupNewcastle UniversityNewcastle upon TyneUK
| | - Anil Wipat
- Interdisciplinary Computing and Complex BioSystems GroupNewcastle UniversityNewcastle upon TyneUK
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex BioSystems GroupNewcastle UniversityNewcastle upon TyneUK
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Rihacek M, Kosaristanova L, Fialova T, Kuthanova M, Eichmeier A, Hakalova E, Cerny M, Berka M, Palkovicova J, Dolejska M, Svec P, Adam V, Zurek L, Cihalova K. Zinc effects on bacteria: insights from Escherichia coli by multi-omics approach. mSystems 2023; 8:e0073323. [PMID: 37905937 PMCID: PMC10734530 DOI: 10.1128/msystems.00733-23] [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: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE A long-term exposure of bacteria to zinc oxide and zinc oxide nanoparticles leads to major alterations in bacterial morphology and physiology. These included biochemical and physiological processes promoting the emergence of strains with multi-drug resistance and virulence traits. After the removal of zinc pressure, bacterial phenotype reversed back to the original state; however, certain changes at the genomic, transcriptomic, and proteomic level remained. Why is this important? The extensive and intensive use of supplements in animal feed effects the intestinal microbiota of livestock and this may negatively impact the health of animals and people. Therefore, it is crucial to understand and monitor the impact of feed supplements on intestinal microorganisms in order to adequately assess and prevent potential health risks.
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Affiliation(s)
- Martin Rihacek
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ludmila Kosaristanova
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Tatiana Fialova
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Michaela Kuthanova
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ales Eichmeier
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Brno, Czechia
| | - Eliska Hakalova
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Brno, Czechia
| | - Martin Cerny
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, Brno, Czechia
| | - Miroslav Berka
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences Mendel University in Brno, Brno, Czechia
| | - Jana Palkovicova
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czechia
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Monika Dolejska
- Faculty of Medicine in Pilsen, Biomedical Center, Charles University, Pilsen, Czechia
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czechia
| | - Pavel Svec
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Ludek Zurek
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Kristyna Cihalova
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
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Chen L, Wang C, Su J. Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis. Microorganisms 2023; 11:2401. [PMID: 37894061 PMCID: PMC10609351 DOI: 10.3390/microorganisms11102401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.
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Affiliation(s)
- Liping Chen
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Chenglong Wang
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jianyu Su
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
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Wan Y, Wai Chi Chan E, Chen S. Maintenance and generation of proton motive force are both essential for expression of phenotypic antibiotic tolerance in bacteria. Microbiol Spectr 2023; 11:e0083223. [PMID: 37623371 PMCID: PMC10580908 DOI: 10.1128/spectrum.00832-23] [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: 02/25/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023] Open
Abstract
Bacterial antibiotic tolerance, a phenomenon first observed in 1944, is known to be responsible for both onset and exacerbation of recurrent and chronic bacterial infections. The development of antibiotic tolerance was previously thought to be due to a switch to physiological dormancy when bacteria encounter adverse growth conditions. Our recent laboratory findings, however, showed that a set of genes related to the maintenance of proton motive force (PMF) are up-regulated under starvation, indicating that the tolerant sub-population, which are commonly known as persisters, can actively maintain their tolerance phenotypes. In this study, we investigated the relative functional roles of proteins involved in the maintenance and active generation of PMF in mediating tolerance formation in bacteria and found that the PspA and RcsB proteins play a key role in PMF maintenance in persisters, as deletion of genes encoding these two proteins resulted in significantly lower tolerance levels. Consistently, expression of the OsmC and Bdm proteins, which is under regulation by RcsB, is required to maintain PMF and the antibiotic tolerance phenotypes. On the other hand, the NuoL, Ndh, AppC, CyoB, and NuoF proteins, which are electron transport chain (ETC) components, were also found to be actively expressed in persisters in order to generate PMF to support functioning of various tolerance mechanisms such as efflux activities. Our data show that active generation of PMF is even more important than the PMF maintenance functions of PspA and RcsB in the expression of antibiotic tolerance phenotypes in persisters. Assessment of double- and triple-gene knockout strains, in which the PMF maintenance genes and those encoding ETC components were simultaneously deleted, confirms that these two groups of genes are both required for the expression of antibiotic tolerance phenotypes and that a lack of these functions would result in complete PMF dissipation and accumulation of antibiotics in the intracellular compartment of persisters and eventually cell death. Products of these genes are, therefore, ideal targets for future development of anti-tolerance agents. IMPORTANCE In this work, bacteria were found to undergo active generation and maintenance of proton motive force (PMF) under adverse conditions, such as starvation so as to support a range of physiological functions in order to survive under such conditions for a prolonged period. The ability to maintain a substantial level of PMF was found to be directly linked to that exhibiting phenotypic antibiotic tolerance under nutrient starvation or other adverse conditions. These findings infer that bacteria do not simply become physiologically dormant when they become antibiotic tolerant, instead they need to produce a wide range of proteins including those which help prevent PMF dissipation, such as PspA and RcsB, and the electron transport chain components, such as NuoL and Ndh, that actively generate PMF even during long-term starvation. As antibiotic tolerant sub-population is known to play a role in eliciting recurrent and chronic infections, especially among patients with a weakened immune system, the PMF maintenance mechanisms identified in this work are potential targets for the development of new strategies to control recurrent and chronic infections.
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Affiliation(s)
- Yingkun Wan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- Department of Applied Biology and Chemical Technology, State Key Lab of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Department of Applied Biology and Chemical Technology, State Key Lab of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- City University of Hong Kong Chendu Research Institute, Chengdu, China
- Shenzhen Key Lab for Food Biological Safety Control, Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China
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Young M, Chojnacki M, Blanchard C, Cao X, Johnson WL, Flaherty D, Dunman PM. Genetic Determinants of Acinetobacter baumannii Serum-Associated Adaptive Efflux-Mediated Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1173. [PMID: 37508269 PMCID: PMC10376123 DOI: 10.3390/antibiotics12071173] [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: 06/09/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen of serious healthcare concern that is becoming increasingly difficult to treat due to antibiotic treatment failure. Recent studies have revealed that clinically defined antibiotic-susceptible strains upregulate the expression of a repertoire of putative drug efflux pumps during their growth under biologically relevant conditions, e.g., in human serum, resulting in efflux-associated resistance to physiologically achievable antibiotic levels within a patient. This phenomenon, termed Adaptive Efflux Mediated Resistance (AEMR), has been hypothesized to account for one mechanism by which antibiotic-susceptible A. baumannii fails to respond to antibiotic treatment. In the current study, we sought to identify genetic determinants that contribute to A. baumannii serum-associated AEMR by screening a transposon mutant library for members that display a loss of the AEMR phenotype. Results revealed that mutation of a putative pirin-like protein, YhaK, results in a loss of AEMR, a phenotype that could be complemented by a wild-type copy of the yhaK gene and was verified in a second strain background. Ethidium bromide efflux assays confirmed that the loss of AEMR phenotype due to pirin-like protein mutation correlated with reduced overarching efflux capacity. Further, flow cytometry and confocal microscopy measures of a fluorophore 7-(dimethylamino)-coumarin-4-acetic acid (DMACA)-tagged levofloxacin isomer, ofloxacin, further verified that YhaK mutation reduces AEMR-mediated antibiotic efflux. RNA-sequencing studies revealed that YhaK may be required for the expression of multiple efflux-associated systems, including MATE and ABC families of efflux pumps. Collectively, the data indicate that the A. baumannii YhaK pirin-like protein plays a role in modulating the organism's adaptive efflux-mediated resistance phenotype.
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Affiliation(s)
- Mikaeel Young
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Michaelle Chojnacki
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Catlyn Blanchard
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Xufeng Cao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, Lafayette, IN 47907, USA
| | - William L. Johnson
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
| | - Daniel Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University College of Pharmacy, Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN 47907, USA
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (M.Y.); (M.C.); (W.L.J.)
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12
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Transcriptome analysis reveals reasons for the low tolerance of Clostridium tyrobutyricum to furan derivatives. Appl Microbiol Biotechnol 2022; 107:327-339. [DOI: 10.1007/s00253-022-12281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
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13
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Roth M, Goodall ECA, Pullela K, Jaquet V, François P, Henderson IR, Krause KH. Transposon-Directed Insertion-Site Sequencing Reveals Glycolysis Gene gpmA as Part of the H2O2 Defense Mechanisms in Escherichia coli. Antioxidants (Basel) 2022; 11:antiox11102053. [PMID: 36290776 PMCID: PMC9598634 DOI: 10.3390/antiox11102053] [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: 09/30/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a common effector of defense mechanisms against pathogenic infections. However, bacterial factors involved in H2O2 tolerance remain unclear. Here we used transposon-directed insertion-site sequencing (TraDIS), a technique allowing the screening of the whole genome, to identify genes implicated in H2O2 tolerance in Escherichia coli. Our TraDIS analysis identified 10 mutants with fitness defect upon H2O2 exposure, among which previously H2O2-associated genes (oxyR, dps, dksA, rpoS, hfq and polA) and other genes with no known association with H2O2 tolerance in E. coli (corA, rbsR, nhaA and gpmA). This is the first description of the impact of gpmA, a gene involved in glycolysis, on the susceptibility of E. coli to H2O2. Indeed, confirmatory experiments showed that the deletion of gpmA led to a specific hypersensitivity to H2O2 comparable to the deletion of the major H2O2 scavenger gene katG. This hypersensitivity was not due to an alteration of catalase function and was independent of the carbon source or the presence of oxygen. Transcription of gpmA was upregulated under H2O2 exposure, highlighting its role under oxidative stress. In summary, our TraDIS approach identified gpmA as a member of the oxidative stress defense mechanism in E. coli.
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Affiliation(s)
- Myriam Roth
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- Correspondence:
| | - Emily C. A. Goodall
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Karthik Pullela
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Vincent Jaquet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- READS Unit, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals of Geneva, University Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland
| | - Ian R. Henderson
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
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14
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Zheng EJ, Andrews IW, Grote AT, Manson AL, Alcantar MA, Earl AM, Collins JJ. Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies. Nat Commun 2022; 13:2525. [PMID: 35534481 PMCID: PMC9085803 DOI: 10.1038/s41467-022-30272-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/22/2022] [Indexed: 01/21/2023] Open
Abstract
Antibiotic tolerance, or the ability of bacteria to survive antibiotic treatment in the absence of genetic resistance, has been linked to chronic and recurrent infections. Tolerant cells are often characterized by a low metabolic state, against which most clinically used antibiotics are ineffective. Here, we show that tolerance readily evolves against antibiotics that are strongly dependent on bacterial metabolism, but does not arise against antibiotics whose efficacy is only minimally affected by metabolic state. We identify a mechanism of tolerance evolution in E. coli involving deletion of the sodium-proton antiporter gene nhaA, which results in downregulated metabolism and upregulated stress responses. Additionally, we find that cycling of antibiotics with different metabolic dependencies interrupts evolution of tolerance in vitro, increasing the lifetime of treatment efficacy. Our work highlights the potential for limiting the occurrence and extent of tolerance by accounting for antibiotic dependencies on bacterial metabolism.
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Affiliation(s)
- Erica J Zheng
- Program in Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ian W Andrews
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexandra T Grote
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Miguel A Alcantar
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - James J Collins
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA.
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