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Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction. Cell Rep 2024; 43:113517. [PMID: 38142397 DOI: 10.1016/j.celrep.2023.113517] [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: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bacteria and their interactions with the host. However, construction of high-quality libraries with uniform representation can be challenging. In this review, we survey various strategies for barcoded library construction, including transposition systems, methods of transposon delivery, optimal library size, and transconjugant selection schemes. We discuss the advantages and limitations of each approach, as well as factors to consider when selecting a strategy. In addition, we highlight experimental and computational advances in arraying condensed libraries from mutant pools. We focus on examples of successful library construction in gut bacteria and their application to gene function studies and drug discovery. Given the need for understanding gene function and organization in gut bacteria, we provide a comprehensive guide for researchers to construct randomly barcoded transposon mutant libraries.
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Affiliation(s)
- Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Mary Anderson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Po-Hsun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nazgul Sakenova
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tümay Capraz
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentine Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Zimmerman
- Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Justin L Sonnenburg
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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Zhang S, Shu Y, Zhang W, Xu Z, Li Y, Li S, Li Q, Xiong R, Long Y, Liu J, Zhang Y, Chen C, Lu Y. Quorum sensing N-acyl homoserine lactones-SdiA enhances the biofilm formation of E. coli by regulating sRNA CsrB expression. Heliyon 2023; 9:e21658. [PMID: 38027585 PMCID: PMC10651509 DOI: 10.1016/j.heliyon.2023.e21658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
As an important virulence phenotype of Escherichia coli, the regulation mechanism of biofilm by non-coding RNA and quorum sensing system has not been clarified. Here, by transcriptome sequencing and RT-PCR analysis, we found CsrB, a non-coding RNA of the carbon storage regulation system, was positively regulated by the LuxR protein SdiA. Furthermore, β-galactosidase reporter assays showed that SdiA enhanced promoter transcriptional activity of csrB. The consistent dynamic expression levels of SdiA and CsrB during Escherichia coli growth were also detected. Moreover, curli assays and biofilm assays showed sdiA deficiency in Escherichia coli SM10λπ or BW25113 led to a decreased formation of biofilm, and was significantly restored by over-expression of CsrB. Interestingly, the regulations of SdiA on CsrB in biofilm formation were enhanced by quorum sensing signal molecules AHLs. In conclusion, SdiA plays a crucial role in Escherichia coli biofilm formation by regulating the expression of non-coding RNA CsrB. Our study provides new insights into SdiA-non-coding RNA regulatory network involved in Escherichia coli biofilm formation.
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Affiliation(s)
- Shebin Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yurong Shu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Weizheng Zhang
- Department of Laboratory Medicine, Guangzhou No.11 People's Hospital, Guangzhou Cadre Health Management Center, Guangzhou, PR China
| | - Zhenjie Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Youqiang Li
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, PR China
| | - Song Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Qiwei Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Rui Xiong
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yifei Long
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Jianping Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yunyan Zhang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yang Lu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital Guangzhou, Qingyuan, PR China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
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Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes. Antibiotics (Basel) 2023; 12:antibiotics12020333. [PMID: 36830244 PMCID: PMC9952537 DOI: 10.3390/antibiotics12020333] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.
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Banu Raza F, Vijayaragavalu S, Kandasamy R, Krishnaswami V, Kumar V A. Microbiome and the inflammatory pathway in peri-implant health and disease with an updated review on treatment strategies. J Oral Biol Craniofac Res 2023; 13:84-91. [PMID: 36504486 PMCID: PMC9730223 DOI: 10.1016/j.jobcr.2022.11.005] [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: 03/12/2022] [Revised: 08/30/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
Crestal bone preservation around the dental implant for aesthetic and functional success is widely researched and documented over a decade. Several etiological factors were put forth for crestal bone loss; of which biofilm plays a major role. Biofilm is formed by the colonization of wide spectra of bacteria inhabited around dental implants. Bacterial adherence affects the regulators of bone growth and an early intervention preserves the peri-implant bone. Primary modes of therapy stated in early literature were either prevention or treatment of infection caused by biofilm. This narrative review overviews the microbiome during different stages of peri-implant health, the mechanism of bone destruction, and the expression of the biomarkers at each stage. Microbial contamination and the associated biomarkers varied depending on the stage of peri-implant infection. The comprehensive review helps in formulating a research plan, both in diagnostics and treatment aspects in improving peri-implant health.
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Key Words
- Antibiotics
- Biomarkers
- CD14, Cluster of Differentiation 14
- CSF, Colony-Stimulating Factor
- Gene expression
- IL, Interleukins
- MMP 8, Matrix MetalloProteinase 8
- Microbiota
- OPG, Osteoprotegerin
- PSMB 2, Proteasome subunit beta type-2
- Peri-implant
- RANK, Receptor Activator of Nuclear factor Kappa-Β
- RANKL, Receptor Activator of Nuclear factor Kappa-ΒLigand
- TIMP, Tissue inhibitor of Metalloproteinase
- TNF, Tumor Necrosis Factor
- TWEAK, TNF-related weak inducer of apoptosis
- VEGF, Vascular Endothelial Growth Factor
- sRANKL, soluble Receptor Activator of Nuclear Factor-κB Ligand
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Affiliation(s)
- Fathima Banu Raza
- Department of Prosthodontics, Faculty of Dental Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | | | - Ruckmani Kandasamy
- Centre for Excellence in Nanobio Translational REsearch (CENTRE), Department of Pharmaceutical Technology, University College of Engineering, Anna University, BIT Campus, Tiruchirappalli, Tamil Nadu, India
| | - Venkateshwaran Krishnaswami
- Centre for Excellence in Nanobio Translational REsearch (CENTRE), Department of Pharmaceutical Technology, University College of Engineering, Anna University, BIT Campus, Tiruchirappalli, Tamil Nadu, India
| | - Anand Kumar V
- Department of Prosthodontics, Faculty of Dental Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
- Corresponding author. Department of Prosthodontics, Faculty of Dental Sciences, SRIHER (DU), Porur, Chennai, Tamil Nadu, India.
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Falà AK, Álvarez-Ordóñez A, Filloux A, Gahan CGM, Cotter PD. Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting. Front Microbiol 2022; 13:1002185. [PMID: 36504831 PMCID: PMC9733432 DOI: 10.3389/fmicb.2022.1002185] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
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Affiliation(s)
- A. Kate Falà
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland,*Correspondence: Paul D. Cotter,
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Lu Y, Liu Y, Zhou C, Liu Y, Long Y, Lin D, Xiong R, Xiao Q, Huang B, Chen C. Quorum sensing regulates heteroresistance in Pseudomonas aeruginosa. Front Microbiol 2022; 13:1017707. [PMID: 36386621 PMCID: PMC9650436 DOI: 10.3389/fmicb.2022.1017707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/07/2022] [Indexed: 10/29/2023] Open
Abstract
The prevalence and genetic mechanism of antibiotic heteroresistance (HR) have attracted significant research attention recently. However, non-genetic mechanism of HR has not been adequately explored. The present study aimed to evaluate the role of quorum sensing (QS), an important mechanism of behavioral coordination in different subpopulations and consequent heteroresistance. First, the prevalence of HR to 7 antibiotics was investigated in 170 clinical isolates of P. aeruginosa using population analysis profiles. The results showed that P. aeruginosa was significantly heteroresistant to meropenem (MEM), amikacin (AMK), ciprofloxacin (CIP), and ceftazidime (CAZ). The observed HR was correlated with down-regulation of QS associated genes lasI and rhlI. Further, loss-of-function analysis results showed that reduced expression of lasI and rhlI enhanced HR of P. aeruginosa to MEM, AMK, CIP, and CAZ. Conversely, overexpression of these genes or treatment with 3-oxo-C12-HSL/C4-HSL lowered HR of P. aeruginosa to the four antibiotics. Additionally, although downregulation of oprD and upregulation of efflux-associated genes was evident in heteroresistant subpopulations, their expression was not regulated by LasI and RhlI. Moreover, fitness cost measurements disclosed higher growth rates of PAO1ΔlasI and PAO1ΔrhlI in the presence of sub-MIC antibiotic as compared with that of wild-type PAO1. Our data suggest that under temporary antibiotic pressure, downregulation of QS might result in less fitness cost and promote HR of P. aeruginosa.
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Affiliation(s)
- Yang Lu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuyang Liu
- Department of Laboratory Medicine, Chengdu First People's Hospital, Chengdu, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chenxu Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaqin Liu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
| | - Yifei Long
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongling Lin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Rui Xiong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qian Xiao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements. Appl Environ Microbiol 2022; 88:e0099122. [PMID: 36036594 PMCID: PMC9499024 DOI: 10.1128/aem.00991-22] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the “life cycle” (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as “signatures” of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses.
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Zhu Y, Fan Y, Cao X, Lu R, Chu S, Ding A. Regulation of Carbapenemase Gene Conjugation in Escherichia coli Clinical Isolates. Microb Drug Resist 2022; 28:551-558. [PMID: 35319308 DOI: 10.1089/mdr.2021.0190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: The purpose of this study is to raise awareness of the hazards of carbapenemase epidemics and provide theoretical support for preventing the spread of carbapenemase-producing organisms. Methods: A total of 893 non-duplicate E. coil strains were recruited from three major local hospitals. The carbapenemase genotype of each imipenem-resistant strain was analyzed. Molecular typing and homology analysis of the main carbapenemase-producing strains reveal the transmission mode of resistance genes. Through the conjugation experiment, the potential spreading risk of carbapenemase genes was analyzed. Extended-spectrum beta-lactamase genes and replicon detection of the conjugant carrying plasmid were performed. The unannotated Escherichia coli bacterial small non-coding RNAs (sRNAs) interacting with sdiA were predicted through a bioinformatics tool. The sRNAs overexpression and knockout strains were constructed, and the effect of sRNA on conjugation was analyzed. Results: A total of 8 carbapenemase-producing strains were detected (0.90%, 8/893). The main carbapenemase genotype was blaKPC -2 (7 strains). Multilocus sequence typing indicated that 7 E. coli isolates belonged to ST-10, ST-101, ST-131, ST-405, ST-410, and ST-1193, ST-2562, respectively. Homologous cluster analysis revealed that the sequence types among the 7 E. coli were high diversity. The blaKPC -2 genes were successfully transferred from these isolates to EC600 by conjugation. All transconjugant cells exhibited significantly reduced susceptibility to the imipenem. IncFII was the most common conjugative plasmid type (85.7%, 6/7). Bioinformatics predicted the interaction between RydB and sdiA. Further experiments found that the interaction between RydB and sdiA improved the bacterial conjugation rate between MG1655 and EC600. The regulation effect of RydB on E. coli conjugation was not affected by the replicon type and/or harboring resistance coding genotype in conjugative plasmids. Conclusion: Our findings emphasized the epidemiological characteristics of carbapenemase-resistant E. coli. A functional phenotype of the new sRNA RydB was identified, and the regulation effect of RydB on E. coli conjugation was improved.
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Affiliation(s)
- Yihua Zhu
- Clinical Laboratory, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu, P.R. China
| | - Yuping Fan
- Clinical Laboratory, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu, P.R. China
| | - Xinjian Cao
- Clinical Laboratory, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu, P.R. China
| | - Renfei Lu
- Clinical Laboratory, The Third Affiliated Hospital of Nantong University, Nantong, Jiangsu, P.R. China
| | - Shaopeng Chu
- Clinical Laboratory, Nantong University Affiliated Hospital, Nantong, Jiangsu, P.R. China
| | - Aimin Ding
- Department of Nursing, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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Sun R, Yu P, Zuo P, Alvarez PJ. Bacterial Concentrations and Water Turbulence Influence the Importance of Conjugation Versus Phage-Mediated Antibiotic Resistance Gene Transfer in Suspended Growth Systems. ACS ENVIRONMENTAL AU 2022; 2:156-165. [PMID: 37101581 PMCID: PMC10114721 DOI: 10.1021/acsenvironau.1c00027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite the abundance of phage-borne antibiotic resistance genes (ARGs) in the environment, the frequency of ARG propagation via phage-mediated transduction (relative to via conjugation) is poorly understood. We investigated the influence of bacterial concentration and water turbulence level [quantified as Reynold's number (Re)] in suspended growth systems on the frequency of ARG transfer by two mechanisms: delivery by a lysogenic phage (phage λ carrying gentamycin-resistance gene, genR) and conjugation mediated by the self-transmissible plasmid RP4. Using Escherichia coli (E. coli) as the recipient, phage delivery had a comparable frequency (1.2 ± 0.9 × 10-6) to that of conjugation (1.1 ± 0.9 × 10-6) in suspensions with low cell concentration (104 CFU/mL) and moderate turbulence (Re = 5 × 104). Turbulence affected cell (or phage)-to-cell contact rates and detachment (due to shear force), and thus, it affected the relative importance of conjugation versus phage delivery. At 107 CFU/mL, no significant difference was observed between the frequencies of ARG transfer by the two mechanisms under quiescent water conditions (2.8 ± 0.3 × 10-5 for conjugation vs 2.2 ± 0.5 × 10-5 for phage delivery, p = 0.19) or when Re reached 5 × 105 (3.4 ± 1.5 × 10-5 for conjugation vs 2.9 ± 1.0 × 10-5 for phage delivery, p = 0.52). Transcriptomic analysis of genes related to conjugation and phage delivery and simulation of cell (or phage)-to-cell collisions at different Re values corroborate that the importance of phage delivery relative to conjugation increases under either quiescent or turbulent conditions. This finding challenges the prevailing view that conjugation is the dominant ARG transfer mechanism and underscores the need to consider and mitigate potential ARG dissemination via transduction.
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Affiliation(s)
- Ruonan Sun
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pengxiao Zuo
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J.J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
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Xiao Q, Luo Y, Shi W, Lu Y, Xiong R, Wu X, Huang H, Zhao C, Zeng J, Chen C. The effects of LL-37 on virulence factors related to the quorum sensing system of Pseudomonas aeruginosa. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:284. [PMID: 35434009 PMCID: PMC9011280 DOI: 10.21037/atm-22-617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/04/2022] [Indexed: 11/24/2022]
Abstract
Background Antimicrobial peptides (AMPs) have shown promise in the treatment of multi-resistant pathogens. It was therefore of interest to analyze the effects of the AMP LL-37 on the regulation of several virulence factors related to the quorum sensing (QS) system of Pseudomonas aeruginosa (P. aeruginosa) in vitro. Methods The minimum inhibitory concentration (MIC) was evaluated by the micro broth dilution method. The expression of QS-related and QS-regulated virulence factor genes was also evaluated. Exotoxin A activity was measured with the nicotinamide adenine dinucleotide (NAD) (Coenzyme I) method; Elastase activity was detected with the elastin-Congo red (ECR) method; Pyocyanin detection was performed using the chloroform extraction method. The effects of LL-37 were assessed by measuring the expression changes of the virulence protein-encoding genes of the strains with quantitative polymerase chain reaction (PCR). Results The MIC of LL-37 against both P. aeruginosa reference strain (ATCC 15692 PAO1) and PA-ΔlasI/rhII was therefore determined to be 256 µg/mL. LL-37 at sub-minimum inhibitory concentrations (sub-MICs) had no significant effects on P. aeruginosa bacterial growth (P>0.05), but significantly downregulated the expression of all 3 virulence factors. Conclusions Interestingly, this effect appeared to be dose-related. These findings suggest that LL-37 could be a potential candidate for QS inhibition against bacterial infection and may have significant clinical potential in the treatment of P. aeruginosa biofilms.
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Affiliation(s)
- Qian Xiao
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yanfen Luo
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wen Shi
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yang Lu
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Rui Xiong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xinggui Wu
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haihao Huang
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chanjing Zhao
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianming Zeng
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
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11
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Synergistic Inhibitory Effect of Polymyxin B in Combination with Ceftazidime against Robust Biofilm Formed by Acinetobacter baumannii with Genetic Deficiency in AbaI/AbaR Quorum Sensing. Microbiol Spectr 2022; 10:e0176821. [PMID: 35196792 PMCID: PMC8865539 DOI: 10.1128/spectrum.01768-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenem resistance of Acinetobacter baumannii poses challenges to public health. Biofilm contributes to the persistence of A. baumannii cells. This study was designed to investigate the genetic relationships among carbapenem resistance, polymyxin resistance, multidrug resistance, biofilm formation, and surface-associated motility and evaluate the antibiofilm effect of polymyxin in combination with other antibiotics. A total of 103 clinical A. baumannii strains were used to determine antibiotic susceptibility, biofilm formation capacity, and motility. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting was used to determine the genetic variation among strains. The distribution of 17 genes related to the resistance-nodulation-cell division (RND)-type efflux, autoinducer-receptor (AbaI/AbaR) quorum sensing, oxacillinases (OXA)-23, and insertion sequence of ISAba1 element was investigated. The representative strains were chosen to evaluate the gene transcription and the antibiofilm activity by polymyxin B (PB) in combination with merapenem, levofloxacin, and ceftazidime, respectively. ERIC-PCR-dependent fingerprints were found to be associated with carbapenem resistance and multidrug resistance. The presence of blaOXA-23 was found to correlate with genes involved in ISAba1 insertion, AbaI/AbaR quorum sensing, and AdeABC efflux. Carbapenem resistance was observed to be negatively correlated with biofilm formation and positively correlated with motility. PB in combination with ceftazidime displayed a synergistic antibiofilm effect against robust biofilm formed by an A. baumannii strain with deficiency in AbaI/AbaR quorum sensing. Our results not only clarify the genetic correlation among carbapenem resistance, biofilm formation, and pathogenicity in a certain level but also provide a theoretical basis for clinical applications of polymyxin-based combination of antibiotics in antibiofilm therapy. IMPORTANCE Deeper explorations of molecular correlation among antibiotic resistance, biofilm formation, and pathogenicity could provide novel insights that would facilitate the development of therapeutics and prevention against A. baumannii biofilm-related infections. The major finding that polymyxin B in combination with ceftazidime displayed a synergistic antibiofilm effect against robust biofilm formed by an A. baumannii strain with genetic deficiency in AbaI/AbaR quorum sensing further provides a theoretical basis for clinical applications of antibiotics in combination with quorum quenching in antibiofilm therapy.
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12
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Feng G, Huang H, Chen Y. Effects of emerging pollutants on the occurrence and transfer of antibiotic resistance genes: A review. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126602. [PMID: 34273886 DOI: 10.1016/j.jhazmat.2021.126602] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The emergence and spread of antibiotic resistance genes (ARGs) have become major concerns for both public health and environmental ecosystems. Emerging pollutants (EPs) that accumulate in environmental compartments also pose a potential risk for the enrichment of ARGs in indigenous microorganisms. This paper presents a comprehensive review of the effects and intrinsic mechanisms of EPs, including microplastics, engineered nanomaterials, disinfection byproducts, pharmaceuticals, and personal care products, on the occurrence and dissemination of ARGs. State-of-the-art methods for identifying culture-independent ARG-host interactions and monitoring horizontal gene transfer (HGT) processes in real-time are first reviewed. The contributions of EPs to the abundance and diversity of ARGs are then summarized. Finally, we discussed the underlying mechanisms related to the regulation of HGT, increased mutagenesis, and the evolution of microbial communities. Further details of three HGT (i.e., conjugation, transformation, and transduction) frequency patterns in response to various EPs are also examined. This review contemplates and reassesses the risks of ARG evolution posed by the manufacture and application of EPs.
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Affiliation(s)
- Guanqun Feng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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13
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Bier E, Nizet V. Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance. Trends Genet 2021; 37:745-757. [PMID: 33745750 DOI: 10.1016/j.tig.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.
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Affiliation(s)
- Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA.
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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14
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Pacheco T, Gomes AÉI, Siqueira NMG, Assoni L, Darrieux M, Venter H, Ferraz LFC. SdiA, a Quorum-Sensing Regulator, Suppresses Fimbriae Expression, Biofilm Formation, and Quorum-Sensing Signaling Molecules Production in Klebsiella pneumoniae. Front Microbiol 2021; 12:597735. [PMID: 34234747 PMCID: PMC8255378 DOI: 10.3389/fmicb.2021.597735] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has become a worldwide concern due to the emergence of multidrug-resistant isolates responsible for various invasive infectious diseases. Biofilm formation constitutes a major virulence factor for K. pneumoniae and relies on the expression of fimbrial adhesins and aggregation of bacterial cells on biotic or abiotic surfaces in a coordinated manner. During biofilm aggregation, bacterial cells communicate with each other through inter- or intra-species interactions mediated by signallng molecules, called autoinducers, in a mechanism known as quorum sensing (QS). In most Gram-negative bacteria, intra-species communication typically involves the LuxI/LuxR system: LuxI synthase produces N-acyl homoserine lactones (AHLs) as autoinducers and the LuxR transcription factor is their cognate receptor. However, K. pneumoniae does not produce AHL but encodes SdiA, an orphan LuxR-type receptor that responds to exogenous AHL molecules produced by other bacterial species. While SdiA regulates several cellular processes and the expression of virulence factors in many pathogens, the role of this regulator in K. pneumoniae remains unknown. In this study, we describe the characterization of sdiA mutant strain of K. pneumoniae. The sdiA mutant strain has increased biofilm formation, which correlates with the increased expression of type 1 fimbriae, thus revealing a repressive role of SdiA in fimbriae expression and bacterial cell adherence and aggregation. On the other hand, SdiA acts as a transcriptional activator of cell division machinery assembly in the septum, since cells lacking SdiA regulator exhibited a filamentary shape rather than the typical rod shape. We also show that K. pneumoniae cells lacking SdiA regulator present constant production of QS autoinducers at maximum levels, suggesting a putative role for SdiA in the regulation of AI-2 production. Taken together, our results demonstrate that SdiA regulates cell division and the expression of virulence factors such as fimbriae expression, biofilm formation, and production of QS autoinducers in K. pneumoniae.
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Affiliation(s)
- Thaisy Pacheco
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Ana Érika Inácio Gomes
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | | | - Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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15
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Zoolkefli FIRM, Moriguchi K, Cho Y, Kiyokawa K, Yamamoto S, Suzuki K. Isolation and Analysis of Donor Chromosomal Genes Whose Deficiency Is Responsible for Accelerating Bacterial and Trans-Kingdom Conjugations by IncP1 T4SS Machinery. Front Microbiol 2021; 12:620535. [PMID: 34093458 PMCID: PMC8174662 DOI: 10.3389/fmicb.2021.620535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Conjugal transfer is a major driving force of genetic exchange in eubacteria, and the system in IncP1-type broad-host-range plasmids transfers DNA even to eukaryotes and archaea in a process known as trans-kingdom conjugation (TKC). Although conjugation factors encoded on plasmids have been extensively analyzed, those on the donor chromosome have not. To identify the potential conjugation factor(s), a genome-wide survey on a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors to Saccharomyces cerevisiae recipients was performed using a conjugal transfer system mediated by the type IV secretion system (T4SS) of the IncP1α plasmid. Out of 3,884 mutants, three mutants (ΔfrmR, ΔsufA, and ΔiscA) were isolated, which showed an increase by one order of magnitude in both E. coli-E. coli and E. coli-yeast conjugations without an increase in the mRNA accumulation level for the conjugation related genes examined. The double-knockout mutants for these genes (ΔfrmRΔsufA and ΔiscAΔfrmR) did not show synergistic effects on the conjugation efficiency, suggesting that these factors affect a common step in the conjugation machinery. The three mutants demonstrated increased conjugation efficiency in IncP1β-type but not in IncN- and IncW-type broad-host-range plasmid transfers, and the homologous gene knockout mutants against the three genes in Agrobacterium tumefaciens also showed increased TKC efficiency. These results suggest the existence of a specific regulatory system in IncP1 plasmids that enables the control of conjugation efficiency in different hosts, which could be utilized for the development of donor strains as gene introduction tools into bacteria, eukaryotes, and archaea.
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Affiliation(s)
| | - Kazuki Moriguchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Yunjae Cho
- Department of Biological Science, Faculty of Science, Hiroshima University, Higashihiroshima, Japan
| | - Kazuya Kiyokawa
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
| | - Katsunori Suzuki
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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16
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Xiong R, Liu Y, Pu J, Liu J, Zheng D, Zeng J, Chen C, Lu Y, Huang B. Indole Inhibits IncP-1 Conjugation System Mainly Through Promoting korA and korB Expression. Front Microbiol 2021; 12:628133. [PMID: 33815310 PMCID: PMC8017341 DOI: 10.3389/fmicb.2021.628133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/12/2021] [Indexed: 11/26/2022] Open
Abstract
Indole works as an interspecies signal molecule to regulate multiple physiological activities, like antibiotic resistance, acid resistance, and virulence. However, the effect of indole on conjugation is unknown. Here, with Escherichia coli SM10λπ as a donor strain that carries a chromosomally integrated conjugative RP4 plasmid, we explored the effect of indole on conjugation of a mobilizable pUCP24T plasmid imparting gentamycin resistance. The results showed that exogenous indole treatment inhibited conjugative transfer of pUCP24T from SM10λπ to recipient strains, Pseudomonas aeruginosa PAO1 and E. coli EC600. Furthermore, raising endogenous indole production through overexpression of TnaA, a tryptophanase, in SM10λπ significantly inhibited both SM10λπ-PAO1 and SM10λπ-EC600 conjugation, whereas deficiency of tnaA reversed the phenotype. Subsequent mechanistic studies revealed that exogenous indole significantly inhibited the expression of mating pair formation gene (trbB) and the DNA transfer and replication gene (trfA), mainly due to the promotion of regulatory genes (korA and korB), and the result was confirmed in tnaA knockout and overexpression strains. Additionally, we found that both extracellular indole production and tnaA expression of SM10λπ were downregulated by ciprofloxacin (CIP). Intriguingly, one-eighth minimum inhibitory concentration of CIP treatment clearly facilitated both SM10λπ-PAO1 and SM10λπ-EC600 conjugation, and indole inhibited CIP-induced conjugation frequency. These data suggest that indole may play a negative role in the process of CIP-induced conjugation. This is the first study to reveal the biological function of indole-inhibiting conjugation and its role in CIP-induced conjugation, which may be developed into a new way of controlling the spread of antibiotic resistance.
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Affiliation(s)
- Rui Xiong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuyang Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jieying Pu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Jianping Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Dexiang Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Jianming Zeng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Yang Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
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17
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In Vitro Assessment of Antimicrobial Resistance Dissemination Dynamics during Multidrug-Resistant-Bacterium Invasion Events by Using a Continuous-Culture Device. Appl Environ Microbiol 2021; 87:AEM.02659-20. [PMID: 33361364 DOI: 10.1128/aem.02659-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/11/2020] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial-resistant pathogens display significant public health threats by causing difficulties in clinical treatment of bacterial infection. Antimicrobial resistance (AMR) is transmissible between bacteria, significantly increasing the appearance of antimicrobial-resistant pathogens and aggravating the AMR problem. In this work, the dissemination dynamics of AMR from invading multidrug-resistant (MDR) Escherichia coli to a community of pathogenic Salmonella enterica was investigated using a continuous-culture device, and the behaviors of dissemination dynamics under different levels of antibiotic stress were investigated. Three MDR E. coli invasion events were analyzed in this work: MDR E. coli-S. enterica cocolonization, MDR E. coli invasion after antibiotic treatment of S. enterica, and MDR E. coli invasion before antibiotic treatment of S. enterica It was found that both horizontal gene transfer (HGT) and vertical gene transfer (VGT) play significant roles in AMR dissemination, although different processes contribute differently under different circumstances, that environmental levels of antibiotics promote AMR dissemination by enhancing HGT rather than leading to selective advantage for resistant bacteria, and that early invasion of MDR E. coli completely and quickly sabotages the effectiveness of antibiotic treatment. These findings contribute to understanding the drivers of AMR dissemination under different antibiotic stresses, the detrimental impact of environmental tetracycline contamination, and the danger of nosocomial presence and dissemination of MDR nonpathogens.IMPORTANCE Antimicrobial resistance poses a grave threat to public health and reduces the effectiveness of antimicrobial drugs in treating bacterial infections. Antimicrobial resistance is transmissible, either by horizontal gene transfer between bacteria or by vertical gene transfer following inheritance of genetic traits. The dissemination dynamics and behaviors of this threat, however, have not been rigorously investigated. In this work, with a continuous-culture device, we studied antimicrobial resistance dissemination processes by simulating antimicrobial-resistant Escherichia coli invasion to a pathogenic Salmonella enterica community. Using this novel tool, we provide evidence on the drivers of antimicrobial resistance dissemination, on the detrimental impact of environmental antibiotic contamination, and on the danger of antimicrobial resistance in hospitals, even if what harbors the antimicrobial resistance is not a pathogen. This work furthers our understanding of antimicrobial resistance and its dissemination between bacteria and of antibiotic therapy, our most powerful tool against bacterial infection.
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18
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Styles MJ, Early SA, Tucholski T, West KHJ, Ge Y, Blackwell HE. Chemical Control of Quorum Sensing in E. coli: Identification of Small Molecule Modulators of SdiA and Mechanistic Characterization of a Covalent Inhibitor. ACS Infect Dis 2020; 6:3092-3103. [PMID: 33124430 DOI: 10.1021/acsinfecdis.0c00654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is the causative agent of severe diarrheal disease in humans. Cattle are the natural reservoir of EHEC, and approximately 75% of EHEC infections in humans stem from bovine products. Many common bacterial pathogens, including EHEC, rely on chemical communication systems, such as quorum sensing (QS), to regulate virulence and facilitate host colonization. EHEC uses SdiA from E. coli (SdiAEC), an orphan LuxR-type receptor, to sense N-acyl l-homoserine lactone (AHL) QS signals produced by other members of the bovine enteric microbiome. SdiAEC regulates two phenotypes critical for colonizing cattle: acid resistance and the formation of attaching and effacing lesions. Despite the importance of SdiAEC, there is very little known about its selectivity for different AHL signals, and no chemical inhibitors that act specifically on SdiAEC have been reported. Such compounds would represent valuable tools to study the roles of QS in EHEC virulence. To identify chemical modulators of SdiAEC and delineate the structure-activity relationships (SARs) for AHL activity in this receptor, we report herein the screening of a focused library composed largely of AHLs and AHL analogues in an SdiAEC reporter assay. We describe the identity and SARs of potent modulators of SdiAEC activity, examine the promiscuity of SdiAEC, characterize the mechanism of a covalent inhibitor, and provide phenotypic assay data to support that these compounds can control SdiAEC-dependent acid resistance in E. coli. These SdiAEC modulators could be used to advance the study of LuxR-type receptor/ligand interactions, the biological roles of orphan LuxR-type receptors, and potential QS-based therapeutic approaches.
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Affiliation(s)
- Matthew J. Styles
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Stephen A. Early
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Korbin H. J. West
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, Wisconsin Institute for Medical Research, University of Wisconsin−Madison, 1111 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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19
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Pourciau C, Lai YJ, Gorelik M, Babitzke P, Romeo T. Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA. Front Microbiol 2020; 11:601352. [PMID: 33193284 PMCID: PMC7652899 DOI: 10.3389/fmicb.2020.601352] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
The carbon storage regulator (Csr) or repressor of stationary phase metabolites (Rsm) system of Gammaproteobacteria is among the most complex and best-studied posttranscriptional regulatory systems. Based on a small RNA-binding protein, CsrA and homologs, it controls metabolism, physiology, and bacterial lifestyle decisions by regulating gene expression on a vast scale. Binding of CsrA to sequences containing conserved GGA motifs in mRNAs can regulate translation, RNA stability, riboswitch function, and transcript elongation. CsrA governs the expression of dozens of transcription factors and other regulators, further expanding its influence on cellular physiology, and these factors can participate in feedback to the Csr system. Expression of csrA itself is subject to autoregulation via translational inhibition and indirect transcriptional activation. CsrA activity is controlled by small noncoding RNAs (sRNAs), CsrB and CsrC in Escherichia coli, which contain multiple high affinity CsrA binding sites that compete with those of mRNA targets. Transcription of CsrB/C is induced by certain nutrient limitations, cellular stresses, and metabolites, while these RNAs are targeted for degradation by the presence of a preferred carbon source. Consistent with these findings, CsrA tends to activate pathways and processes that are associated with robust growth and repress stationary phase metabolism and stress responses. Regulatory loops between Csr components affect the signaling dynamics of the Csr system. Recently, systems-based approaches have greatly expanded our understanding of the roles played by CsrA, while reinforcing the notion that much remains to be learned about the Csr system.
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Affiliation(s)
- Christine Pourciau
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Ying-Jung Lai
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Mark Gorelik
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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20
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Virolle C, Goldlust K, Djermoun S, Bigot S, Lesterlin C. Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level. Genes (Basel) 2020; 11:genes11111239. [PMID: 33105635 PMCID: PMC7690428 DOI: 10.3390/genes11111239] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
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21
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Ma X, Zhang S, Xu Z, Li H, Xiao Q, Qiu F, Zhang W, Long Y, Zheng D, Huang B, Chen C, Lu Y. SdiA Improves the Acid Tolerance of E. coli by Regulating GadW and GadY Expression. Front Microbiol 2020; 11:1078. [PMID: 32582066 PMCID: PMC7286202 DOI: 10.3389/fmicb.2020.01078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/30/2020] [Indexed: 01/20/2023] Open
Abstract
The acid tolerance mechanism is important for Escherichia coli to resist acidic conditions encountered in mammalian host digestive tract environment. Here, we explored how the LuxR protein SdiA influenced E. coli acid tolerance ability in the context of the glutamate- and glutamine-dependent acid resistance system (AR2). First, using a growth and acid shock assay under different acid stresses, we demonstrated that the deletion of sdiA in SM10λpir or BW25113 led to impaired growth under the acidic environment of pH 3–6, which was restored by complementary expression of SdiA. Next, transcriptome sequencing and qPCR disclosed that the expression of glutamate decarboxylase W (GadW) and GadY, the key members of the AR2 system, were regulated by SdiA. Further, β-galactosidase reporter assays showed that the promoter activity of gadW and gadY was positively regulated by SdiA. Moreover, qPCR and β-galactosidase reporter assays confirmed that the regulation of SdiA on GadW, but not GadY, could be enhanced by quorum sensing (QS) signal molecules AHLs. Collectively, these data suggest that SdiA plays a crucial role in acid tolerance regulation of E. coli. Our findings provide new insights into the important contribution of quorum sensing system AHLs–SdiA to the networks that regulate acid tolerance.
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Affiliation(s)
- Xingyan Ma
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shebin Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhenjie Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Honglin Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qian Xiao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Feng Qiu
- Department of Laboratory Medicine, Nanhai Hospital, Southern Medical University, Foshan, China
| | - Weizheng Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yifei Long
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dexiang Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yang Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
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22
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Lu Y, Li H, Pu J, Xiao Q, Zhao C, Cai Y, Liu Y, Wang L, Li Y, Huang B, Zeng J, Chen C. Identification of a novel RhlI/R-PrrH-LasI/Phzc/PhzD signalling cascade and its implication in P. aeruginosa virulence. Emerg Microbes Infect 2020; 8:1658-1667. [PMID: 31718472 PMCID: PMC6853234 DOI: 10.1080/22221751.2019.1687262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Small regulatory RNAs (sRNAs) act as key regulators in many bacterial signalling cascades. However, in P. aeruginosa, the sRNAs involved in quorum sensing (QS) regulation and their function are still largely unknown. Here, we explored how the prrH locus sRNA influences P. aeruginosa virulence in the context of the QS regulatory network. First, gain- and loss-of-function studies showed that PrrH affects pyocyanin, elastase and rhamnolipid production; biofilm formation; and swimming and swarming motility and impaired the viability of P. aeruginosa in human whole blood. Next, our investigation disclosed that LasI and PhzC/D were directly repressed by PrrH. In addition, RhlI, the key member of the rhl QS system, diminished the expression of PrrH and enhanced the expression of downstream genes. Bioinformatics analysis found two binding sites of RhlR, the transcription factor of the rhl system, on the promoter region of prrH. Further β-galactosidase reporter and qPCR assays confirmed that PrrH was transcriptionally repressed by RhlR. Collectively, our data identified a novel RhlI/R-PrrH-LasI/PhzC/PhzD regulatory circuitry that may contribute to P. aeruginosa pathogenesis. Our findings indicate that PrrH is a quorum regulatory RNA (Qrr) in P. aeruginosa and provide new insight into PrrH’s function.
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Affiliation(s)
- Yang Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Honglin Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China.,The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Jieying Pu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Qian Xiao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Chanjing Zhao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Yimei Cai
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Yuyang Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Lina Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Youqiang Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. People's Republic of China
| | - Jianming Zeng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P. R. People's Republic of China
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23
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Schwab M, Bergonzi C, Sakkos J, Staley C, Zhang Q, Sadowsky MJ, Aksan A, Elias M. Signal Disruption Leads to Changes in Bacterial Community Population. Front Microbiol 2019; 10:611. [PMID: 30984139 PMCID: PMC6449428 DOI: 10.3389/fmicb.2019.00611] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/11/2019] [Indexed: 01/02/2023] Open
Abstract
The disruption of bacterial signaling (quorum quenching) has been proven to be an innovative approach to influence the behavior of bacteria. In particular, lactonase enzymes that are capable of hydrolyzing the N-acyl homoserine lactone (AHL) molecules used by numerous bacteria, were reported to inhibit biofilm formation, including those of freshwater microbial communities. However, insights and tools are currently lacking to characterize, understand and explain the effects of signal disruption on complex microbial communities. Here, we produced silica capsules containing an engineered lactonase that exhibits quorum quenching activity. Capsules were used to design a filtration cartridge to selectively degrade AHLs from a recirculating bioreactor. The growth of a complex microbial community in the bioreactor, in the presence or absence of lactonase, was monitored over a 3-week period. Dynamic population analysis revealed that signal disruption using a quorum quenching lactonase can effectively reduce biofilm formation in the recirculating bioreactor system and that biofilm inhibition is concomitant to drastic changes in the composition, diversity and abundance of soil bacterial communities within these biofilms. Effects of the quorum quenching lactonase on the suspension community also affected the microbial composition, suggesting that effects of signal disruption are not limited to biofilm populations. This unexpected finding is evidence for the importance of signaling in the competition between bacteria within communities. This study provides foundational tools and data for the investigation of the importance of AHL-based signaling in the context of complex microbial communities.
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Affiliation(s)
- Michael Schwab
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Celine Bergonzi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Jonathan Sakkos
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Christopher Staley
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Surgery, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Qian Zhang
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Michael J Sadowsky
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Alptekin Aksan
- Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Department of Mechanical Engineering, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, St. Paul, MN, United States.,Biotechnology Institute, University of Minnesota, Twin Cities, St. Paul, MN, United States
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24
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Yang Y, Zhou M, Hardwidge PR, Cui H, Zhu G. Isolation and Characterization of N-acyl Homoserine Lactone-Producing Bacteria From Cattle Rumen and Swine Intestines. Front Cell Infect Microbiol 2018; 8:155. [PMID: 29868511 PMCID: PMC5954215 DOI: 10.3389/fcimb.2018.00155] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/24/2018] [Indexed: 11/15/2022] Open
Abstract
Quorum sensing systems regulate gene expression in response to bacterial population density. Acyl-homoserine lactones are a class of quorum sensing molecules found in cattle rumen that are thought to regulate the gene expression of enterohemorrhagic Escherichia coli and thus help this pathogen survive in animal gastrointestinal tracts. However, the specific bacteria that produce these signaling molecules in bovine and porcine gastrointestinal tracts are unknown. Here we developed methods to concentrate gastrointestinal fluids and screen the bacteria that produce acyl-homoserine lactones. We isolated a Pseudomonas aeruginosa strain YZ1 from cattle rumen, and an Aeromonas hydrophila strain YZ2 from pig intestine. Mass spectrometry analysis of culture supernatants indicated at least three specific classes of acyl-homoserine lactones produced by YZ1, and a C4-acyl-homoserine lactone produced by YZ2. Transformation of E. coli with P. aeruginosa or A. hydrophila luxI homologs,which can produce short- or long-chain acyl-homoserine lactones conferred upon E. coli the ability to synthesize acyl-homoserine lactones and affected gene expression, motility, and acid tolerance of E. coli. This is the first study reporting the isolation and characterization of acyl-homoserine lactone synthase-positive bacteria from cattle rumen and swine intestines.
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Affiliation(s)
- Yang Yang
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Mingxu Zhou
- Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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25
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Antibiotics Promote Escherichia coli-Pseudomonas aeruginosa Conjugation through Inhibiting Quorum Sensing. Antimicrob Agents Chemother 2017; 61:AAC.01284-17. [PMID: 28993333 DOI: 10.1128/aac.01284-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/30/2017] [Indexed: 12/19/2022] Open
Abstract
The effect of antibiotics on horizontal gene transfer (HGT) is controversial, and the underlying mechanism remains poorly understood. Here, using Escherichia coli SM10λπ as the donor strain, which carries a chromosomally integrated RP4 plasmid, we investigated the effect of antibiotics on conjugational transfer of a mobilizable gentamicin (Gm) resistance plasmid. The results showed that an exposure to gentamicin that restricted the survival of recipient cells significantly enhanced SM10λπ-Pseudomonas aeruginosa PAO1 conjugation, which was attenuated by a deficiency of lasI-rhlI, genes associated with the generation of the quorum sensing signals N-acyl homoserine lactones (AHLs) in PAO1, or the deletion of the AHL receptor SdiA in SM10λπ. Subsequent mechanistic investigations revealed that a treatment with Gm repressed the mRNA expression of lasI and rhlI in PAO1 and upregulated traI expression in SM10λπ. Moreover, PAO1 treated with other quorum sensing (QS)-inhibiting antibiotics such as azithromycin or chloramphenicol also showed a conjugation-promoting ability. On the other hand, when using non-AHL-producing E. coli strain EC600 as the recipient cells, the promoting effect of Gm on conjugation could not be observed. These data suggest that AHL-SdiA contributes to the effectiveness of antibiotics on plasmid conjugation. Collectively, our findings highlight the HGT-promoting effect of antibiotics and suggest quorum sensing as a promising target for controlling antibiotic resistance dissemination. These findings have implications for assessing the risks of antibiotic use and developing advisable antibiotic treatment protocols.
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