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Liu HY, Prentice EL, Webber MA. Mechanisms of antimicrobial resistance in biofilms. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:27. [PMID: 39364333 PMCID: PMC11445061 DOI: 10.1038/s44259-024-00046-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 09/02/2024] [Indexed: 10/05/2024]
Abstract
Most bacteria in nature exist in aggregated communities known as biofilms, and cells within a biofilm demonstrate major physiological changes compared to their planktonic counterparts. Biofilms are associated with many different types of infections which can have severe impacts on patients. Infections involving a biofilm component are often chronic and highly recalcitrant to antibiotic therapy as a result of intrinsic physical factors including extracellular matrix production, low growth rates, altered antibiotic target production and efficient exchange of resistance genes. This review describes the biofilm lifecycle, phenotypic characteristics of a biofilm, and contribution of matrix and persister cells to biofilms intrinsic tolerance to antimicrobials. We also describe how biofilms can evolve antibiotic resistance and transfer resistance genes within biofilms. Multispecies biofilms and the impacts of various interactions, including cooperation and competition, between species on tolerance to antimicrobials in polymicrobial biofilm communities are also discussed.
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Affiliation(s)
- Ho Yu Liu
- Quadram Institute Biosciences, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
- Norwich Medical School, University of East Anglia, Norwich, Norfolk NR4 7TJ UK
- Centre for Microbial Interactions, Norwich Research Park, Norwich, Norfolk NR4 7UG UK
| | - Emma L Prentice
- Quadram Institute Biosciences, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Mark A Webber
- Quadram Institute Biosciences, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
- Norwich Medical School, University of East Anglia, Norwich, Norfolk NR4 7TJ UK
- Centre for Microbial Interactions, Norwich Research Park, Norwich, Norfolk NR4 7UG UK
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2
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Ojaimi Loibman S, Quintana-Hayashi MP, Santos L, Lindén SK. Aeromonas salmonicida AI-1 and AI-2 quorum sensing pathways are differentially regulated by rainbow trout mucins and during in vivo colonization. FISH & SHELLFISH IMMUNOLOGY 2024; 153:109862. [PMID: 39209006 DOI: 10.1016/j.fsi.2024.109862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Aeromonas salmonicida is an opportunistic pathogen with relevance for aquaculture. Fish epithelia are covered by a mucus layer, composed mainly by highly glycosylated mucins, which are the first point of contact between fish and pathogens. Quorum sensing (QS), a bacterial communication mechanism through secreted autoinducer signals that governs gene expression, influences bacterial growth and virulence. The main A. salmonicida autoinducers are mediated by the luxS and asaI genes, corresponding to inter- and intraspecies communication, respectively. The aim of this study was to determine the effect of the mucins that pathogens encounter during colonization of the gill and skin on A. salmonicida QS. We found that expression of A. salmonicida asaI, but not luxS, was increased after culture at 20 °C compared to 10 °C. Rainbow trout gill and skin mucins up-regulated asaI expression 2-fold but down-regulated luxS 10-fold. The downregulation of luxS was reflected by a reduction in autoinducer-2 secretion. Mucins isolated from skin had a stronger inhibitory effect than mucins isolated from gills on both luxS expression and A1-2 secretion, consistent with a higher relative abundance of N-Acetylneuraminic acid on skin mucins than on gill mucins. Reduction of AI-2 production by mucins or luxS-deletion lead to a reduced A. salmonicida auto-aggregation. Furthermore, after colonization of the gill, luxS was down regulated whereas asaI expression was upregulated. Both in vivo and in vitro, the expression of luxS and asaI were thus differentially regulated, frequently in an inverse manner. The strong AI-2 inhibiting effect of the skin mucins is likely part of the mucin-based defense against pathogens.
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Affiliation(s)
| | | | - Licínia Santos
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, Sweden
| | - Sara K Lindén
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, Sweden.
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3
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Gopalakrishnan AV, Kanagaraja A, Sakthivelu M, Devadasan V, Gopinath SCB, Raman P. Role of fatty acids in modulating quorum sensing in Pseudomonas aeruginosa and Chromobacterium violaceum: an integrated experimental and computational analysis. Int Microbiol 2024:10.1007/s10123-024-00590-y. [PMID: 39292411 DOI: 10.1007/s10123-024-00590-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/15/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024]
Abstract
The broad-spectrum antibacterial capabilities of fatty acids (FAs) and their reduced propensity to promote resistance have rendered as a promising substitute for conventional antibiotics. The structural significance of fatty acid production with the other lipids is a major energy source, and signal transduction has drawn a great deal of research attention to these biomolecules. Saturated and monounsaturated fatty acids reduce virulence by preventing harmful opportunistic bacteria like Pseudomonas aeruginosa and Chromobacterium violaceum from activating their quorum sensing (QS) systems. In this finding, the fatty acids capric acid, caprylic acid, and monoelaidin were selected to evaluate their anti-QS activity against the C. violaceum and P. aeruginosa. At the minimum inhibitory concentration (MIC) and sub-MIC concentration of the three fatty acids, the virulence factor production of both the bacteria was quantified. The virulence factors like EPS, biofilm quantification and visualization, and motility assays were inhibited in the dose-dependent manner (MIC and sub-MIC) for both the organisms whereas this pattern was followed in the pyocyanin, pyoverdine, rhamnolipid, protease of P. aeruginosa and the violacein, and chitinase of C. violaceum. In all these biochemical assays, the capric acid could effectively reduce the production and further validated at gene expression level by RT-qPCR. The study on the gene expression for all these virulence factors reveals that the capric acid inhibited the growth of both the organisms in a higher fold than the caprylic and monoelaidin. The in silico approach of structural validation for the binding of ligands with the proteins in the QS circuit was studied by molecular docking in Schrodinger software. The Las I and Las R in P. aeruginosa and the CviR of C. violaceum protein structures were docked with the selected three fatty acids. The capric acid binds to the pocket with the highest binding score of all the proteins than the caprylic and monoelaidin fatty acids. Thus, capric acid proves to be the therapeutic biomolecule for the anti-QS activity of opportunistic bacteria.
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Affiliation(s)
- Allwyn Vyas Gopalakrishnan
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chengalpet, Dt. Tamil Nadu, India
| | - Abinaya Kanagaraja
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chengalpet, Dt. Tamil Nadu, India
| | - Meenakumari Sakthivelu
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chengalpet, Dt. Tamil Nadu, India
| | - Velmurugan Devadasan
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chengalpet, Dt. Tamil Nadu, India
| | - Subash C B Gopinath
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602 105, Tamil Nadu, India
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), 02600, Arau, Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000, Kangar, Perlis, Malaysia
- Department of Technical Sciences, Western Caspian University, Baku, AZ, 1075, Azerbaijan
| | - Pachaiappan Raman
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, 603 203, Chengalpet, Dt. Tamil Nadu, India.
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Hilliard GM, Wilkinson TS, Harris LG, Jenkins RE, Shornick LP. PCL-gelatin honey scaffolds promote Staphylococcus aureus agrA expression in biofilms with Pseudomonas aeruginosa. Front Microbiol 2024; 15:1440658. [PMID: 39290512 PMCID: PMC11405313 DOI: 10.3389/fmicb.2024.1440658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
Introduction Bacterial infection and biofilm formation contribute to impaired healing in chronic diabetic wounds. Staphylococcus aureus and Pseudomonas aeruginosa are found in human diabetic wound biofilms. They may develop antibiotic resistance, increasing the urgency for alternative or complementary therapies. Diabetic wound healing may be improved with the use of biomedically engineered scaffolds, which can also serve as delivery systems for antibacterial compounds. Manuka honey is a potent antibacterial and wound care agent due to its high osmolarity, low pH, and constituents (such as methylglyoxal). Honey exhibits bacteriostatic and bactericidal effects, modulates the expression of biofilm forming genes, and restores antibiotic susceptibility in previously drug resistant pathogens. Methods In this study, we created a dermal regeneration template (DRT) composed of polycaprolactone-gelatin (PCL-gelatin) and Manuka honey to retain honey in the wound and also provide a scaffold for tissue regeneration. Results and discussion Soluble Manuka honey inhibited the planktonic and biofilm growth of both S. aureus (UWH3) and P. aeruginosa (PA14) co-cultures. Manuka honey embedded PCL-gelatin scaffolds did not exhibit bacteriostatic or bactericidal effects on cocultures of UHW3 and PA14; however, they promoted the expression of AgrA, a gene associated with dispersal of S. aureus biofilms.
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Affiliation(s)
| | | | - Llinos G Harris
- Biomedical Sciences at University of Swansea, Swansea, Wales, United Kingdom
| | - Rowena E Jenkins
- Biomedical Sciences at University of Swansea, Swansea, Wales, United Kingdom
| | - Laurie P Shornick
- Department of Biology at Saint Louis University, St. Louis, MO, United States
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Kamran M, Raza M, Ullah R, Alotaibi A, Bano R, Zaman A, Chaman S, Iqbal K, Rasool S, Amin A. Activity of Fluoroquinolones and Proton Pump Inhibitors against Resistant Oral Bacterial Biofilms, in silico and in vitro Analysis. Pol J Microbiol 2024; 73:329-342. [PMID: 39268954 PMCID: PMC11395420 DOI: 10.33073/pjm-2024-028] [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: 03/29/2024] [Accepted: 06/02/2024] [Indexed: 09/15/2024] Open
Abstract
Oral bacterial infections are a great health concern worldwide especially in diabetic patients. Emergence of antimicrobial resistance with reference to biofilms in oral cavity is of great concern. We investigated antibiotics combination with proton pump inhibitors against oral clinical isolates. The strains were identified as Staphylococcus epidermidis and Staphylococcus aureus by the 16S rRNA gene sequencing. In molecular docking, ciprofloxacin, levofloxacin, and omeprazole best fit to active pockets of transcriptional regulators 4BXI and 3QP1. None of the proton pump inhibitors were active against S. epidermidis, whereas omeprazole showed significant inhibition (MIC 3.9 μg/ml). Fluoroquinolones were active against both S. epidermidis and S. aureus. In combination analysis, a marked decrease in minimum inhibitory concentration was noticed with omeprazole (MIC 0.12 μg/ml). In antiquorum sensing experiments, a significant inhibitory zone was shown for all fluoroquinolones (14-20 mm), whereas among proton pump inhibitors, only omeprazole (12 ± 0.12 mm) was active against Chromobacterium violaceum. In combination analysis, a moderate increase in antiquorum sensing activity was recorded for ciprofloxacin, ofloxacin, and proton pump inhibitors. Further, significant S. aureus biofilm eradication was recorded using of ciprofloxacin, levofloxacin, and omeprazole combination (78 ± 2.1%). The time-kill kinetic studies indicated a bactericidal effect by ciprofloxacin: levofloxacin: omeprazole combination over 24 hrs. It was concluded that fluoroquinolone combined with omeprazole could be an effective treatment option for eradicating oral bacterial biofilms.
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Affiliation(s)
- Muhammad Kamran
- Natural Products Research Lab (NPRL), Gomal Centre of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Raza
- Peshawar Dental College, Riphah International University, Islamabad, Pakistan
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Centre, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alotaibi
- Department of Basic Science, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ràheela Bano
- Department of Pathology, Gomal Medical College, Dera Ismail Khan, Pakistan
| | - Ali Zaman
- Institute of Microbiology, Faculty of Veterinary and Animal Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Sadia Chaman
- Institute of Pharmaceutical Sciences, UVAS, Lahore, Pakistan
| | - Kashif Iqbal
- Faculty of Pharmacy, Ibadat International University, Islamabad, Pakistan
| | - Shahid Rasool
- College of Pharmacy, University of Sargodha, Sargodha, Pakistan
| | - Adnan Amin
- Natural Products Research Lab (NPRL), Gomal Centre of Pharmaceutical Sciences, Faculty of Pharmacy, Gomal University, Dera Ismail Khan, Pakistan
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He Y, Bright R, Vasilev K, Zilm P. Development of "Intelligent particles" for the treatment of dental caries. Eur J Pharm Biopharm 2024; 202:114374. [PMID: 38942176 DOI: 10.1016/j.ejpb.2024.114374] [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: 04/24/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
Dental caries is one of the most prevalent non-communicable diseases worldwide, mediated by a multispecies biofilm that consists of high levels of acidogenic bacteria which ferment sugar to acid and cause teeth demineralization. Current treatment practice remains insufficient in addressing 1) rapid clearance of therapeutic agents from the oral environment 2) destroying bacteria that contribute to the healthy oral microbiome. In addition, increasing concerns over antibiotic resistance calls for innovative alternatives. In this study, we developed a pH responsive nano-carrier for delivery of polycationic silver nanoparticles. Branched-PEI capped silver nanoparticles (BPEI-AgNPs) were encapsulated in a tannic acid - Fe (III) complex-modified poly(D,L-lactic-co-glycolic acid) (PLGA) particle (Fe(III)-TA/PLGA@BPEI-AgNPs) to enhance binding to the plaque biofilm and demonstrate "intelligence" by releasing BPEI-AgNPs under acidic conditions that promote dental caries The constructed Fe(III)-TA/PLGA@BPEI-AgNPs (intelligent particles - IPs) exhibited significant binding to an axenic S. mutans biofilm grown on hydroxyapatite. Ag+ ions were released faster from the IPs at pH 4.0 (cariogenic pH) compared to pH 7.4. The antibiofilm results indicated that IPs can significantly reduce S. mutans biofilm volume and viability under acidic conditions. Cytotoxicity on differentiated Caco-2 cells and human gingival fibroblasts indicated that IPs were not cytotoxic. These findings demonstrate great potential of IPs in the treatment of dental caries.
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Affiliation(s)
- Yanping He
- Adelaide Dental School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Richard Bright
- College of Medicine and Public Health, Flinders University, Bedford Park SA 5042, Australia
| | - Krasimir Vasilev
- College of Medicine and Public Health, Flinders University, Bedford Park SA 5042, Australia
| | - Peter Zilm
- Adelaide Dental School, University of Adelaide, Adelaide, SA 5000, Australia.
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Pereira O, Qin W, Galand PE, Debroas D, Lami R, Hochart C, Zhou Y, Zhou J, Zhang C. Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing. MLIFE 2024; 3:417-429. [PMID: 39359677 PMCID: PMC11442133 DOI: 10.1002/mlf2.12144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/22/2024] [Accepted: 06/18/2024] [Indexed: 10/04/2024]
Abstract
Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.
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Affiliation(s)
- Olivier Pereira
- Shenzhen Key Laboratory of Marine Geo-Omics of Archaea, Department of Science and Engineering Southern University of Science and Technology Shenzhen China
- Institut WUT-AMU Wuhan University of Technology and Aix-Marseille Université Wuhan China
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics University of Oklahoma Norman Oklahoma USA
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB) Banyuls sur Mer France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement Clermont-Ferrand France
| | - Raphael Lami
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM) Banyuls sur Mer France
| | - Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB) Banyuls sur Mer France
| | - Yangkai Zhou
- Shenzhen Key Laboratory of Marine Geo-Omics of Archaea, Department of Science and Engineering Southern University of Science and Technology Shenzhen China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Shenzhen International Graduate School Tsinghua University Shenzhen China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics of Archaea, Department of Science and Engineering Southern University of Science and Technology Shenzhen China
- Shanghai Sheshan National Geophysical Observatory Shanghai Earthquake Agency Shanghai China
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Pham TT, Nguyen TD, Nguyen TT, Pham MN, Nguyen PT, Nguyen TUT, Huynh TTN, Nguyen HT. Rhizosphere bacterial exopolysaccharides: composition, biosynthesis, and their potential applications. Arch Microbiol 2024; 206:388. [PMID: 39196410 DOI: 10.1007/s00203-024-04113-1] [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: 07/04/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 08/29/2024]
Abstract
Bacterial exopolysaccharides (EPS) are biopolymers of carbohydrates, often released from cells into the extracellular environment. Due to their distinctive physicochemical properties, biocompatibility, biodegradability, and non-toxicity, EPS finds applications in various industrial sectors. However, the need for alternative EPS has grown over the past few decades as lactic acid bacteria's (LAB) low-yield EPS is unable to meet the demand. In this case, rhizosphere bacteria with the diverse communities in soil leading to variations in composition and structure, are recognized as a potential source of EPS applicable in various industries. In addition, media components and cultivation conditions have an impact on EPS production, which ultimately affects the quantity, structure, and biological functions of the EPS. Therefore, scientists are currently working on manipulating bacterial EPS by developing cultures and applying abiotic and biotic stresses, so that better production of exopolysaccharides can be attained. This review highlights the composition, biosynthesis, and effects of environmental factors on EPS production along with the potential applications in different fields of industry. Ultimately, an overview of potential future paths and tactics for improving EPS implementation and commercialization is pointed out.
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Affiliation(s)
| | | | - Thi-Tho Nguyen
- Hutech Institute of Applied Science, HUTECH University, Ho Chi Minh City, Vietnam.
| | - Minh-Nhut Pham
- Hutech Institute of Applied Science, HUTECH University, Ho Chi Minh City, Vietnam
| | - Phu-Tho Nguyen
- An Giang University, An Giang, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - To-Uyen Thi Nguyen
- Graduate University of Sciences and Technology, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | | | - Huu-Thanh Nguyen
- An Giang University, An Giang, Vietnam.
- Vietnam National University, Ho Chi Minh City, Vietnam.
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Jung JM, Rahman A, Schiffer AM, Weisberg AJ. Beav: a bacterial genome and mobile element annotation pipeline. mSphere 2024; 9:e0020924. [PMID: 39037262 PMCID: PMC11351099 DOI: 10.1128/msphere.00209-24] [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: 03/12/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024] Open
Abstract
Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional Agrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at https://github.com/weisberglab/beav. IMPORTANCE Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
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Affiliation(s)
- Jewell M. Jung
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Arafat Rahman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Andrea M. Schiffer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
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10
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Mendoza ASG, Acosta MFM, Sánchez JAM, Vázquez LEC. Principles and challenges of whole cell microbial biosensors in the food industry. J Food Sci 2024. [PMID: 39175184 DOI: 10.1111/1750-3841.17294] [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: 04/25/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Whole cell microbial biosensors (WCMB) are mostly genetically modified microorganisms used to detect target molecules as indicators of biological and chemical contaminants as well as in the identification of compounds of interest in the food industry. The specificity and sensitivity of these biosensors are achieved through the design of genetic circuits that make use of genetic sequences such as promoters, terminators, genes encoding regulatory proteins or reporter proteins, among others. Despite the advances of WCMBs for their application, significant challenges are faced, such as cell stability, regulatory restrictions, and the need to optimize response times so that they can be a competitive detection tool in the market. This review explores the technological progress, potential and limitations of WCMBs in the food industry, starting by reviewing the operating principles of biosensors. The importance of selecting appropriate chassis cells and the integration of recognition elements and transducers to maximize their effectiveness in the detection of contaminants and compounds of interest in the food industry is highlighted.
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Affiliation(s)
- América Selene Gaona Mendoza
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
| | - María Fernanda Mendoza Acosta
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
| | - Julio Armando Massange Sánchez
- Plant Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco A.C. (CIATEJ), Guadalajara, Mexico
| | - Luz Edith Casados Vázquez
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- CONAHCyT-University of Guanajuato, Guanajuato, México
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11
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Cianciotto NP. The type II secretion system as an underappreciated and understudied mediator of interbacterial antagonism. Infect Immun 2024; 92:e0020724. [PMID: 38980047 PMCID: PMC11320942 DOI: 10.1128/iai.00207-24] [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: 07/10/2024] Open
Abstract
Interbacterial antagonism involves all major phyla, occurs across the full range of ecological niches, and has great significance for the environment, clinical arena, and agricultural and industrial sectors. Though the earliest insight into interbacterial antagonism traces back to the discovery of antibiotics, a paradigm shift happened when it was learned that protein secretion systems (e.g., types VI and IV secretion systems) deliver toxic "effectors" against competitors. However, a link between interbacterial antagonism and the Gram-negative type II secretion system (T2SS), which exists in many pathogens and environmental species, is not evident in prior reviews on bacterial competition or T2SS function. A current examination of the literature revealed four examples of a T2SS or one of its known substrates having a bactericidal activity against a Gram-positive target or another Gram-negative. When further studied, the T2SS effectors proved to be peptidases that target the peptidoglycan of the competitor. There are also reports of various bacteriolytic enzymes occurring in the culture supernatants of some other Gram-negative species, and a link between these bactericidal activities and T2SS is suggested. Thus, a T2SS can be a mediator of interbacterial antagonism, and it is possible that many T2SSs have antibacterial outputs. Yet, at present, the T2SS remains relatively understudied for its role in interbacterial competition. Arguably, there is a need to analyze the T2SSs of a broader range of species for their role in interbacterial antagonism. Such investigation offers, among other things, a possible pathway toward developing new antimicrobials for treating disease.
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Affiliation(s)
- Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University School of Medicine, Chicago, Illinois, USA
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Mini M, Jayakumar D, Kumar P. In-silico and in-vitro assessment of the antibiofilm potential of azo dye, carmoisine against Pseudomonas aeruginosa. J Biomol Struct Dyn 2024; 42:6700-6710. [PMID: 37485898 DOI: 10.1080/07391102.2023.2237579] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
Biofilm is a community of microorganisms attached to the substrate and plays a significant role in microbial pathogenesis and medical device-related infection. Pseudomonas aeruginosa (PA) is a highly infectious gram-negative opportunistic biofilm-forming bacterium with high antibiotic resistance. Several reports underscore the antimicrobial activity of natural and synthetic food coloring agents, including carmoisine, turmeric dye, red amaranth dye, and phloxine B. However, their ability to suppress the PA biofilm is not clearly understood. Carmoisine is a red-colored synthetic azo dye containing naphthalene subunits and sulfonic groups and is widely used as a food coloring agent. This study investigated the antibiofilm potential and possible mechanism of biofilm inhibition by carmoisine against PA. Computational studies through molecular docking revealed that carmoisine strongly binds to QS regulator LasR (-12.7) and relatively less strongly but significantly with WspR (-6.9). Further analysis of the docked LasR-carmoisine complex using 100 ns MD simulation (Desmond, Schrödinger) validated the bonding strength and stability. Crystal violet assay, triphenyl tetrazolium chloride salt assay, and confocal microscopic studies were adopted for biofilm quantification, and the results indicated the dose-dependent antibiofilm activity of carmoisine against PA. We hypothesise that the carmoisine-mediated reduction of biofilm in PA is due to its interaction with LasR and interference with the QS system. The computational and biochemical analysis of another compound, 1,2-naphthoquinone-4-sulphonic acid, reiterated the role of the naphthalene ring in biofilm inhibition. Hence, this work will pave the way for the future discovery of antibiofilm drugs based on naphthalene ring-based lead compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Minsa Mini
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
| | - Devi Jayakumar
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
| | - Praveen Kumar
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
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13
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Shapiro JA. A very brief note on why bacterial evolution has physiology. J Physiol 2024; 602:2395-2399. [PMID: 37641409 DOI: 10.1113/jp284409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
The majority of bacteria live and evolve in surface biofilms. Both growth in biofilms and horizontal transfer of DNA are regulated by quorum-sensing pheromone signals. The common regulation of bacterial surface growth and DNA transfers illustrates how physiology contributes to bacterial evolution.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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14
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Surur AK, de Oliveira AB, De Annunzio SR, Ferrisse TM, Fontana CR. Bacterial resistance to antimicrobial photodynamic therapy: A critical update. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 255:112905. [PMID: 38703452 DOI: 10.1016/j.jphotobiol.2024.112905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/06/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024]
Abstract
Bacterial antibiotic resistance is one of the most significant challenges for public health. The increase in bacterial resistance, mainly due to microorganisms harmful to health, and the need to search for alternative treatments to contain infections that cannot be treated by conventional antibiotic therapy has been aroused. An alternative widely studied in recent decades is antimicrobial photodynamic therapy (aPDT), a treatment that can eliminate microorganisms through oxidative stress. Although this therapy has shown satisfactory results in infection control, it is still controversial in the scientific community whether bacteria manage to develop resistance after successive applications of aPDT. Thus, this work provides an overview of the articles that performed successive aPDT applications in models using bacteria published since 2010, focusing on sublethal dose cycles, highlighting the main PSs tested, and addressing the possible mechanisms for developing tolerance or resistance to aPDT, such as efflux pumps, biofilm formation, OxyR and SoxRS systems, catalase and superoxide dismutase enzymes and quorum sensing.
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Affiliation(s)
- Amanda Koberstain Surur
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Clinical Analysis, Araraquara, São Paulo, Brazil.
| | - Analú Barros de Oliveira
- São Paulo State University (UNESP), School of Dentistry, Department of Dental Materials and Prosthodontics, Araraquara, São Paulo, Brazil.
| | - Sarah Raquel De Annunzio
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Clinical Analysis, Araraquara, São Paulo, Brazil.
| | - Túlio Morandin Ferrisse
- São Paulo State University (UNESP), School of Dentistry, Department of Dental Materials and Prosthodontics, Araraquara, São Paulo, Brazil.
| | - Carla Raquel Fontana
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Department of Clinical Analysis, Araraquara, São Paulo, Brazil.
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15
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Widanarni W, Gustilatov M, Ekasari J, Julyantoro PGS, Waturangi DE, Sukenda S. Unveiling the positive impact of biofloc culture on Vibrio parahaemolyticus infection of Pacific white shrimp by reducing quorum sensing and virulence gene expression and enhancing immunity. JOURNAL OF FISH DISEASES 2024; 47:e13932. [PMID: 38373053 DOI: 10.1111/jfd.13932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024]
Abstract
This study aimed to evaluate and unveil the positive impact of biofloc culture on Vibrio parahaemolyticus infection of Pacific white shrimp by reducing quorum sensing (QS) and virulence gene expression and enhancing shrimp's immunity. The shrimp with an average body weight of 0.50 ± 0.09 g were reared in containers with a volume of 2.5 L, 21 units, and a density of 20 shrimp L-1. The shrimp were cultured for 5 days, with each treatment including biofloc system maintenance with a C/N ratio of 10 and a control treatment without biofloc, followed by a challenge test through immersion using V. parahaemolyticus at densities of 103, 105, and 107 CFU mL-1 initially. The results of the in vitro experiment showed that biofloc suspension can inhibit and disperse biofilm formation, as well as reduce the exo-enzyme activity (amylase, protease, and chitinase) of V. parahaemolyticus. Furthermore, the biofloc treatment significantly reduced the expression of the QS regulatory gene OpaR, the PirB toxin gene, and the virulence factor genes T6SS1 and T6SS2 in both in vitro and in vivo. The biofloc system also increased the expression of shrimp immunity-related genes (LGBP, proPO, SP, and PE) and the survival rate of white shrimp challenged with V. parahaemolyticus.
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Affiliation(s)
- Widanarni Widanarni
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia
| | - Muhamad Gustilatov
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia
| | - Julie Ekasari
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia
| | - Pande Gde Sasmita Julyantoro
- Department of Aquatic Resources Management, Faculty of Marine Science and Fisheries, University of Udayana, Denpasar, Bali, Indonesia
| | | | - Sukenda Sukenda
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia
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16
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Manisha Y, Srinivasan M, Jobichen C, Rosenshine I, Sivaraman J. Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens. Biol Rev Camb Philos Soc 2024; 99:837-863. [PMID: 38217090 DOI: 10.1111/brv.13047] [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: 10/20/2021] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.
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Affiliation(s)
- Yadav Manisha
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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17
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Song T, Gupta S, Sorokin Y, Frenkel O, Cytryn E, Friedman J. A Burkholderia cenocepacia-like environmental isolate strongly inhibits the plant fungal pathogen Zymoseptoria tritici. Appl Environ Microbiol 2024; 90:e0222223. [PMID: 38624199 PMCID: PMC11107150 DOI: 10.1128/aem.02222-23] [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: 12/21/2023] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
Fungal phytopathogens cause significant reductions in agricultural yields annually, and overusing chemical fungicides for their control leads to environmental pollution and the emergence of resistant pathogens. Exploring natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We isolated and characterized a novel bacterial strain associated with the species Burkholderia cenocepacia, termed APO9, which strongly inhibits Zymoseptoria tritici, a commercially important pathogenic fungus causing Septoria tritici blotch in wheat. Additionally, this strain exhibits inhibitory activity against four other phytopathogens. We found that physical contact plays a crucial role for APO9's antagonistic capacity. Genome sequencing of APO9 and biosynthetic gene cluster (BGC) analysis identified nine classes of BGCs and three types of secretion systems (types II, III, and IV), which may be involved in the inhibition of Z. tritici and other pathogens. To identify genes driving APO9's inhibitory activity, we screened a library containing 1,602 transposon mutants and identified five genes whose inactivation reduced inhibition efficiency. One such gene encodes for a diaminopimelate decarboxylase located in a terpenoid biosynthesis gene cluster. Phylogenetic analysis revealed that while some of these genes are also found across the Burkholderia genus, as well as in other Betaproteobacteria, the combination of these genes is unique to the Burkholderia cepacia complex. These findings suggest that the inhibitory capacity of APO9 is complex and not limited to a single mechanism, and may play a role in the interaction between various Burkholderia species and various phytopathogens within diverse plant ecosystems. IMPORTANCE The detrimental effects of fungal pathogens on crop yields are substantial. The overuse of chemical fungicides contributes not only to environmental pollution but also to the emergence of resistant pathogens. Investigating natural isolates with strong antagonistic effects against pathogens can improve our understanding of their ecology and develop new treatments for the future. We discovered and examined a unique bacterial strain that demonstrates significant inhibitory activity against several phytopathogens. Our research demonstrates that this strain has a wide spectrum of inhibitory actions against plant pathogens, functioning through a complex mechanism. This plays a vital role in the interactions between plant microbiota and phytopathogens.
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Affiliation(s)
- Tingting Song
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Suyash Gupta
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon Lezion, Israel
- Institute of Plant Protection, Agricultural Research Organization, Rishon Lezion, Israel
| | - Yael Sorokin
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Omer Frenkel
- Institute of Plant Protection, Agricultural Research Organization, Rishon Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon Lezion, Israel
| | - Jonathan Friedman
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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18
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Bendary MM, Ali MAM, Abdel Halim AS, Boufahja F, Chaudhary AA, Elkelish A, Soliman RHM, Hegazy WAH. Investigating Sulforaphane's anti-virulence and anti-quorum sensing properties against Pseudomonas aeruginosa. Front Pharmacol 2024; 15:1406653. [PMID: 38835668 PMCID: PMC11148281 DOI: 10.3389/fphar.2024.1406653] [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: 03/25/2024] [Accepted: 04/29/2024] [Indexed: 06/06/2024] Open
Abstract
Background P. aeruginosa, a significant bacterium, can cause severe illness and resistance to antibiotics. Quorum sensing (QS) systems regulate virulence factors production. Targeting QS could reduce bacteria pathogenicity and prevent antibiotic resistance. Cruciferous vegetables contain sulforaphane, known for its anti-inflammatory, antioxidant, anticancer, and antimicrobial properties. Aim We aimed to examine the inhibitory influences of sulforaphane, at a sub-inhibitory concentration (¼ minimum inhibitory concentration, MIC), on virulence and QS in P. aeruginosa. Materials and methods The sulforaphane's anti-virulence actions at sub-inhibitory concentrations were explored in vitro and in vivo. A sub-MIC concentration of sulforaphane was combined with anti-pseudomonal drugs, and the results of this combination were assessed. The virtual affinity of sulforaphane for the receptors of QS was studied, and its effect on the expression of QS genes was quantified. Results Sulforaphane significantly decreased the biofilm formation, motility, ability to withstand oxidative stress, and the synthesis of virulence extracellular enzymes such as proteases, hemolysins, and elastase, as well as other virulence factors like pyocyanin. In addition, sulforaphane lessened the severity of P. aeruginosa infection in mice. Sulforaphane reduced the antipseudomonal antibiotics' MICs when used together, resulting in synergistic effects. The observed anti-virulence impacts were attributed to the ability of sulforaphane to inhibit QS via suppressing the QS genes' expression. Conclusion Sulforaphane shows promise as a potent anti-virulence and anti-QS agent that can be used alongside conventional antimicrobials to manage severe infections effectively. Furthermore, this study paves the way for further investigation of sulforaphane and similar structures as pharmacophores for anti-QS candidates.
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Affiliation(s)
- Mahmoud M Bendary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Mohamed A M Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Alyaa S Abdel Halim
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Fehmi Boufahja
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Amr Elkelish
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Rania H M Soliman
- Department of Anatomy and Embryology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Wael A H Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat, Oman
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19
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Stege PB, Beekman JM, Hendrickx APA, van Eijk L, Rogers MRC, Suen SWF, Vonk AM, Willems RJL, Paganelli FL. Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: unraveling the transcriptional dynamics of host-enterococcal interactions. FEMS MICROBES 2024; 5:xtae014. [PMID: 38813098 PMCID: PMC11134301 DOI: 10.1093/femsmc/xtae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/27/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Enterococcus faecium is an opportunistic pathogen able to colonize the intestines of hospitalized patients. This initial colonization is an important step in the downstream pathogenesis, which includes outgrowth of the intestinal microbiota and potential infection of the host. The impact of intestinal overgrowth on host-enterococcal interactions is not well understood. We therefore applied a RNAseq approach in order to unravel the transcriptional dynamics of E. faecium upon co-culturing with human derived colonic epithelium. Co-cultures of colonic epithelium with a hospital-associated vancomycin resistant (vanA-type) E. faecium (VRE) showed that VRE resided on top of the colonic epithelium when analyzed by microscopy. RNAseq revealed that exposure to the colonic epithelium resulted in upregulation of 238 VRE genes compared to the control condition, including genes implicated in pili expression, conjugation (plasmid_2), genes related to sugar uptake, and biofilm formation (chromosome). In total, 260 were downregulated, including the vanA operon located on plasmid_3. Pathway analysis revealed an overall switch in metabolism to amino acid scavenging and reduction. In summary, our study demonstrates that co-culturing of VRE with human colonic epithelium promotes an elaborate gene response in VRE, enhancing our insight in host-E. faecium interactions, which might facilitate the design of novel anti-infectivity strategies.
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Affiliation(s)
- Paul B Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721MA, The Netherlands
| | - Laura van Eijk
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Sylvia W F Suen
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
- Winclove Probiotics, Amsterdam, 1033JS, The Netherlands
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20
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Rahman NIA, Ramzi MM, Rawi NN, Siong JYF, Bakar K, Bhubalan K, Ariffin F, Saidin J, Azemi AK, Ismail N. Characterization of antibiofilm compound from marine sponge Stylissa carteri. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:37552-37563. [PMID: 38780848 DOI: 10.1007/s11356-024-33704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The fouling phenomenon grabbed global attention and caused huge economic losses specifically in marine-related industries. Sessile behavior exposed the sponge to the risk of fouling. However, their bodies remained free from foulers, which were attributed to the chemical defense system. The objectives of this study were to determine the antibiofilm activity of the marine sponge, Stylissa carteri, and to characterize the isolated compound involved. The antibiofilm activity of S. carteri methanolic crude extract (MCE) and fractions was tested against biofilm-producing bacteria, Pseudomonas aeruginosa, using two different modes of crystal violet biofilm assays: preventive and detachment. Besides that, the disc-diffusion test was conducted to screen the antibacterial activity against gram-positive and gram-negative bacteria while a cytotoxicity assay was conducted on the HepG2 cell line. Bioassay-guided fractionation was carried out using vacuum liquid chromatography (VLC) and solid phase extraction using a C18 Sep-Pak Cartridge. The crystal compound was isolated and characterized through thin-layer chromatography (TLC), Fourier transform infrared (FTIR) spectroscopy, liquid chromatography-mass spectrometry (LCMS), and nuclear magnetic resonance (NMR) spectroscopy. The S. carteri MCE showed a promising result with a half-maximal inhibitory concentration (IC50) of 20.22 μg/mL in the preventive assay, while no IC50 was determined in the detachment assay since all inhibitions < 50%. The S. carteri MCE exhibited broad-spectrum antibacterial activity and displayed a non-cytotoxic effect. Fraction 4 from MCE of S. carteri (IC50 = 2.40 μg/mL) reduced the biofilm in the preventive assay at all concentrations and exhibited no antibacterial activity indicating the independence of antibiofilm from antibacterial properties. Based on the data obtained, an alkaloid named debromohymenialdisine (DBH) was identified from Fraction 4 of S. carteri MCE. In conclusion, S. carteri was able to reduce the establishment of the biofilm formed by P. aeruginosa and could serve as a prominent source of natural antifouling agents.
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Affiliation(s)
- Nor Izzati Abd Rahman
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Mujahidah Mohd Ramzi
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Nurul Najihah Rawi
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Julius Yong Fu Siong
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Kamariah Bakar
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Fazilah Ariffin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Jasnizat Saidin
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Ahmad Khusairi Azemi
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Noraznawati Ismail
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia.
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21
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Monzón-Atienza L, Bravo J, Torrecillas S, Gómez-Mercader A, Montero D, Ramos-Vivas J, Galindo-Villegas J, Acosta F. An In-Depth Study on the Inhibition of Quorum Sensing by Bacillus velezensis D-18: Its Significant Impact on Vibrio Biofilm Formation in Aquaculture. Microorganisms 2024; 12:890. [PMID: 38792721 PMCID: PMC11123725 DOI: 10.3390/microorganisms12050890] [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: 04/03/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Amid growing concerns about antibiotic resistance, innovative strategies are imperative in addressing bacterial infections in aquaculture. Quorum quenching (QQ), the enzymatic inhibition of quorum sensing (QS), has emerged as a promising solution. This study delves into the QQ capabilities of the probiotic strain Bacillus velezensis D-18 and its products, particularly in Vibrio anguillarum 507 communication and biofilm formation. Chromobacterium violaceum MK was used as a biomarker in this study, and the results confirmed that B. velezensis D-18 effectively inhibits QS. Further exploration into the QQ mechanism revealed the presence of lactonase activity by B. velezensis D-18 that degraded both long- and short-chain acyl homoserine lactones (AHLs). PCR analysis demonstrated the presence of a homologous lactonase-producing gene, ytnP, in the genome of B. velezensis D-18. The study evaluated the impact of B. velezensis D-18 on V. anguillarum 507 growth and biofilm formation. The probiotic not only controls the biofilm formation of V. anguillarum but also significantly restrains pathogen growth. Therefore, B. velezensis D-18 demonstrates substantial potential for preventing V. anguillarum diseases in aquaculture through its QQ capacity. The ability to disrupt bacterial communication and control biofilm formation positions B. velezensis D-18 as a promising eco-friendly alternative to conventional antibiotics in managing bacterial diseases in aquaculture.
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Affiliation(s)
- Luis Monzón-Atienza
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
| | - Jimena Bravo
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentáries (IRTA), Centre de Sant Carles de la Rápita (IRTA-SCR), 43540 Sant Carles de la Rápita, Spain
| | - Antonio Gómez-Mercader
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
| | - José Ramos-Vivas
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39010 Santander, Spain
| | - Jorge Galindo-Villegas
- Deparment of Genomics, Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway;
| | - Félix Acosta
- Grupo de Investigación en Acuicultura (GIA), Instituto Ecoaqua, Universidad de Las Palmas de Gran Canaria, 35001 Las Palmas de Gran Canaria, Spain; (L.M.-A.); (S.T.); (A.G.-M.); (J.R.-V.)
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Pacwa-Płociniczak M, Kumor A, Bukowczan M, Sinkkonen A, Roslund M, Płociniczak T. The potential of enhanced phytoremediation to clean up multi-contaminated soil - insights from metatranscriptomics. Microbiol Res 2024; 284:127738. [PMID: 38692035 DOI: 10.1016/j.micres.2024.127738] [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: 11/29/2023] [Revised: 03/29/2024] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Abstract
This study aimed to (i) investigate the potential for enhanced phytoremediation to remove contaminants from soil historically co-contaminated with petroleum hydrocarbons (PHs) and heavy metals (HMs) and (ii) analyze the expression of crucial bacterial genes and whole metatranscriptomics profiles for better understanding of soil processes during applied treatment. Phytoremediation was performed using Zea mays and supported by the Pseudomonas qingdaonensis ZCR6 strain and a natural biofertilizer: meat and bone meal (MBM). In previous investigations, mechanisms supporting plant growth and PH degradation were described in the ZCR6 strain. Here, ZCR6 survived in the soil throughout the experiment, but the efficacy of PH removal from all soils fertilized with MBM reached 32 % regardless of the bacterial inoculation. All experimental groups contained 2 % (w/w) MBM. The toxic effect of this amendment on plants was detected 30 days after germination, irrespective of ZCR6 inoculation. Among the 17 genes tested using the qPCR method, only expression of the acdS gene, encoding 1-aminocyclopropane-1-carboxylic acid deaminase, and the CYP153 gene, encoding cytochrome P450-type alkane hydroxylase, was detected in soils. Metatranscriptomic analysis of soils indicated increased expression of methane particulated ammonia monooxygenase subunit A (pmoA-amoA) by Nitrosomonadales bacteria in all soils enriched with MBM compared to the non-fertilized control. We suggest that the addition of 2 % (w/w) MBM caused the toxic effect on plants via the rapid release of ammonia, and this led to high pmoA-amoA expression. In parallel, due to its wide substrate specificity, enhanced bacterial hydrocarbon removal in MBM-treated soils was observed. The metatranscriptomic results indicate that MBM application should be considered to improve bioremediation of soils polluted with PHs rather than phytoremediation. However, lower concentrations of MBM could be considered for phytoremediation enhancement. From a broader perspective, these results indicated the superior capability of metatranscriptomics to investigate the microbial mechanisms driving various bioremediation techniques.
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Affiliation(s)
- Magdalena Pacwa-Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, Katowice 40-032, Poland.
| | - Agata Kumor
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, Katowice 40-032, Poland.
| | - Marta Bukowczan
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, Katowice 40-032, Poland.
| | - Aki Sinkkonen
- Horticulture Technologies, Natural Resources Institute Finland, Itäinen Pitkäkatu 4A, Turku, Finland.
| | - Marja Roslund
- Horticulture Technologies, Natural Resources Institute Finland, Itäinen Pitkäkatu 4A, Turku, Finland.
| | - Tomasz Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, Katowice 40-032, Poland.
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Rojo-Bezares B, Casado C, Ceniceros T, López M, Chichón G, Lozano C, Ruiz-Roldán L, Sáenz Y. Pseudomonas aeruginosa from river water: antimicrobial resistance, virulence and molecular typing. FEMS Microbiol Ecol 2024; 100:fiae028. [PMID: 38444209 PMCID: PMC11004943 DOI: 10.1093/femsec/fiae028] [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: 06/20/2023] [Revised: 12/04/2023] [Accepted: 03/04/2024] [Indexed: 03/07/2024] Open
Abstract
Pseudomonas aeruginosa isolates were recovered from surface river water samples in La Rioja region (Spain) to characterise their antibiotic resistance, molecular typing and virulence mechanisms. Fifty-two P. aeruginosa isolates were isolated from 15 different water samples (45.4%) and belonged to 23 different pulsed-field electrophoresis (PFGE) patterns. All isolates were susceptible to all antibiotics tested, except one carbapenem-resistant P. aeruginosa that showed a premature stop codon in OprD porin. Twenty-two sequence types (STs) (six new ones) were detected among 29 selected P. aeruginosa (one strain with a different PFGE pattern per sample), with ST274 (14%) being the most frequent one. O:6 and O:3 were the predominant serotypes (31%). Seven virulotypes were detected, being 59% exoS-exoY-exoT-exoA-lasA-lasB-lasI-lasR-rhlAB-rhlI-rhlR-aprA-positive P. aeruginosa. It is noteworthy that the exlA gene was identified in three strains (10.3%), and the exoU gene in seven (24.1%), exoS in 18 (62.1%), and both exoS and exoU genes in one strain. High motility ranges were found in these strains. Twenty-seven per cent of strains produced more biofilm biomass, 90% more pyorubin, 83% more pyocyanin and 65.5% more than twice the elastase activity compared with the PAO1 strain. These results highlight the importance of rivers as temporary reservoirs and sources of P. aeruginosa transmission, and show the importance of their epidemiological surveillance in the environment.
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Affiliation(s)
- Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Cristina Casado
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Tania Ceniceros
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Gabriela Chichón
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Carmen Lozano
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Lidia Ruiz-Roldán
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
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24
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Yang JH, Fu JJ, Jia ZY, Geng YC, Ling YR, Fan NS, Jin RC. Microbial response and recovery strategy of the anammox process under ciprofloxacin stress from pure strain and consortia perspectives. ENVIRONMENT INTERNATIONAL 2024; 186:108599. [PMID: 38554504 DOI: 10.1016/j.envint.2024.108599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/01/2024]
Abstract
Ciprofloxacin (CIP) poses a high risk of resistance development in water environments. Therefore, comprehensive effects and recovery strategies of CIP in anaerobic ammonia oxidation (anammox) process were systematically elucidated from consortia and pure strains perspectives. The anammox consortia was not significantly affected by the stress of 10 mg L-1 CIP, while the higher concentration (20 mg L-1) of CIP caused a dramatic reduction in the nitrogen removal performance of anammox system. Simultaneously, the abundances of dominant functional bacteria and corresponding genes also significantly decreased. Such inhibition could not be mitigated by the recovery strategy of adding hydrazine and hydroxylamine. Reducing nitrogen load rate from 5.1 to 1.4 kg N m-3 d-1 promoted the restoration of three reactors. In addition, the robustness and recovery of anammox systems was evaluated using starvation and shock strategies. Simultaneously, antibiotic resistance genes and key metabolic pathways of anammox consortia were upregulated, such as carbohydrate and energy metabolisms. In addition, 11 pure stains were isolated from the anammox system and identified through phylogenetic analysis, 40 % of which showed multidrug resistance, especially Pseudomonas. These findings provide deep insights into the responding mechanism of anammox consortia to CIP stress and promote the application of anammox process for treating wastewater containing antibiotics.
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Affiliation(s)
- Jun-Hui Yang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jin-Jin Fu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zi-Yu Jia
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yin-Ce Geng
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yi-Rong Ling
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Nian-Si Fan
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China; Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
| | - Ren-Cun Jin
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, China; Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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25
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Yang X, Zeng Q, Gou S, Wu Y, Ma X, Zou H, Zhao K. Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates. Front Microbiol 2024; 15:1327675. [PMID: 38410387 PMCID: PMC10895058 DOI: 10.3389/fmicb.2024.1327675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Colonization of Pseudomonas aeruginosa in the lung environments frequently leads to the enrichment of strains displaying enhanced antibiotic resistance and reduced production of quorum-sensing (QS) controlled products. However, the relationship between the emergence of QS deficient variants and antibiotic resistance remains less understood. In this study, 67 P. aeruginosa strains were isolated from the lungs of 14 patients with chronic obstructive pulmonary disease, followed by determining their genetic relationship, QS-related phenotypes and resistance to commonly used antibiotics. The integrity of P. aeruginosa QS system was checked by DNA sequencing. The relationship between the QS system and antibiotic resistance was then assessed by correlation analyses. The function of the LasR protein and bacterial virulence were evaluated through homology modeling and nematode-infection assay. The influence of antibiotic on the development of extracellular protease production ability of P. aeruginosa was tested by an evolutionary experiment. The results showed that P. aeruginosa clinical strains displayed abundant diversity in phenotype and genotype. The production of extracellular proteases was significantly negatively correlated with antibiotic resistance. The strains with enhanced antibiotic resistance also showed a notable overlap with the mutation of lasR gene, which is the core regulatory gene of P. aeruginosa QS system. Molecular docking and Caenorhabditis elegans infection assays further suggested that P. aeruginosa with impaired LasR protein could also have varying pathogenicity. Moreover, in vitro evolution experiments demonstrated that antibiotic-mediated selective pressure, particularly from Levofloxacin contributed to the emergence of extracellular protease-negative strains. Therefore, this study provides evidence for the connection of P. aeruginosa QS system and antibiotic resistance, and holds significance for developing targeted strategies to address antibiotic resistance and improving the management of antibiotic-resistant infections in chronic respiratory diseases.
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Affiliation(s)
- Xiting Yang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Qianglin Zeng
- Affiliated Hospital of Chengdu University, Chengdu University, Chengdu, Sichuan, China
| | - Shiyi Gou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Yi Wu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Xiaoling Ma
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Hang Zou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
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26
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Gómez-Salgado MDRH, Beltrán-Gómez JÁ, Díaz-Nuñez JL, Rivera-Chávez JA, García-Contreras R, Estrada-Velasco ÁY, Quezada H, Serrano Bello CA, Castillo-Juárez I. Efficacy of a Mexican folk remedy containing cuachalalate (Amphipterygium adstringens (Schltdl.) Schiede ex Standl) for the treatment of burn wounds infected with Pseudomonas aeruginosa. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117305. [PMID: 37848078 DOI: 10.1016/j.jep.2023.117305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Cuachalalate (Amphipterygium adstringens) stem bark has been used to heal wounds and counteract microbial infections since pre-Hispanic times. However, its effect in treating infected burns remains unclear. STUDY OBJECTIVES To determine the antipathogenic capacity of a folk remedy (FR) containing cuachalalate stem bark to treat lesions caused by thermal damage and bacterial infection. MATERIALS AND METHODS The antipathogenic capacity of the hexanic extract (HE) and FR was evaluated in a burned mouse model infected with Pseudomonas aeruginosa. Second to third-degree burns were induced with 95 °C water in CD1 mice in similar ratios of males to females. The mice were randomly grouped into non-inoculated (Group 1) and P. aeruginosa inoculated. The latter were divided into untreated infection (Group 2) and infection topically treated with HE (Group 3), silver sulfadiazine (Group 4), and tween 80 (Group 5). In the case of FR, the lesions were washed with an aqueous extract (AE) and applied powdered stem bark (Group 6). Animal survival, establishment of the bacteria in the lesions, and systemic dispersion were determined. In addition, histopathological analysis was performed. The chemical composition of the AE was analyzed through molecular networking analysis, and the antivirulence capacity was determined through the inhibition of pyocyanin production and caseinolytic activity. RESULTS Only the FR showed antipathogenic activity and increased animal survival by 50% by reducing the systemic dispersion of P. aeruginosa. In addition, it stimulated the formation of granulation tissue and the generation of new blood vessels. The AE did not show bactericidal activity but reduced bacterial virulence, and glycosylated flavonoids and catechins were identified as its main constituents. CONCLUSIONS The results of this study contribute to validating the effectiveness of a popular remedy containing cuachalalate stem bark for treating burns infected with P. aeruginosa.
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Affiliation(s)
| | - José Ángel Beltrán-Gómez
- Laboratorio de Investigación y Aplicación de Fitoquímicos Bioactivos, Posgrado en Botánica, Colegio de Postgraduados, Texcoco, 56230, Mexico.
| | - José Luis Díaz-Nuñez
- Laboratorio de Investigación y Aplicación de Fitoquímicos Bioactivos, Posgrado en Botánica, Colegio de Postgraduados, Texcoco, 56230, Mexico.
| | - José Alberto Rivera-Chávez
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, CDMX, Mexico.
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, 04510, Mexico.
| | - Ángel Yahir Estrada-Velasco
- Departamento de Microbiología y Parasitología, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX, 04510, Mexico.
| | - Héctor Quezada
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, CDMX, 06720, Mexico.
| | - Carlos Alberto Serrano Bello
- Departamento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, CDMX, 06720, Mexico.
| | - Israel Castillo-Juárez
- Laboratorio de Investigación y Aplicación de Fitoquímicos Bioactivos, Posgrado en Botánica, Colegio de Postgraduados, Texcoco, 56230, Mexico.
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27
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [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: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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28
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Vadakkan K, Ngangbam AK, Sathishkumar K, Rumjit NP, Cheruvathur MK. A review of chemical signaling pathways in the quorum sensing circuit of Pseudomonas aeruginosa. Int J Biol Macromol 2024; 254:127861. [PMID: 37939761 DOI: 10.1016/j.ijbiomac.2023.127861] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Pseudomonas aeruginosa, an increasingly common competitive and biofilm organism in healthcare infection with sophisticated, interlinked and hierarchic quorum systems (Las, Rhl, PQS, and IQS), creates the greatest threats to the medical industry and has rendered prevailing chemotherapy medications ineffective. The rise of multidrug resistance has evolved into a concerning and potentially fatal occurrence for human life. P. aeruginosa biofilm development is assisted by exopolysaccharides, extracellular DNA, proteins, macromolecules, cellular signaling and interaction. Quorum sensing is a communication process between cells that involves autonomous inducers and regulators. Quorum-induced infectious agent biofilms and the synthesis of virulence factors have increased disease transmission, medication resistance, infection episodes, hospitalizations and mortality. Hence, quorum sensing may be a potential therapeutical target for bacterial illness, and developing quorum inhibitors as an anti-virulent tool could be a promising treatment strategy for existing antibiotics. Quorum quenching is a prevalent technique for treating infections caused by microbes because it diminishes microbial pathogenesis and increases microbe biofilm sensitivity to antibiotics, making it a potential candidate for drug development. This paper examines P. aeruginosa quorum sensing, the hierarchy of quorum sensing mechanism, quorum sensing inhibition and quorum sensing inhibitory agents as a drug development strategy to supplement traditional antibiotic strategies.
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Affiliation(s)
- Kayeen Vadakkan
- Department of Biology, St. Mary's College, Thrissur, Kerala 680020, India; Manipur International University, Imphal, Manipur 795140, India.
| | | | - Kuppusamy Sathishkumar
- Rhizosphere Biology Laboratory, Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India; Department of Computational Biology, Institute of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai 602 105, Tamil Nadu, India
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29
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Rebollar EA. Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent. Microb Genom 2024; 10:001181. [PMID: 38240649 PMCID: PMC10868611 DOI: 10.1099/mgen.0.001181] [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: 09/13/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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30
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Zhou T, Wang J, Todd JD, Zhang XH, Zhang Y. Quorum Sensing Regulates the Production of Methanethiol in Vibrio harveyi. Microorganisms 2023; 12:35. [PMID: 38257862 PMCID: PMC10819757 DOI: 10.3390/microorganisms12010035] [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: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Methanethiol (MeSH) and dimethyl sulfide (DMS) are important volatile organic sulfur compounds involved in atmospheric chemistry and climate regulation. However, little is known about the metabolism of these compounds in the ubiquitous marine vibrios. Here, we investigated MeSH/DMS production and whether these processes were regulated by quorum-sensing (QS) systems in Vibrio harveyi BB120. V. harveyi BB120 exhibited strong MeSH production from methionine (Met) (465 nmol mg total protein-1) and weak DMS production from dimethylsulfoniopropionate (DMSP) cleavage. The homologs of MegL responsible for MeSH production from L-Met widely existed in vibrio genomes. Using BB120 and its nine QS mutants, we found that the MeSH production was regulated by HAI-1, AI-2 and CAI-1 QS pathways, as well as the luxO gene located in the center of this QS cascade. The regulation role of HAI-1 and AI-2 QS systems in MeSH production was further confirmed by applying quorum-quenching enzyme MomL and exogenous autoinducer AI-2. By contrast, the DMS production from DMSP cleavage showed no significant difference between BB120 and its QS mutants. Such QS-regulated MeSH production may help to remove excess Met that can be harmful for vibrio growth. These results emphasize the importance of QS systems and the MeSH production process in vibrios.
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Affiliation(s)
- Tiantian Zhou
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.Z.); (J.W.); (X.-H.Z.)
| | - Jinyan Wang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.Z.); (J.W.); (X.-H.Z.)
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.Z.); (J.W.); (X.-H.Z.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Yunhui Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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31
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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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Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
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Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [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: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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Nazeer RR, Wang M, Welch M. More than just a gel: the extracellular matrixome of Pseudomonas aeruginosa. Front Mol Biosci 2023; 10:1307857. [PMID: 38028553 PMCID: PMC10679415 DOI: 10.3389/fmolb.2023.1307857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Armed with an arsenal of protein secretion systems, antibiotic efflux pumps, and the occasional proclivity for explosive self-destruction, Pseudomonas aeruginosa has become a model for the study of bacterial pathogenesis and biofilm formation. There is accruing evidence to suggest that the biofilm matrix-the bioglue that holds the structure together-acts not only in a structural capacity, but is also a molecular "net" whose function is to capture and retain certain secreted products (including proteins and small molecules). In this perspective, we argue that the biofilm matrixome is a distinct extracellular compartment, and one that is differentiated from the bulk secretome. Some of the points we raise are deliberately speculative, but are becoming increasingly accessible to experimental investigation.
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Affiliation(s)
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Kaur M, Buyck JM, Goormaghtigh F, Decout JL, Mozaheb N, Mingeot-Leclercq MP. Deficient Pseudomonas aeruginosa in MlaA/VacJ outer membrane lipoprotein shows decrease in rhamnolipids secretion, motility, and biofilm formation, and increase in fluoroquinolones susceptibility and innate immune response. Res Microbiol 2023; 174:104132. [PMID: 37660742 DOI: 10.1016/j.resmic.2023.104132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium that causes severe hospital acquired infections poses threat by its ability for adaptation to various growth modes and environmental conditions and by its intrinsic resistance to antibiotics. The latter is mainly due to the outer membrane (OM) asymmetry which is maintained by the Mla pathway resulting in the retrograde transport of glycerophospholipids from the OM to the inner membrane. It comprises six Mla proteins, including MlaA, an OM lipoprotein involved in the removal of glycerophospholipids mislocalized at the outer leaflet of OM. To investigate the role of P. aeruginosa OM asymmetry especially MlaA, this study investigated the effect of mlaA deletion on (i) the susceptibility to antibiotics, (ii) the secretion of virulence factors, the motility, biofilm formation, and (iii) the inflammatory response. mlaA deletion in P. aeruginosa ATCC27853 results in phenotypic changes including, an increase in fluoroquinolones susceptibility and in PQS (Pseudomonas Quinolone Signal) and TNF-α release and a decrease in rhamnolipids secretion, motility and biofilm formation. Investigating how the mlaA knockout impacts on antibiotic susceptibility, bacterial virulence and innate immune response will help to elucidate the biological significance of the Mla system and contribute to the understanding of MlaA in P. aeruginosa OM asymmetry.
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Affiliation(s)
- M Kaur
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
| | - J M Buyck
- University of Poitiers, INSERM U1070, Poitiers, France.
| | - F Goormaghtigh
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
| | - J-L Decout
- Université Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire, Rue de la Chimie, F-38041 Grenoble, France.
| | - N Mozaheb
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
| | - M-P Mingeot-Leclercq
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
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36
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Bayat M, Nahand JS, Farsad-Akhatr N, Memar MY. Bile effects on the Pseudomonas aeruginosa pathogenesis in cystic fibrosis patients with gastroesophageal reflux. Heliyon 2023; 9:e22111. [PMID: 38034726 PMCID: PMC10685303 DOI: 10.1016/j.heliyon.2023.e22111] [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: 06/06/2023] [Revised: 09/10/2023] [Accepted: 11/05/2023] [Indexed: 12/02/2023] Open
Abstract
Gastroesophageal reflux (GER) occurs in most cystic fibrosis (CF) patients and is the primary source of bile aspiration in the airway tract of CF individuals. Aspirated bile is associated with the severity of lung diseases and chronic inflammation caused by Pseudomonas aeruginosa as the most common pathogen of CF respiratory tract infections. P. aeruginosa is equipped with several mechanisms to facilitate the infection process, including but not limited to the expression of virulence factors, biofilm formation, and antimicrobial resistance, all of which are under the strong regulation of quorum sensing (QS) mechanism. By increasing the expression of lasI, rhlI, and pqsA-E, bile exposure directly impacts the QS network. An increase in psl expression and pyocyanin production can promote biofilm formation. Along with the loss of flagella and reduced swarming motility, GER-derived bile can repress the expression of genes involved in creating an acute infection, such as expression of Type Three Secretion (T3SS), hydrogen cyanide (hcnABC), amidase (amiR), and phenazine (phzA-E). Inversely, to cause persistent infection, bile exposure can increase the Type Six Secretion System (T6SS) and efflux pump expression, which can trigger resistance to antibiotics such as colistin, polymyxin B, and erythromycin. This review will discuss the influence of aspirated bile on the pathogenesis, resistance, and persistence of P. aeruginosa in CF patients.
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Affiliation(s)
- Mobina Bayat
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nader Farsad-Akhatr
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Zhang C, Hammer BK. Sociomicrobiology: Coexistence of conflict and cooperation in the squid light organ. Curr Biol 2023; 33:R1063-R1064. [PMID: 37875083 DOI: 10.1016/j.cub.2023.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The Hawaiian bobtail squid's Vibrio fischeri symbionts use quorum sensing for both bioluminescence and to modulate antagonism. New research finds quorum sensing unexpectedly represses V. fischeri's type 6 secretion system, highlighting intricate connections between cooperative and competitive microbial behaviors.
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Affiliation(s)
- Christopher Zhang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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38
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Ballante F, Turkina MV, Ntzouni M, Magnusson KE, Vikström E. Modified N-acyl-L-homoserine lactone compounds abrogate Las-dependent quorum-sensing response in human pathogen Pseudomonas aeruginosa. Front Mol Biosci 2023; 10:1264773. [PMID: 37908228 PMCID: PMC10613653 DOI: 10.3389/fmolb.2023.1264773] [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: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
Quorum sensing (QS) is a mode of cell-cell communication that bacteria use to sense population density and orchestrate collective behaviors. The common opportunistic human pathogen Pseudomonas aeruginosa employs QS to regulate a large set of genes involved in virulence and host-pathogen interactions. The Las circuit positioned on the top of the QS hierarchy in P. aeruginosa makes use of N-acyl-L-homoserine lactones (AHLs) as signal molecules, like N-3-oxo-dodecanoyl-L-homoserine lactone (3O-C12-HSL). Disabling QS circuits by certain small-molecule compounds, known as quorum-sensing inhibitors (QSIs), has been proposed as a strategy to attenuate bacterial pathogenicity. In this study, four new AHL analogs were designed by incorporating a tert-butoxycarbonyl Boc group in amide and β-keto (3-oxo) moiety. Compounds were evaluated on a molecular and phenotypic basis as a QSI using the screening strategy linked to the assignment of the Las QS system in P. aeruginosa. Using a LasR-based bioreporter, we found that the compounds decreased LasR-controlled light activity and competed efficiently with natural 3O-C12-HSL. The compounds reduced the production of the cognate 3O-C12-HSL and certain virulence traits, like total protease activity, elastase activity, pyocyanin production, and extracellular DNA release. Furthermore, a quantitative proteomic approach was used to study the effect of the compounds on QS-regulated extracellular proteins. Among the four compounds tested, one of them showed the most significant difference in the appearance of the 3O-C12-HSL-responsive reference proteins related to QS communication and virulence, i.e., a distinct activity as a QSI. Moreover, by combining experimental data with computational chemistry, we addressed the effect of LasR protein flexibility on docking precision and assessed the advantage of using a multi-conformational docking procedure for binding mode prediction of LasR modulators. Thus, the four new AHL compounds were tested for their interaction with the AHL-binding site in LasR to identify the key interferences with the activity of LasR. Our study provides further insight into molecular features that are required for small-molecule modulation of LasR-dependent QS communication in P. aeruginosa. This should facilitate rational design of the next generation of antivirulence tools to study and manipulate QS-controlled fitness in bacteria and, thereby, handle bacterial infections in a new way.
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Affiliation(s)
- Flavio Ballante
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Maria Ntzouni
- Core Facility, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Karl-Eric Magnusson
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Elena Vikström
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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Meir A, Macé K, Vegunta Y, Williams SM, Waksman G. Substrate recruitment mechanism by gram-negative type III, IV, and VI bacterial injectisomes. Trends Microbiol 2023; 31:916-932. [PMID: 37085348 DOI: 10.1016/j.tim.2023.03.005] [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: 10/28/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/23/2023]
Abstract
Bacteria use a wide arsenal of macromolecular substrates (DNA and proteins) to interact with or infect prokaryotic and eukaryotic cells. To do so, they utilize substrate-injecting secretion systems or injectisomes. However, prior to secretion, substrates must be recruited to specialized recruitment platforms and then handed over to the secretion apparatus for secretion. In this review, we provide an update on recent advances in substrate recruitment and delivery by gram-negative bacterial recruitment platforms associated with Type III, IV, and VI secretion systems.
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Affiliation(s)
- Amit Meir
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Current address: MRC Centre for Virus Research, School of Infection and Immunity, University of Glasgow, Glasgow, UK.
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Yogesh Vegunta
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Sunanda M Williams
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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40
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Gerner E, Giraldo-Osorno PM, Johansson Loo A, Firdaus R, Ben Amara H, Werthén M, Palmquist A, Thomsen P, Omar O, Almqvist S, Trobos M. Targeting Pseudomonas aeruginosa quorum sensing with sodium salicylate modulates immune responses in vitro and in vivo. Front Cell Infect Microbiol 2023; 13:1183959. [PMID: 37614559 PMCID: PMC10442818 DOI: 10.3389/fcimb.2023.1183959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
Introduction Chronic infections are a major clinical challenge in hard-to-heal wounds and implanted devices. Pseudomonas aeruginosa is a common causative pathogen that produces numerous virulence factors. Due to the increasing problem of antibiotic resistance, new alternative treatment strategies are needed. Quorum sensing (QS) is a bacterial communication system that regulates virulence and dampens inflammation, promoting bacterial survival. QS inhibition is a potent strategy to reduce bacterial virulence and alleviate the negative impact on host immune response. Aim This study investigates how secreted factors from P. aeruginosa PAO1, cultured in the presence or absence of the QS inhibitor sodium salicylate (NaSa), influence host immune response. Material and methods In vitro, THP-1 macrophages and neutrophil-like HL-60 cells were used. In vivo, discs of titanium were implanted in a subcutaneous rat model with local administration of P. aeruginosa culture supernatants. The host immune response to virulence factors contained in culture supernatants (+/-NaSa) was characterized through cell viability, migration, phagocytosis, gene expression, cytokine secretion, and histology. Results In vitro, P. aeruginosa supernatants from NaSa-containing cultures significantly increased THP-1 phagocytosis and HL-60 cell migration compared with untreated supernatants (-NaSa). Stimulation with NaSa-treated supernatants in vivo resulted in: (i) significantly increased immune cell infiltration and cell attachment to titanium discs; (ii) increased gene expression of IL-8, IL-10, ARG1, and iNOS, and (iii) increased GRO-α protein secretion and decreased IL-1β, IL-6, and IL-1α secretion, as compared with untreated supernatants. Conclusion In conclusion, treating P. aeruginosa with NaSa reduces the production of virulence factors and modulates major immune events, such as promoting phagocytosis and cell migration, and decreasing the secretion of several pro-inflammatory cytokines.
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Affiliation(s)
- Erik Gerner
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Mölnlycke Health Care AB, Gothenburg, Sweden
| | - Paula Milena Giraldo-Osorno
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Anna Johansson Loo
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rininta Firdaus
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Heithem Ben Amara
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria Werthén
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Anders Palmquist
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter Thomsen
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Omar Omar
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Margarita Trobos
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
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Nicholas-Haizelden K, Murphy B, Hoptroff M, Horsburgh MJ. Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products. Microorganisms 2023; 11:1899. [PMID: 37630459 PMCID: PMC10456854 DOI: 10.3390/microorganisms11081899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial or therapeutic applications. The human skin is an ecological niche which harbours a rich and compositional diversity microbiome stemming from the multifactorial interactions between the host and microbiota facilitated by exploitable effector compounds. Advances in the understanding of microbial colonisation mechanisms alongside species and strain interactions have revealed a novel chemical and biological understanding which displays applicative potential. Studies elucidating the organismal interfaces and concomitant understanding of the central processes of skin biology have begun to unravel a potential wealth of molecules which can exploited for their proposed functions. A variety of skin-microbiome-derived compounds display prospective therapeutic applications, ranging from antioncogenic agents relevant in skin cancer therapy to treatment strategies for antimicrobial-resistant bacterial and fungal infections. Considerable opportunities have emerged for the translation to personal care products, such as topical agents to mitigate various skin conditions such as acne and eczema. Adjacent compound developments have focused on cosmetic applications such as reducing skin ageing and its associated changes to skin properties and the microbiome. The skin microbiome contains a wealth of prospective compounds with therapeutic and commercial applications; however, considerable work is required for the translation of in vitro findings to relevant in vivo models to ensure translatability.
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Affiliation(s)
- Keir Nicholas-Haizelden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
| | - Barry Murphy
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Wirral CH63 3JW, UK; (B.M.); (M.H.)
| | - Malcolm J. Horsburgh
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK;
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Yang M, Zhou X, Bao Y, Zhang Y, Liu B, Gan L, Tao W, Tuo J, Gong H. Comprehensive Genomic Analysis Reveals Extensive Diversity of Type I and Type IV Secretion Systems in Klebsiella pneumoniae. Curr Microbiol 2023; 80:270. [PMID: 37402963 DOI: 10.1007/s00284-023-03362-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
The diversity and distribution of secretion systems in Klebsiella pneumoniae are unclear. In this study, the six common secretion systems (T1SS-T6SS) were comprehensively investigated in the genomes of 952 K. pneumoniae strains. T1SS, T2SS, type T subtype of T4SS, T5SS, and subtype T6SSi of T6SS were found. The findings indicated fewer types of secretion systems in K. pneumoniae than reported in Enterobacteriaceae, such as Escherichia coli. One conserved T2SS, one conserved T5SS, and two conserved T6SS were detected in more than 90% of the strains. In contrast, the strains displayed extensive diversity of T1SS and T4SS. Notably, T1SS and T4SS were enriched in the hypervirulent and classical multidrug resistance pathotypes of K. pneumoniae, respectively. The results expand the epidemiological knowledge of the virulence and transmissibility of pathogenic K. pneumoniae and contribute to identify the potential strains for safe applications.
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Affiliation(s)
- Menglei Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiaoqin Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yangyang Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Boya Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Luxi Gan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Weihua Tao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jinyou Tuo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Heng Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Chang HY, Gui CY, Huang TC, Hung YC, Chen TY. Quantitative Proteomic Analysis on the Slightly Acidic Electrolyzed Water Triggered Viable but Non-Culturable Listeria monocytogenes. Int J Mol Sci 2023; 24:10616. [PMID: 37445793 DOI: 10.3390/ijms241310616] [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: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
This study undertakes a comprehensive exploration of the impact of slightly acidic electrolyzed water (SAEW) on Listeria monocytogenes, a common foodborne pathogen, with a particular focus on understanding the molecular mechanisms leading to the viable but nonculturable (VBNC) state. Given the widespread application of SAEW as an effective disinfectant in the food industry, uncovering these molecular pathways is crucial for improving food safety measures. We employed tandem mass tags (TMT), labeling proteomic techniques and LC-MS/MS to identify differentially expressed proteins under two doses of SAEW conditions. We indicated 203 differential expressed proteins (DEPs), including 78 up-regulated and 125 down-regulated DEPs. The functional enrichment analysis of these proteins indicated that ribosomes, biosynthesis of secondary metabolites, and aminoacyl-tRNA biosynthesis were enriched functions affected by SAEW. Further, we delved into the role of protein chlorination, a potential consequence of reactive chlorine species generated during the SAEW production process, by identifying 31 chlorinated peptides from 22 proteins, with a dominant sequence motif of Rxxxxx[cY] and functionally enriched in translation. Our findings suggest that SAEW might prompt alterations in the protein translation process and trigger compensatory ribosome biosynthesis. However, an imbalance in the levels of elongation factors and AARSs could hinder recovery, leading to the VBNC state. This research carries substantial implications for food safety and sanitation, as it adds to our understanding of the SAEW-induced VBNC state in L. monocytogenes and offers potential strategies for its control.
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Affiliation(s)
- Hsin-Yi Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan
- Department of Research and Development, National Defense Medical Center, Taipei 11490, Taiwan
| | - Chin-Ying Gui
- Department of Food Science, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Tsui-Chin Huang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yen-Con Hung
- Department of Food Science & Technology, University of Georgia, Griffin, GA 30223-1797, USA
| | - Tai-Yuan Chen
- Department of Food Science, National Taiwan Ocean University, Keelung 20224, Taiwan
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Shen Y, Gao S, Fan Q, Zuo J, Wang Y, Yi L, Wang Y. New antibacterial targets: Regulation of quorum sensing and secretory systems in zoonotic bacteria. Microbiol Res 2023; 274:127436. [PMID: 37343493 DOI: 10.1016/j.micres.2023.127436] [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: 03/17/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Quorum sensing (QS) is a communication mechanism that controls bacterial communication and can influence the transcriptional expression of multiple genes through one or more signaling molecules, thereby coordinating the population response of multiple bacterial pathogens. Secretion systems (SS) play an equally important role in bacterial information exchange, relying on the secretory systems to secrete proteins that act as virulence factors to promote adhesion to host cells. Eight highly efficient SS have been described, all of which are involved in the secretion or transfer of virulence factors, and the effector proteins they secrete play a key role in the virulence and pathogenicity of bacteria. It has been shown that many bacterial SS are directly or indirectly regulated by QS and thus influence bacterial virulence and antibiotic resistance. This review describes the relationship between QS and SS of several common zoonotic pathogenic bacteria and outlines the molecular mechanisms of how QS systems regulate SS, to provide a theoretical basis for the study of bacterial pathogenicity and the development of novel antibacterial drugs.
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Affiliation(s)
- Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Shuji Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Qingying Fan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China
| | - Li Yi
- Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China; College of Life Science, Luoyang Normal University, Luoyang, China.
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China; Henan Engineering Research Center of Livestock and Poultry Emerging Disease Detection and Control, Luoyang, China.
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Carezzano ME, Paletti Rovey MF, Cappellari LDR, Gallarato LA, Bogino P, Oliva MDLM, Giordano W. Biofilm-Forming Ability of Phytopathogenic Bacteria: A Review of its Involvement in Plant Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112207. [PMID: 37299186 DOI: 10.3390/plants12112207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Phytopathogenic bacteria not only affect crop yield and quality but also the environment. Understanding the mechanisms involved in their survival is essential to develop new strategies to control plant disease. One such mechanism is the formation of biofilms; i.e., microbial communities within a three-dimensional structure that offers adaptive advantages, such as protection against unfavorable environmental conditions. Biofilm-producing phytopathogenic bacteria are difficult to manage. They colonize the intercellular spaces and the vascular system of the host plants and cause a wide range of symptoms such as necrosis, wilting, leaf spots, blight, soft rot, and hyperplasia. This review summarizes up-to-date information about saline and drought stress in plants (abiotic stress) and then goes on to focus on the biotic stress produced by biofilm-forming phytopathogenic bacteria, which are responsible for serious disease in many crops. Their characteristics, pathogenesis, virulence factors, systems of cellular communication, and the molecules implicated in the regulation of these processes are all covered.
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Affiliation(s)
- María Evangelina Carezzano
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Córdoba X5804BYA, Argentina
- Departamento de Biología Molecular; Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba X5804BYA, Argentina
- Departamento de Microbiología e Inmunología, UNRC, Río Cuarto, Córdoba X5804BYA, Argentina
| | - María Fernanda Paletti Rovey
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Córdoba X5804BYA, Argentina
- Departamento de Microbiología e Inmunología, UNRC, Río Cuarto, Córdoba X5804BYA, Argentina
| | - Lorena Del Rosario Cappellari
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Córdoba X5804BYA, Argentina
- Departamento de Biología Molecular; Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba X5804BYA, Argentina
| | | | - Pablo Bogino
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Córdoba X5804BYA, Argentina
- Departamento de Biología Molecular; Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba X5804BYA, Argentina
| | - María de Las Mercedes Oliva
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Córdoba X5804BYA, Argentina
- Departamento de Microbiología e Inmunología, UNRC, Río Cuarto, Córdoba X5804BYA, Argentina
| | - Walter Giordano
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Córdoba X5804BYA, Argentina
- Departamento de Biología Molecular; Universidad Nacional de Río Cuarto (UNRC), Río Cuarto, Córdoba X5804BYA, Argentina
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Mbock MA, Kamkumo RG, Shukla R, Fouatio WF, Fokou PVT, Tsofack FN, Noussi CD, Fifen R, Nkengfack AE, Singh TR, Ndjakou BL, Sewald N, Boyom FF, Ngang JJE, Boyomo O, Dimo T. Curative anti-typhoid effect of Detarium microcarpum Guill. & Perr. (Leguminosae) hydroethanolic extract root bark based-on in vivo and molecular docking analyses. JOURNAL OF ETHNOPHARMACOLOGY 2023; 307:116209. [PMID: 36706937 DOI: 10.1016/j.jep.2023.116209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Detarium microcarpum is used to treat typhoid fever, a major public health problem, by indigenous population in Africa. Though its preventive activities have been documented, the curative effect is still to be confirmed. AIM OF THE STUDY This study aimed at evaluating the curative effects of the hydroethanolic extract of Detarium microcarpum root bark on Salmonella typhimurium-induced typhoid in rat and exploring the in-silico inhibition of some bacterial key enzymes. STUDY DESIGN In vitro antioxydant, in vivo antisalmonella of the extract and in silico molecular docking assay on the isolated compounds were carried out to explore the anti-salmonella effects of Detarium microcarpum. MATERIAL AND METHODS The in vitro antioxidant properties of the extract were evaluated using DPPH, ABTS and FRAP tests. The anti-salmonella activity of the extract was assessed through feacal sample from Salmonella typhimurium-infected rat cultured in Salmonella-Shigella agar (SS agar) medium. The affinity of isolated compounds (Rhinocerotinoic acid and Microcarposide) from the extract were performed on four key enzymes (Adenylosuccinate lyase, Acetyl coenzyme A synthetase, Thymidine phosphorylase and LuxS-Quorum sensor) using molecular docking simulation to elucidate the molecular level inhibition mechanism. RESULTS Crude extract of D. microcarpum root bark showed variable activities on DPPH (RSa50: 6.09 ± 1.04 μg/mL), ABTS (RSa50: 24.46 ± 0.27), and FRAP (RSa50: 23.30 ± 0.23). The extract at all the doses exhibited significant healing effect of infected rats, with the complete clearance. The extract restored hematological, biochemical and histological parameters closed to the normal control. The molecular docking results indicates that rhinocerotinoic acid and microcarposide present more affinity to the LuxS-Quorum sensor and Acetyl coenzyme A synthetase protein as compared to the others. CONCLUSION These results demonstrate potent anti-typhoid activities of the hydroethanolic of Detarium microcarpum root bark extract through antioxidant properties and high inhibitory affinity of its compounds on some bacterial key enzymes that justify its use as traditional medicine to typhoid fever.
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Affiliation(s)
- Michel Arnaud Mbock
- Department of Microbiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon; Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon; Department of Biochemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon; Department of Biochemistry, Laboratory of Biochemistry, Faculty of Science, University of Douala, PO Box 24 157, Douala, Cameroon
| | - Raceline Gounoue Kamkumo
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon; Department of Biochemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon.
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology Waknaghat, Solan, 173215, H.P., India
| | - William Feudjou Fouatio
- Department of Chemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Patrick Valère Tsouh Fokou
- Department of Biochemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon; Department of Biochemistry, Faculty of Science, University of Bamenda, P.O. box 39, Bamenda, Cameroon
| | - Florence Ngueguim Tsofack
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon
| | - Clarice Djouwoug Noussi
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon
| | - Rodrigue Fifen
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon
| | - Augustin Ephrem Nkengfack
- Department of Chemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology Waknaghat, Solan, 173215, H.P., India
| | - Bruno Lenta Ndjakou
- Department of Chemistry, Higher Teacher Training College, University of Yaoundé 1, P.O. Box 47, Yaoundé, Cameroon
| | - Norbert Sewald
- Department of Chemistry, Bielefeld University, P.O. Box 100131, 33501, Bielefeld, Germany
| | - Fabrice Fekam Boyom
- Department of Biochemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Jean Justin Essia Ngang
- Department of Microbiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon
| | - Onana Boyomo
- Department of Microbiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon
| | - Theophile Dimo
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaoundé, Cameroon.
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Cañellas-Santos M, Rosell-Vives E, Montell L, Bilbao A, Goñi-de-Cerio F, Fernandez-Campos F. Anti-Inflammatory and Anti-Quorum Sensing Effect of Camellia sinensis Callus Lysate for Treatment of Acne. Curr Issues Mol Biol 2023; 45:3997-4016. [PMID: 37232724 PMCID: PMC10217533 DOI: 10.3390/cimb45050255] [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: 02/13/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/27/2023] Open
Abstract
Cutibacterium acnes (C. acnes) is involved in the pathogenesis of acne by inducing inflammation and biofilm formation, along with other virulence factors. A Camellia sinensis (C. sinensis) callus lysate is proposed to reduce these effects. The aim of the present work is to study the anti-inflammatory properties of a callus extract from C. sinensis on C. acnes-stimulated human keratinocytes and the quorum-quenching activities. Keratinocytes were stimulated with thermo-inactivated pathogenic C. acnes and were treated with the herbal lysate (0.25% w/w) to evaluate its anti-inflammatory effect. C. acnes biofilm was developed in vitro and treated with 2.5 and 5% w/w of the lysate to evaluate quorum sensing and the lipase activity. The results showed that the lysate was able to reduce the production of interleukin-6 (IL-6), interleukin-8 (IL-8), tumor necrosis factor-α (TNF-α), and C-X-C motif chemokine ligand 1 (CXCL1), and decrease the nuclear translocation of nuclear factor kappa light chain enhancer of activated B cells (NF-κB). The lysate did not show bactericidal activity but showed diminished biofilm formation, the lipase activity, and the production of autoinducer 2 (AI-2), a member of a family of signaling molecules used in quorum sensing. Therefore, the proposed callus lysate could have the potential to reduce acne-related symptoms without the eradication of C. acnes, which is part of the natural skin microbiome.
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Affiliation(s)
| | | | - Laia Montell
- Laboratory Reig Jofre, Avda del Flors s/n, 08970 Sant Joan Despí, Barcelona, Spain
| | - Ainhoa Bilbao
- GAIKER Technology Centre, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Edif. 202, 48170 Zamudio, Spain
| | - Felipe Goñi-de-Cerio
- GAIKER Technology Centre, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Edif. 202, 48170 Zamudio, Spain
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Verdial C, Serrano I, Tavares L, Gil S, Oliveira M. Mechanisms of Antibiotic and Biocide Resistance That Contribute to Pseudomonas aeruginosa Persistence in the Hospital Environment. Biomedicines 2023; 11:biomedicines11041221. [PMID: 37189839 DOI: 10.3390/biomedicines11041221] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen responsible for multiple hospital- and community-acquired infections, both in human and veterinary medicine. P. aeruginosa persistence in clinical settings is worrisome and is a result of its remarkable flexibility and adaptability. This species exhibits several characteristics that allow it to thrive under different environmental conditions, including the ability to colonize inert materials such as medical equipment and hospital surfaces. P. aeruginosa presents several intrinsic mechanisms of defense that allow it to survive external aggressions, but it is also able to develop strategies and evolve into multiple phenotypes to persevere, which include antimicrobial-tolerant strains, persister cells, and biofilms. Currently, these emergent pathogenic strains are a worldwide problem and a major concern. Biocides are frequently used as a complementary/combination strategy to control the dissemination of P. aeruginosa-resistant strains; however, tolerance to commonly used biocides has also already been reported, representing an impediment to the effective elimination of this important pathogen from clinical settings. This review focuses on the characteristics of P. aeruginosa responsible for its persistence in hospital environments, including those associated with its antibiotic and biocide resistance ability.
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Affiliation(s)
- Cláudia Verdial
- Gato Escondido-Veterinary Clinic, Av. Bombeiros Voluntários n°22B, 2950-209 Palmela, Portugal
| | - Isa Serrano
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Luís Tavares
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Solange Gil
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Manuela Oliveira
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
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Khayat MT, Elbaramawi SS, Nazeih SI, Safo MK, Khafagy ES, Ali MAM, Abbas HA, Hegazy WAH, Seleem NM. Diminishing the Pathogenesis of the Food-Borne Pathogen Serratia marcescens by Low Doses of Sodium Citrate. BIOLOGY 2023; 12:biology12040504. [PMID: 37106705 PMCID: PMC10135860 DOI: 10.3390/biology12040504] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023]
Abstract
Protecting food from bacterial contamination is crucial for ensuring its safety and avoiding foodborne illness. Serratia marcescens is one of the food bacterial contaminants that can form biofilms and pigments that spoil the food product and could cause infections and illness to the consumer. Food preservation is essential to diminish such bacterial contaminants or at least reduce their pathogenesis; however, it should not affect food odor, taste, and consistency and must be safe. Sodium citrate is a well-known safe food additive and the current study aims to evaluate its anti-virulence and anti-biofilm activity at low concentrations against S. marcescens. The anti-virulence and antibiofilm activities of sodium citrate were evaluated phenotypically and genotypically. The results showed the significant effect of sodium citrate on decreasing the biofilm formation and other virulence factors, such as motility and the production of prodigiosin, protease, and hemolysins. This could be owed to its downregulating effect on the virulence-encoding genes. An in vivo investigation was conducted on mice and the histopathological examination of isolated tissues from the liver and kidney of mice confirmed the anti-virulence activity of sodium citrate. In addition, an in silico docking study was conducted to evaluate the sodium citrate binding ability to S. marcescens quorum sensing (QS) receptors that regulates its virulence. Sodium citrate showed a marked virtual ability to compete on QS proteins, which could explain sodium citrate’s anti-virulence effect. In conclusion, sodium citrate is a safe food additive and can be used at low concentrations to prevent contamination and biofilm formation by S. marcescens and other bacteria.
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Affiliation(s)
- Maan T. Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (M.T.K.); (W.A.H.H.)
| | - Samar S. Elbaramawi
- Medicinal Chemistry Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Shaimaa I. Nazeih
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Martin K. Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia 41552, Egypt
| | - Mohamed A. M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11432, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Hisham A. Abbas
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Wael A. H. Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat 113, Oman
- Correspondence: (M.T.K.); (W.A.H.H.)
| | - Noura M. Seleem
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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Meng L, Cao X, Li C, Li J, Xie H, Shi J, Han M, Shen H, Liu C. Housekeeping gene stability in Pesudomonas aeruginosa PAO1 under the pressure of commonly used antibiotics in molecular microbiology assays. Front Microbiol 2023; 14:1140515. [PMID: 36992935 PMCID: PMC10040570 DOI: 10.3389/fmicb.2023.1140515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen notorious for its remarkable capacity of multi-drug resistance, and has become one of the most important model bacteria in clinical bacteriology research. Quantitative real-time PCR is a reliable method widely used in gene expression analysis, for which the selection of a set of appropriate housekeeping genes is a key prerequisite for the accuracy of the results. However, it is easy to overlook that the expression level of housekeeping gene may vary in different conditions, especially in the condition of molecular microbiology assays, where tested strains are generally cultured under the pre-set antibiotic selection pressures, and how this affects the stability of commonly used housekeeping genes remains unclear. In this study, the expression stability of ten classic housekeeping genes (algD, gyrA, anr, nadB, recA, fabD, proC, ampC, rpoS, and rpsL) under the pressure of eight laboratory commonly used antibiotics (kanamycin, gentamycin, tetracycline, chloramphenicol, hygromycin B, apramycin, tellurite, and zeocin) were tested. Results showed that the stability of housekeeping gene expression was indeed affected by the types of antibiotics added, and of course the best reference gene set varied for different antibiotics. This study provides a comprehensive summary of the effects of laboratory antibiotics on the stability of housekeeping genes in P. aeruginosa, highlighting the necessity to select housekeeping genes according to the type of antibiotics used in the initial stage of experiment.
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Affiliation(s)
- Lingning Meng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jia Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jiping Shi
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Mei Han
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Han Shen,
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- *Correspondence: Chang Liu,
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