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Pal A, Ghosh D, Thakur P, Nagpal P, Irulappan M, Maruthan K, Mukherjee S, Patil N, Dutta T, Veeraraghavan B, Vivekanandan P. Clinically relevant mutations in regulatory regions of metabolic genes facilitate early adaptation to ciprofloxacin in Escherichia coli. Nucleic Acids Res 2024; 52:10385-10399. [PMID: 39180403 PMCID: PMC11417348 DOI: 10.1093/nar/gkae719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
The genomic landscape associated with early adaptation to ciprofloxacin is poorly understood. Although the interplay between core metabolism and antimicrobial resistance is being increasingly recognized, mutations in metabolic genes and their biological role remain elusive. Here, we exposed Escherichia coli to increasing gradients of ciprofloxacin with intermittent transfer-bottlenecking and identified mutations in three non-canonical targets linked to metabolism including a deletion (tRNA-ArgΔ414-bp) and point mutations in the regulatory regions of argI (ARG box) and narU. Our findings suggest that these mutations modulate arginine and carbohydrate metabolism, facilitate anaerobiosis and increased ATP production during ciprofloxacin stress. Furthermore, mutations in the regulatory regions of argI and narU were detected in over 70% of sequences from clinical E. coli isolates and were overrepresented among ciprofloxacin-resistant isolates. In sum, we have identified clinically relevant mutations in the regulatory regions of metabolic genes as a central theme that drives physiological changes necessary for adaptation to ciprofloxacin stress.
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Affiliation(s)
- Arijit Pal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Department of Zoology, Raiganj Surendranath Mahavidyalaya, Sudarshanpur, Raiganj, Uttar Dinajpur, West Bengal733134, India
| | - Dipannita Ghosh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pratyusha Thakur
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priya Nagpal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Madhumathi Irulappan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthik Maruthan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Sanket Mukherjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Nikita G Patil
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Amity Institute of Virology and Immunology, Amity University, Noida, Uttar Pradesh, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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2
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Wang X, Zhang X, Zhang J, Zhou Y, Wang F, Wang Z, Li X. Advances in microbial production of geraniol: from metabolic engineering to potential industrial applications. Crit Rev Biotechnol 2024:1-16. [PMID: 39266251 DOI: 10.1080/07388551.2024.2391881] [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: 05/09/2023] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 09/14/2024]
Abstract
Geraniol, an acyclic monoterpene alcohol, has significant potential applications in various fields, including: food, cosmetics, biofuels, and pharmaceuticals. However, the current sources of geraniol mainly include plant tissue extraction or chemical synthesis, which are unsustainable and suffer severely from high energy consumption and severe environmental problems. The process of microbial production of geraniol has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Escherichia coli (13.2 g/L) and Saccharomyces cerevisiae (5.5 g/L) laid a solid foundation for the microbial production of geraniol. In this review, recent advances in the development of geraniol-producing strains, including: metabolic pathway construction, key enzyme improvement, genetic modification strategies, and cytotoxicity alleviation, are critically summarized. Furthermore, the key challenges in scaling up geraniol production and future perspectives for the development of robust geraniol-producing strains are suggested. This review provides theoretical guidance for the industrial production of geraniol using microbial cell factories.
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Affiliation(s)
- Xun Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Xinyi Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Jia Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Yujunjie Zhou
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Fei Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Zhiguo Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
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Yan X, Lin J, Liu Z, David SD, Liang D, Nie S, Ge M, Xue Z, Li W, Qiao J. The Recent Progress of Tricyclic Aromadendrene-Type Sesquiterpenoids: Biological Activities and Biosynthesis. Biomolecules 2024; 14:1133. [PMID: 39334899 PMCID: PMC11430642 DOI: 10.3390/biom14091133] [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: 08/02/2024] [Revised: 08/28/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
The tricyclic-aromadendrene-type sesquiterpenes are widely distributed and exhibit a range of biological activities, including anti-inflammatory, analgesic, antioxidant, antibacterial, insecticidal and cytotoxic properties. Several key sesquiterpene synthases (STSs) of this type have been identified, of which, viridiflorol synthase has been engineered for efficiently biosynthesizing viridiflorol in an Escherichia coli strain. This paper comprehensively summarizes the distribution and biological activity of aromadendrene-type sesquiterpenes in plant essential oils and microorganisms. The progress in aromadendrene-type sesquiterpene biosynthesis research, including the modifications of key STSs and the optimization of synthetic pathways, is reviewed. Finally, the prospects and associated challenges for the application and biosynthesis of these natural products are also discussed.
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Affiliation(s)
- Xiaoguang Yan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Jiaqi Lin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Ziming Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Sichone Daniel David
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Dongmei Liang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Shengxin Nie
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Mingyue Ge
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Zhaohui Xue
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Weiguo Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Zhejiang Institute of Tianjin University, Shaoxing 312300, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
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4
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Dulanto Chiang A, Dekker JP. Efflux pump-mediated resistance to new beta lactam antibiotics in multidrug-resistant gram-negative bacteria. COMMUNICATIONS MEDICINE 2024; 4:170. [PMID: 39210044 PMCID: PMC11362173 DOI: 10.1038/s43856-024-00591-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
The emergence and spread of bacteria resistant to commonly used antibiotics poses a critical threat to modern medical practice. Multiple classes of bacterial efflux pump systems play various roles in antibiotic resistance, and members of the resistance-nodulation-division (RND) transporter superfamily are among the most important determinants of efflux-mediated resistance in gram-negative bacteria. RND pumps demonstrate broad substrate specificities, facilitating extrusion of multiple chemical classes of antibiotics from the bacterial cell. Several newer beta-lactams and beta-lactam/beta-lactamase inhibitor combinations (BL/BLI) have been developed to treat infections caused by multidrug resistant bacteria. Here we review recent studies that suggest RND efflux pumps in clinically relevant gram-negative bacteria may play critical but underappreciated roles in the development of resistance to beta-lactams and novel BL/BLI combinations. Improved understanding of the genetic and structural basis of RND efflux pump-mediated resistance may identify new antibiotic targets as well as strategies to minimize the emergence of resistance.
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Affiliation(s)
- Augusto Dulanto Chiang
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
- Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - John P Dekker
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA.
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA.
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5
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Gravey F, Michel A, Langlois B, Gérard M, Galopin S, Gakuba C, Du Cheyron D, Fazilleau L, Brossier D, Guérin F, Giard JC, Le Hello S. Central role of the ramAR locus in the multidrug resistance in ESBL -Enterobacterales. Microbiol Spectr 2024; 12:e0354823. [PMID: 38916360 PMCID: PMC11302662 DOI: 10.1128/spectrum.03548-23] [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: 10/03/2023] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
The aim of this study was to evaluate the proportion of resistance to a temocillin, tigecycline, ciprofloxacin, and chloramphenicol phenotype called t2c2 that resulted from mutations within the ramAR locus among extended-spectrum β-lactamases-Enterobacterales (ESBL-E) isolated in three intensive care units for 3 years in a French university hospital. Two parallel approaches were performed on all 443 ESBL-E included: (i) the minimal inhibitory concentrations of temocillin, tigecycline, ciprofloxacin, and chloramphenicol were determined and (ii) the genomes obtained from the Illumina sequencing platform were analyzed to determine multilocus sequence types, resistomes, and diversity of several tetR-associated genes including ramAR operon. Among the 443 ESBL-E strains included, isolates of Escherichia coli (n = 194), Klebsiella pneumoniae (n = 122), and Enterobacter cloacae complex (Ecc) (n = 127) were found. Thirty-one ESBL-E strains (7%), 16 K. pneumoniae (13.1%), and 15 Ecc (11.8%) presented the t2c2 phenotype in addition to their ESBL profile, whereas no E. coli presented these resistances. The t2c2 phenotype was invariably reversible by the addition of Phe-Arg-β-naphthylamide, indicating a role of resistance-nodulation-division pumps in these observations. Mutations associated with the t2c2 phenotype were restricted to RamR, the ramAR intergenic region (IR), and AcrR. Mutations in RamR consisted of C- or N-terminal deletions and amino acid substitutions inside its DNA-binding domain or within key sites of protein-substrate interactions. The ramAR IR showed nucleotide substitutions involved in the RamR DNA-binding domain. This diversity of sequences suggested that RamR and the ramAR IR represent major genetic events for bacterial antimicrobial resistance.IMPORTANCEMorbimortality caused by infectious diseases is very high among patients hospitalized in intensive care units (ICUs). A part of these outcomes can be explained by antibiotic resistance, which delays the appropriate therapy. The transferable antibiotic resistance gene is a well-known mechanism to explain the high rate of multidrug resistance (MDR) bacteria in ICUs. This study describes the prevalence of chromosomal mutations, which led to additional antibiotic resistance among MDR bacteria. More than 12% of Klebsiella pneumoniae and Enterobacter cloacae complex strains presented mutations within the ramAR locus associated with a dysregulation of an efflux pump called AcrAB-TolC and a porin: OmpF. These dysregulations led to an increase in antibiotic output notably tigecycline, ciprofloxacin, and chloramphenicol associated with a decrease of input for beta-lactam, especially temocillin. Mutations within transcriptional regulators such as ramAR locus played a major role in antibiotic resistance dissemination and need to be further explored.
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Affiliation(s)
- François Gravey
- Department of Infectious Agents, Bacteriology, Université de Caen Normandie, Univ Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, CHU Caen Normandie, Caen, France
| | - Alice Michel
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Bénédicte Langlois
- Department of Infectious Agents, Bacteriology, Université de Caen Normandie, Univ Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, CHU Caen Normandie, Caen, France
| | - Mattéo Gérard
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Sébastien Galopin
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Clément Gakuba
- Service de Réanimation Chirurgicale, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - Damien Du Cheyron
- Service de Réanimation Médicale, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - Laura Fazilleau
- Service de Réanimation Néonatale, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - David Brossier
- Service de Réanimation Pédiatrique, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - François Guérin
- Service de Bactériologie, CHU de Rennes Pontchaillou, Rennes, France
| | - Jean-Christophe Giard
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Simon Le Hello
- Department of Infectious Agents, Bacteriology, Université de Caen Normandie, Univ Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, CHU Caen Normandie, Caen, France
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6
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Vignolini T, Capitanio M, Caldini C, Gardini L, Pavone FS. Highly inclined light sheet allows volumetric super-resolution imaging of efflux pumps distribution in bacterial biofilms. Sci Rep 2024; 14:12902. [PMID: 38839922 PMCID: PMC11153600 DOI: 10.1038/s41598-024-63729-x] [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: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
Bacterial biofilms are highly complex communities in which isogenic bacteria display different gene expression patterns and organize in a three-dimensional mesh gaining enhanced resistance to biocides. The molecular mechanisms behind such increased resistance remain mostly unknown, also because of the technical difficulties in biofilm investigation at the sub-cellular and molecular level. In this work we focus on the AcrAB-TolC protein complex, a multidrug efflux pump found in Enterobacteriaceae, whose overexpression is associated with most multiple drug resistance (MDR) phenotypes occurring in Gram-negative bacteria. We propose an optical method to quantify the expression level of the AcrAB-TolC pump within the biofilm volume at the sub-cellular level, with single-molecule sensitivity. Through a combination of super-resolution PALM with single objective light sheet and precision genome editing, we can directly quantify the spatial distribution of endogenous AcrAB-TolC pumps expressed in both planktonic bacteria and, importantly, within the bacterial biofilm volume. We observe a gradient of pump density within the biofilm volume and over the course of biofilm maturation. Notably, we propose an optical method that could be broadly employed to achieve volumetric super-resolution imaging of thick samples.
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Affiliation(s)
- T Vignolini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy.
- Parasite RNA Biology Group, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
| | - M Capitanio
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - C Caldini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - L Gardini
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
- National Institute of Optics, National Research Council, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy.
| | - F S Pavone
- European Laboratory for Non- Linear Spectroscopy, LENS, Via N. Carrara 1, 50019, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via G. Sansone 1, 50019, Sesto Fiorentino, Italy
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7
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Ntshonga P, Gobe I, Koto G, Strysko J, Paganotti GM. Biocide resistance in Klebsiella pneumoniae: a narrative review. Infect Prev Pract 2024; 6:100360. [PMID: 38571564 PMCID: PMC10988060 DOI: 10.1016/j.infpip.2024.100360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Klebsiella pneumoniae is among the World Health Organization's list of priority pathogens, notorious for its role in causing healthcare-associated infections and neonatal sepsis globally. Containment of K. pneumoniae transmission depends on the continued effectiveness of antimicrobials and of biocides used for topical antisepsis and surface disinfection. Klebsiella pneumoniae is known to disseminate antimicrobial resistance (AMR) through a large auxiliary genome made up of plasmids, transposons and integrons, enabling it to evade antimicrobial killing through the use of efflux systems and biofilm development. Because AMR mechanisms are also known to impart tolerance to biocides, AMR is frequently linked with biocide resistance (BR). However, despite extensive research on AMR, there is a gap in knowledge about BR and the extent to which AMR and BR mechanisms overlap remains debatable. The aim of this paper is to review and summarise the current knowledge on the determinants of BR in K. pneumoniae and highlight content areas that require further inquiry.
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Affiliation(s)
- Pearl Ntshonga
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Garesego Koto
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Jonathan Strysko
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Department of Paediatric and Adolescent Health, Princess Marina Hospital, Gaborone, Botswana
- Department of Global Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical Sciences, University of Botswana, Gaborone, Botswana
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8
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Duffey M, Jumde RP, da Costa RM, Ropponen HK, Blasco B, Piddock LJ. Extending the Potency and Lifespan of Antibiotics: Inhibitors of Gram-Negative Bacterial Efflux Pumps. ACS Infect Dis 2024; 10:1458-1482. [PMID: 38661541 PMCID: PMC11091901 DOI: 10.1021/acsinfecdis.4c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Efflux is a natural process found in all prokaryotic and eukaryotic cells that removes a diverse range of substrates from inside to outside. Many antibiotics are substrates of bacterial efflux pumps, and modifications to the structure or overexpression of efflux pumps are an important resistance mechanism utilized by many multidrug-resistant bacteria. Therefore, chemical inhibition of bacterial efflux to revitalize existing antibiotics has been considered a promising approach for antimicrobial chemotherapy over two decades, and various strategies have been employed. In this review, we provide an overview of bacterial multidrug resistance (MDR) efflux pumps, of which the resistance nodulation division (RND) efflux pumps are considered the most clinically relevant in Gram-negative bacteria, and describe over 50 efflux inhibitors that target such systems. Although numerous efflux inhibitors have been identified to date, none have progressed into clinical use because of formulation, toxicity, and pharmacokinetic issues or a narrow spectrum of inhibition. For these reasons, the development of efflux inhibitors has been considered a difficult and complex area of research, and few active preclinical studies on efflux inhibitors are in progress. However, recently developed tools, including but not limited to computational tools including molecular docking models, offer hope that further research on efflux inhibitors can be a platform for research and development of new bacterial efflux inhibitors.
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Affiliation(s)
- Maëlle Duffey
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Ravindra P. Jumde
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Renata M.A. da Costa
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Henni-Karoliina Ropponen
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Benjamin Blasco
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Laura J.V. Piddock
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
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9
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Korczak L, Majewski P, Iwaniuk D, Sacha P, Matulewicz M, Wieczorek P, Majewska P, Wieczorek A, Radziwon P, Tryniszewska E. Molecular mechanisms of tigecycline-resistance among Enterobacterales. Front Cell Infect Microbiol 2024; 14:1289396. [PMID: 38655285 PMCID: PMC11035753 DOI: 10.3389/fcimb.2024.1289396] [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: 09/05/2023] [Accepted: 02/27/2024] [Indexed: 04/26/2024] Open
Abstract
The global emergence of antimicrobial resistance to multiple antibiotics has recently become a significant concern. Gram-negative bacteria, known for their ability to acquire mobile genetic elements such as plasmids, represent one of the most hazardous microorganisms. This phenomenon poses a serious threat to public health. Notably, the significance of tigecycline, a member of the antibiotic group glycylcyclines and derivative of tetracyclines has increased. Tigecycline is one of the last-resort antimicrobial drugs used to treat complicated infections caused by multidrug-resistant (MDR) bacteria, extensively drug-resistant (XDR) bacteria or even pan-drug-resistant (PDR) bacteria. The primary mechanisms of tigecycline resistance include efflux pumps' overexpression, tet genes and outer membrane porins. Efflux pumps are crucial in conferring multi-drug resistance by expelling antibiotics (such as tigecycline by direct expelling) and decreasing their concentration to sub-toxic levels. This review discusses the problem of tigecycline resistance, and provides important information for understanding the existing molecular mechanisms of tigecycline resistance in Enterobacterales. The emergence and spread of pathogens resistant to last-resort therapeutic options stands as a major global healthcare concern, especially when microorganisms are already resistant to carbapenems and/or colistin.
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Affiliation(s)
- Lukasz Korczak
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Dominika Iwaniuk
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Pawel Sacha
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | | | - Piotr Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | | | - Anna Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Radziwon
- Regional Centre for Transfusion Medicine, Bialystok, Poland
| | - Elzbieta Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Bialystok, Bialystok, Poland
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10
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Liu J, Lin M, Han P, Yao G, Jiang H. Biosynthesis Progress of High-Energy-Density Liquid Fuels Derived from Terpenes. Microorganisms 2024; 12:706. [PMID: 38674649 PMCID: PMC11052473 DOI: 10.3390/microorganisms12040706] [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: 03/07/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
High-energy-density liquid fuels (HED fuels) are essential for volume-limited aerospace vehicles and could serve as energetic additives for conventional fuels. Terpene-derived HED biofuel is an important research field for green fuel synthesis. The direct extraction of terpenes from natural plants is environmentally unfriendly and costly. Designing efficient synthetic pathways in microorganisms to achieve high yields of terpenes shows great potential for the application of terpene-derived fuels. This review provides an overview of the current research progress of terpene-derived HED fuels, surveying terpene fuel properties and the current status of biosynthesis. Additionally, we systematically summarize the engineering strategies for biosynthesizing terpenes, including mining and engineering terpene synthases, optimizing metabolic pathways and cell-level optimization, such as the subcellular localization of terpene synthesis and adaptive evolution. This article will be helpful in providing insight into better developing terpene-derived HED fuels.
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Affiliation(s)
- Jiajia Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.L.)
| | - Man Lin
- College of Biological Engineering, Sichuan University of Science and Engineering, Yibin 644005, China
| | - Penggang Han
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.L.)
| | - Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.L.)
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (J.L.)
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11
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Rong C, Chen H, Wang Z, Zhao S, Dong D, Qu J, Zheng N, Liu H, Hua X. Inactivation of antibiotic resistant bacteria by Fe 3O 4 @MoS 2 activated persulfate and control of antibiotic resistance dissemination risk. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133533. [PMID: 38286046 DOI: 10.1016/j.jhazmat.2024.133533] [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: 10/20/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/31/2024]
Abstract
Antibiotic resistance poses a global environmental challenge that jeopardizes human health and ecosystem stability. Antibiotic resistant bacteria (ARB) significantly promote the spreading and diffusion of antibiotic resistance. This study investigated the efficiency and mechanism of inactivating tetracycline-resistant Escherichia coli (TR E. coli) using Fe3O4 @MoS2 activated persulfate (Fe3O4 @MoS2/PS). Under optimized conditions (200 mg/L Fe3O4 @MoS2, 4 mM PS, 35 °C), TR E. coli (∼7.5 log CFU/mL) could be fully inactivated within 20 min. The primary reactive oxygen species (ROS) responsible for TR E. coli inactivation in the Fe3O4 @MoS2/PS system were hydroxyl radicals (•OH) and superoxide radicals (•O2-). Remarkably, the efflux pump protein was targeted and damaged by the generated ROS during the inactivation process, resulting in cell membrane rupture and efflux of cell content. Additionally, the horizontal transmission ability of residual antibiotic resistance genes (ARGs) harboring in the TR E. coli was also reduced after the inactivation treatment. This study offers an efficient approach for TR E. coli inactivation and substantial mitigation of antibiotic resistance dissemination risk.
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Affiliation(s)
- Chang Rong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Haijun Chen
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Zhuowen Wang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Shiyi Zhao
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Deming Dong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Jiao Qu
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Na Zheng
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Haiyang Liu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China; School of Environment, Northeast Normal University, Changchun 130117, China.
| | - Xiuyi Hua
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130012, China.
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Wilhelm J, Pos KM. Molecular insights into the determinants of substrate specificity and efflux inhibition of the RND efflux pumps AcrB and AdeB. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001438. [PMID: 38358391 PMCID: PMC10924465 DOI: 10.1099/mic.0.001438] [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: 11/01/2022] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Gram-negative bacterial members of the Resistance Nodulation and cell Division (RND) superfamily form tripartite efflux pump systems that span the cell envelope. One of the intriguing features of the multiple drug efflux members of this superfamily is their ability to recognize different classes of antibiotics, dyes, solvents, bile salts, and detergents. This review provides an overview of the molecular mechanisms of multiple drug efflux catalysed by the tripartite RND efflux system AcrAB-TolC from Eschericha coli. The determinants for sequential or simultaneous multiple substrate binding and efflux pump inhibitor binding are discussed. A comparison is made with the determinants for substrate binding of AdeB from Acinetobacter baumannii, which acts within the AdeABC multidrug efflux system. There is an apparent general similarity between the structures of AcrB and AdeB and their substrate specificity. However, the presence of distinct conformational states and different drug efflux capacities as revealed by single-particle cryo-EM and mutational analysis suggest that the drug binding and transport features exhibited by AcrB may not be directly extrapolated to the homolog AdeB efflux pump.
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Affiliation(s)
- Julia Wilhelm
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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Hu EW, Lu HF, Lin YT, Yang TC, Li LH. Modulatory role of SmeQ in SmeYZ efflux pump-involved functions in Stenotrophomonas maltophilia. J Antimicrob Chemother 2024; 79:383-390. [PMID: 38134316 DOI: 10.1093/jac/dkad392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND SmeYZ is a constitutively expressed efflux pump in Stenotrophomonas maltophilia. Previous studies demonstrated that: (i) smeYZ inactivation causes compromised swimming, oxidative stress tolerance and aminoglycoside resistance; and (ii) the ΔsmeYZ-mediated pleiotropic defects, except aminoglycoside susceptibility, result from up-regulation of entSCEBB'FA and sbiAB operons, and decreased intracellular iron level. OBJECTIVES To elucidate the modulatory role of SmeQ, a novel cytoplasmic protein, in ΔsmeYZ-mediated pleiotropic defects. METHODS The presence of operons was verified using RT-PCR. The role of SmeQ in ΔsmeYZ-mediated pleiotropic defects was assessed using in-frame deletion mutants and functional assays. A bacterial adenylate cyclase two-hybrid assay was used to investigate the protein-protein interactions. Gene expression was quantified using quantitative RT-PCR (RT-qPCR). RESULTS SmeYZ and the downstream smeQ formed an operon. SmeQ inactivation in the WT KJ decreased aminoglycoside resistance but did not affect swimming and tolerance to oxidative stress or iron depletion. However, smeQ inactivation in the smeYZ mutant rescued the ΔsmeYZ-mediated pleiotropic defects, except for aminoglycoside susceptibility. In the WT KJ, SmeQ positively modulated SmeYZ pump function by transcriptionally up-regulating the smeYZQ operon. Nevertheless, in the smeYZ mutant, SmeQ exerted its modulatory role by up-regulating entSCEBB'FA and sbiAB operons, decreasing intracellular iron levels, and causing ΔsmeYZ-mediated pleiotropic defects, except for aminoglycoside susceptibility. CONCLUSIONS SmeQ is the first small protein identified to be involved in efflux pump function in S. maltophilia. It exerts modulatory effect by transcriptionally altering the expression of target genes, which are the smeYZQ operon in the WT KJ, and smeYZQ, entSCEBB'FA and sbiAB operons in smeYZ mutants.
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Affiliation(s)
- En-Wei Hu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, Republic of China
| | - Hsu-Feng Lu
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan, Republic of China
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
- Department of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, Republic of China
| | - Tsuey-Ching Yang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, Republic of China
| | - Li-Hua Li
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, Republic of China
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14
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Yu Z, Shi X, Wang Z. Structures and Efflux Mechanisms of the AcrAB-TolC Pump. Subcell Biochem 2024; 104:1-16. [PMID: 38963480 DOI: 10.1007/978-3-031-58843-3_1] [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] [Indexed: 07/05/2024]
Abstract
The global emergence of multidrug resistance (MDR) in gram-negative bacteria has become a matter of worldwide concern. MDR in these pathogens is closely linked to the overexpression of certain efflux pumps, particularly the resistance-nodulation-cell division (RND) efflux pumps. Inhibition of these pumps presents an attractive and promising strategy to combat antibiotic resistance, as the efflux pump inhibitors can effectively restore the potency of existing antibiotics. AcrAB-TolC is one well-studied RND efflux pump, which transports a variety of substrates, therefore providing resistance to a broad spectrum of antibiotics. To develop effective pump inhibitors, a comprehensive understanding of the structural aspect of the AcrAB-TolC efflux pump is imperative. Previous studies on this pump's structure have been limited to individual components or in vitro determination of fully assembled pumps. Recent advancements in cellular cryo-electron tomography (cryo-ET) have provided novel insights into this pump's assembly and functional mechanism within its native cell membrane environment. Here, we present a summary of the structural data regarding the AcrAB-TolC efflux pump, shedding light on its assembly pathway and operational mechanism.
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Affiliation(s)
- Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Xiaodong Shi
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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15
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Xu L, Liaqat F, Sun J, Khazi MI, Xie R, Zhu D. Advances in the vanillin synthesis and biotransformation: A review. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2024; 189:113905. [DOI: 10.1016/j.rser.2023.113905] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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16
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Nanjan P, Bose V. Efflux-mediated Multidrug Resistance in Critical Gram-negative Bacteria and Natural Efflux Pump Inhibitors. Curr Drug Res Rev 2024; 16:349-368. [PMID: 38288795 DOI: 10.2174/0125899775271214240112071830] [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: 08/13/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 09/04/2024]
Abstract
Multidrug Resistance mechanisms in microorganisms confer the slackness of the existing drugs, leading to added difficulty in treating infections. As a consequence, efficient novel drugs and innovative therapies to treat MDR infections are necessarily required. One of the primary contributors to the emergence of multidrug resistance in gram-negative bacteria has been identified as the efflux pumps. These transporter efflux pumps reduce the intracellular concentration of antibiotics and aid bacterial survival in suboptimal low antibiotic concentration environments that may cause treatment failure. The reversal of this resistance via inhibition of the efflux mechanism is a promising method for increasing the effectiveness of antibiotics against multidrug-resistant pathogens. Such EPI, in combination with antibiotics, can make it easier to reintroduce traditional antibiotics into clinical practice. This review mostly examines efflux-mediated multidrug resistance in critical gram-negative bacterial pathogens and EPI of plant origin that have been reported over previous decades.
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Affiliation(s)
- Praveena Nanjan
- Department of Biochemistry, School of Life Science, Jss Academy of Higher Education and Research, Longwood Campus, Mysuru Road, Ooty, India
| | - Vanitha Bose
- Department of Biochemistry, School of Life Science, Jss Academy of Higher Education and Research, Longwood Campus, Mysuru Road, Ooty, India
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Ricci V, Kaur J, Stone J, Piddock LJV. Antibiotics do not induce expression of acrAB directly but via a RamA-dependent pathway. Antimicrob Agents Chemother 2023; 67:e0062023. [PMID: 37815378 PMCID: PMC10649046 DOI: 10.1128/aac.00620-23] [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: 05/12/2023] [Accepted: 08/09/2023] [Indexed: 10/11/2023] Open
Abstract
The aim of this study was to determine if acrAB induction in Salmonella Typhimurium relies solely on RamA or if other transcriptional activator pathways are also involved, and to better understand the kinetics of induction of both acrAB and ramA. We evaluated the expression of acrAB in S. Typhimurium in response to a variety of compounds that are known to induce the expression of one or more of the transcriptional activators, MarA, SoxS, RamA, and Rob. We utilized green fluorescent protein (GFP) transcriptional reporter fusions to investigate the changes in the expression of acrAB, ramA, marA, and soxS following exposure to sub-inhibitory concentrations of antimicrobial compounds. Of the compounds tested, 13 induce acrAB expression in S. Typhimurium via RamA, MarA, SoxS, and Rob-dependent pathways. None of the tested antibiotics induced acrAB expression, and compounds that induced acrAB expression also induced a general stress response. The results from this study show that the majority of compounds tested induced acrAB via the RamA-dependent pathway. However, none of the antibiotic substrates of the AcrB efflux pump directly increased the expression of AcrAB either directly or indirectly via the induction of one of the transcriptional activators. Using a dual GFP/RFP reporter, we investigated the kinetics of the induction of ramA and acrAB simultaneously and found that acrAB gene expression was transient compared to ramA gene expression. ramA gene expression increased with time and would remain high or decrease slowly over the course of the experiment indicating that RamA exerts a wider global effect and is not limited to efflux regulation alone.
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Affiliation(s)
- Vito Ricci
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
| | - Jaswant Kaur
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
| | - Jack Stone
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
| | - Laura J. V. Piddock
- Antimicrobials Research Group, Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
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18
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Dželalija M, Kvesić-Ivanković M, Jozić S, Ordulj M, Kalinić H, Pavlinović A, Šamanić I, Maravić A. Marine resistome of a temperate zone: Distribution, diversity, and driving factors across the trophic gradient. WATER RESEARCH 2023; 246:120688. [PMID: 37806125 DOI: 10.1016/j.watres.2023.120688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
Marine and ocean environments are the most widespread habitats in the world but are still the least studied from the aspect of antibiotic resistance. The indigenous and tetracycline (TET)- and sulfamethoxazole (SXT)-resistant planktonic bacterial communities were simultaneously investigated for the first time along a trophic gradient of a temperate zone, regarding their taxonomic and functional structures as well as biotic and abiotic factors affecting their dynamics as vehicles of antibiotic resistance genes (ARGs), thus impacting the ARGs distribution at seasonal and spatial scales. A total of 80 microbiomes, recovered seasonally from bottom layer and surface waters along a 68-km transect from wastewater-impacted estuary to coastal and pristine open sea in the central Adriatic (Mediterranean Sea), were analysed using 16S rRNA amplicon sequencing, PICRUSt2 bioinformatics and extensive biostatistics. Eighty-one bacterial phyla were identified, with majority (n = 49) in summer when communities were found to be more species enriched across the gradient. Microbial diversity was more site-specific and pronounced in surface microbiomes in winter. Nevertheless, both richness and community diversity decreased with distance from the coast. Although the microbiomes from human-influenced sites significantly differed from those in oligotrophic offshore area, Proteobacteria were still the most abundant phylum during both seasons at the surface and seabed along the gradient, and the major contributors to the marine resistome regarding native and TET- and SXT-resistant microbial communities. Resistome structure was more diverse in winter, whereas peptide, vancomycin and multidrug resistance modules predominated regardless of season, trophic status, or antibiotic. However, multidrug, beta-lactam resistance modules as well as macrolide, phenicol, aminoglycoside, and particularly imipenem resistance genes were much more frequent in winter, suggesting that the diversity of indigenous resistomes is highly dependent on seasonal variations of the water column, driven by thermohaline stratification and nutrients. Moreover, several pathogenic genera stood out as important carriers of multiple resistance traits in TET- and SXT-related resistomes in both seasons, particularly Acinetobacter, Vibrio, Bacillus and Pseudomonas, beside which Proteus, Serratia and Bacteroides prevailed in native resistomes. This study evidenced seasonal and spatial variations of the marine microbiome and resistome and their driving forces along the trophic gradient, providing a comprehensive insight into the diversity and distribution of antibiotic resistance in the marine ecosystem of a temperate zone.
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Affiliation(s)
- Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Marija Kvesić-Ivanković
- Center of Excellence for Science and Technology-Integration of Mediterranean Region, University of Split, Ruđera Boškovića 31, 21000 Split, Croatia; Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Slaven Jozić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - Marin Ordulj
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, 21000 Split, Croatia
| | - Hrvoje Kalinić
- Department of Informatics, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Antonio Pavlinović
- Faculty of Electrical Engineering, Mechanical Engineering and Naval Architecture, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia.
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Han R, Xing J, Sun H, Guo Z, Yi K, Hu G, Zhai Y, Velkov T, Wu H. The antihelminth drug rafoxanide reverses chromosomal-mediated colistin-resistance in Klebsiella pneumoniae. mSphere 2023; 8:e0023423. [PMID: 37747188 PMCID: PMC10597454 DOI: 10.1128/msphere.00234-23] [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: 04/26/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
The emergence and rapid spread of multi-drug-resistant (MDR) bacteria pose a serious threat to global healthcare. Although the synergistic effect of rafoxanide and colistin was reported, little is known regarding the potential mechanism of this synergy, particularly against chromosomal-mediated colistin-resistant Klebsiella pneumoniae. In the present study, we elucidated the synergistic effect of rafoxanide and colistin against chromosomal-mediated colistin-resistant Klebsiella pneumoniae isolates from human (KP-9) and swine (KP-1) infections. Treatment with 1 mg/L rafoxanide overtly reversed the MIC max to 512-fold. Time-kill assays indicated that rafoxanide acted synergistically with colistin against the growth of KP-1 and KP-9. Mechanistically, we unexpectedly found that the combination destroys the inner-membrane integrity, and ATP synthesis was also quenched, albeit, not via F1F0-ATPase; thereby also inhibiting the activity of efflux pumps. Excessive production of reactive oxygen species (ROS) was also an underlying factor contributing to the bacterial-killing effect of the combination. Transcriptomic analysis unraveled overt heterogeneous expression as treated with both administrations compared with monotherapy. Functional analysis of these differentially expressed genes (DEGs) targeted to the plasma membrane and ATP-binding corroborated phenotypic screening results. These novel findings highlight the synergistic mechanism of rafoxanide in combination with colistin which effectively eradicates chromosomal-mediated colistin-resistant Klebsiella pneumoniae. IMPORTANCE The antimicrobial resistance of Klebsiella pneumoniae caused by the abuse of colistin has increased the difficulty of clinical treatment. A promising combination (i.e., rafoxanide+ colistin) has successfully rescued the antibacterial effect of colistin. However, we still failed to know the potential effect of this combination on chromosome-mediated Klebsiella pneumoniae. Through a series of in vitro experiments, as well as transcriptomic profiling, we confirmed that the MIC of colistin was reduced by rafoxanide by destroying the inner-membrane integrity, quenching ATP synthesis, inhibiting the activity of the efflux pump, and increasing the production of reactive oxygen species. In turn, the expression of relevant colistin resistance genes was down-regulated. Collectively, our study revealed rafoxanide as a promising colistin adjuvant against chromosome-mediated Klebsiella pneumoniae.
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Affiliation(s)
- Rongjia Han
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jiabao Xing
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Huarun Sun
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Zeyu Guo
- National Reference Laboratory of Veterinary Drug Residues (SCAU), College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Kaifang Yi
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gongzheng Hu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yajun Zhai
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tony Velkov
- Department of Pharmacology, Biodiscovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hua Wu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Department of Pharmacology, Biodiscovery Institute, Monash University, Clayton, Victoria, Australia
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20
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Leroy EC, Perry TN, Renault TT, Innis CA. Tetracenomycin X sequesters peptidyl-tRNA during translation of QK motifs. Nat Chem Biol 2023; 19:1091-1096. [PMID: 37322159 DOI: 10.1038/s41589-023-01343-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
As antimicrobial resistance threatens our ability to treat common bacterial infections, new antibiotics with limited cross-resistance are urgently needed. In this regard, natural products that target the bacterial ribosome have the potential to be developed into potent drugs through structure-guided design, provided their mechanisms of action are well understood. Here we use inverse toeprinting coupled to next-generation sequencing to show that the aromatic polyketide tetracenomycin X primarily inhibits peptide bond formation between an incoming aminoacyl-tRNA and a terminal Gln-Lys (QK) motif in the nascent polypeptide. Using cryogenic electron microscopy, we reveal that translation inhibition at QK motifs occurs via an unusual mechanism involving sequestration of the 3' adenosine of peptidyl-tRNALys in the drug-occupied nascent polypeptide exit tunnel of the ribosome. Our study provides mechanistic insights into the mode of action of tetracenomycin X on the bacterial ribosome and suggests a path forward for the development of novel aromatic polyketide antibiotics.
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Affiliation(s)
- Elodie C Leroy
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Pessac, France
- Human Technopole, Milan, Italy
| | - Thomas N Perry
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Pessac, France
- Human Technopole, Milan, Italy
| | - Thibaud T Renault
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Pessac, France.
| | - C Axel Innis
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Pessac, France.
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Hasan M, Wang J, Ahn J. Ciprofloxacin and Tetracycline Resistance Cause Collateral Sensitivity to Aminoglycosides in Salmonella Typhimurium. Antibiotics (Basel) 2023; 12:1335. [PMID: 37627755 PMCID: PMC10451331 DOI: 10.3390/antibiotics12081335] [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: 07/25/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The objective of this study was to evaluate collateral sensitivity and cross-resistance of antibiotic-induced resistant Salmonella Typhimurium to various antibiotics. S. Typhimurium ATCC 19585 (STWT) was exposed to ciprofloxacin, gentamicin, kanamycin, and tetracycline to induce antibiotic resistance, respectively, assigned as STCIP, STGEN, STKAN, and STTET. The susceptibilities of the antibiotic-induced resistant mutants to cefotaxime, chloramphenicol, ciprofloxacin, gentamicin, kanamycin, polymyxin B, streptomycin, tetracycline, and tobramycin were determined in the absence and presence of CCCP and PAβN. STCIP showed the cross-resistance to tetracycline and collateral sensitivity to gentamicin (1/2 fold) and kanamycin (1/4 fold). STTET was also cross-resistant to ciprofloxacin (128-fold) and collateral sensitive to gentamicin (1/4-fold) and kanamycin (1/8-fold). The cross-resistance and collateral sensitivity of STCIP and STTET were associated with the AcrAB-TolC efflux pump and outer membrane porin proteins (OmpC). This study provides new insight into the collateral sensitivity phenomenon, which can be used for designing effective antibiotic treatment regimens to control antibiotic-resistant bacteria.
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Affiliation(s)
- Mahadi Hasan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea;
| | - Jun Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
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22
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Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
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23
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Hajiagha MN, Kafil HS. Efflux pumps and microbial biofilm formation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105459. [PMID: 37271271 DOI: 10.1016/j.meegid.2023.105459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/06/2023]
Abstract
Biofilm-related infections are resistant forms of pathogens that are regarded as a medical problem, particularly due to the spread of multiple drug resistance. One of the factors associated with biofilm drug resistance is the presence of various types of efflux pumps in bacteria. Efflux pumps also play a role in biofilm formation by influencing Physical-chemical interactions, mobility, gene regulation, quorum sensing (QS), extracellular polymeric substances (EPS), and toxic compound extrusion. According to the findings of studies based on efflux pump expression analysis, their role in the anatomical position within the biofilm will differ depending on the biofilm formation stage, encoding gene expression level, the type and concentration of substrate. In some cases, the function of the efflux pumps can overlap with each other, so it seems necessary to accurate identify the efflux pumps of biofilm-forming bacteria along with their function in this process. Such studies will help to choose treatment strategy, at least in combination with antibiotics. Furthermore, if the goal of treatment is an efflux pump manipulation, we should not limit it to inhibition.
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Affiliation(s)
- Mahdyeh Neghabi Hajiagha
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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24
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Başaran SN, Öksüz L. The role of efflux pumps ın antıbıotıc resıstance of gram negatıve rods. Arch Microbiol 2023; 205:192. [PMID: 37060362 DOI: 10.1007/s00203-023-03539-3] [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: 03/04/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
Antibiotic resistance is an important public health problem today, causing increased morbidity and mortality. Resistance to antibiotics in bacteria can develop by various mechanisms such as a change in the target site of the drug, a change in the outer membrane permeability, enzymatic defusing of the drug and efflux of the antimicrobial compound. Some bacteria have the potential to develop resistance to more than one drug by using several mechanisms together. One of the important resistance mechanisms of bacteria is active efflux pumps (EPs). EPs are pump proteins found in all cell types, located in the cell membrane. They are responsible for the excretion of various intracellular and extracellular substances (antibiotics, etc.) out of the cell. There is much research on various antimicrobials that cause antibiotic resistance in Gram negative rods, but studies on EPs are relatively few. Due to the concern that antibiotics will be insufficient in the treatment of diseases, a good understanding of EPs and the discovery of new EP inhibitors will shed light on the future of humanity. In this review, the structure of bacterial EPs in Gram negative bacteria, the role of EPs in multidrug resistance, the importance of EP inhibitors in the fight against antibiotic resistance and the phenotypic and genotypic detection methods of EPs are discussed.
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Affiliation(s)
- Sena Nur Başaran
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey.
| | - Lütfiye Öksüz
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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25
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Jiang H, Wang X. Biosynthesis of monoterpenoid and sesquiterpenoid as natural flavors and fragrances. Biotechnol Adv 2023; 65:108151. [PMID: 37037288 DOI: 10.1016/j.biotechadv.2023.108151] [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: 11/03/2022] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023]
Abstract
Terpenoids are a large class of plant-derived compounds, that constitute the main components of essential oils and are widely used as natural flavors and fragrances. The biosynthesis approach presents a promising alternative route in terpenoid production compared to plant extraction or chemical synthesis. In the past decade, the production of terpenoids using biotechnology has attracted broad attention from both academia and the industry. With the growing market of flavor and fragrance, the production of terpenoids directed by synthetic biology shows great potential in promoting future market prospects. Here, we reviewed the latest advances in terpenoid biosynthesis. The engineering strategies for biosynthetic terpenoids were systematically summarized from the enzyme, metabolic, and cellular dimensions. Additionally, we analyzed the key challenges from laboratory production to scalable production, such as key enzyme improvement, terpenoid toxicity, and volatility loss. To provide comprehensive technical guidance, we collected milestone examples of biosynthetic mono- and sesquiterpenoids, compared the current application status of chemical synthesis and biosynthesis in terpenoid production, and discussed the cost drivers based on the data of techno-economic assessment. It is expected to provide critical insights into developing translational research of terpenoid biomanufacturing.
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Affiliation(s)
- Hui Jiang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311200, PR China
| | - Xi Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311200, PR China; College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, PR China.
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26
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Ma X, Hu K, Xiong Y, Li H, Li J, Tang Y, Liu Z. Local Regulator AcrR Regulates Persister Formation by Repression of AcrAB Efflux Pump during Exponential Growth in Aeromonas veronii. Antimicrob Agents Chemother 2023; 67:e0096922. [PMID: 36853030 PMCID: PMC10019292 DOI: 10.1128/aac.00969-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
Bacterial persisters refer to a small fraction of dormant variants that survive treatment with high concentrations of antibiotics. Increasing research indicates that multidrug efflux pumps play a major role in persister formation in many Gram-negative organisms. In the present study, the roles of the repressor of the AcrAB efflux pump, AcrR, in the regulation of the activity and function of the efflux, as well as in the production of persisters, were investigated in the pathogen Aeromonas veronii, which causes huge economic losses in the aquatic industry and threatens human health. We observed that exclusively in exponential-phase cells, not in stationary-phase cells, the deletion of the acrR gene significantly (P < 0.05) promoted the expression of the acrA and acrB genes and reduced the intracellular accumulation of the efflux substrate Hoechst 33342. Moreover, overexpression of acrR triggered decreased transcription of the promoter of the acrAB operon. The persister assay indicated that the loss of the AcrAB pump decreased the formation of persisters under challenge with all tested antibiotic types of chloramphenicol, fluoroquinolone, tetracycline, and β-lactam, while deletion of acrR caused an exponential-phase-specific increase in persister formation against chloramphenicol, tetracycline, and β-lactam. Our results provide molecular insights into the mechanism of bacterial persistence by demonstrating for the first time that the local regulator AcrR is involved in the modulation of persister formation in A. veronii through its repressive activity on the function of the AcrAB efflux pump during the exponential growth period.
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Affiliation(s)
- Xiang Ma
- School of Life Sciences, Hainan University, Haikou, China
| | - Kang Hu
- School of Life Sciences, Hainan University, Haikou, China
| | - Yuesheng Xiong
- School of Life Sciences, Hainan University, Haikou, China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou, China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou, China
| | - Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou, China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
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27
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Ma X, Xi W, Yang D, Zhao L, Yu W, He Y, Ni W, Gao Z. Collateral sensitivity between tetracyclines and aminoglycosides constrains resistance evolution in carbapenem-resistant Klebsiella pneumoniae. Drug Resist Updat 2023; 68:100961. [PMID: 37004351 DOI: 10.1016/j.drup.2023.100961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
AIMS The acquisition of resistance to one antibiotic may confer an increased sensitivity to another antibiotic in bacteria, which is an evolutionary trade-off between different resistance mechanisms, defined as collateral sensitivity (CS). Exploiting the role of CS in treatment design could be an effective method to suppress or even reverse resistance evolution. METHODS Using experimental evolution, we systematically studied the CS between aminoglycosides and tetracyclines in carbapenem-resistant Klebsiella pneumoniae (CRKP) and explored the underlying mechanisms through genomic and transcriptome analyses. The application of CS-based therapies for resistance suppression, including combination therapy and alternating antibiotic therapy, was further evaluated in vitro and in vivo. RESULTS Reciprocal CS existed between tetracyclines and aminoglycosides in CRKP. The increased sensitivity of aminoglycoside-resistant strains to tetracyclines was associated with the alteration of bacterial membrane potential, whereas the unbalanced oxidation-reduction process of tetracycline-resistant strains may lead to an increased bacterial sensitivity to aminoglycosides. CS-based combination therapy could efficiently constrain the evolution of CRKP resistance in vitro and in vivo. In addition, alternating antibiotic therapy can re-sensitize CRKP to previously resistant drugs, thereby maintaining the trade-off. CONCLUSIONS These results provide new insights into constraining the evolution of CRKP resistance through CS-based therapies.
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Affiliation(s)
- Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wen Xi
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Deqing Yang
- Department of Pharmacy, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wentao Ni
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China.
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China.
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28
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Larabi AB, Masson HLP, Bäumler AJ. Bile acids as modulators of gut microbiota composition and function. Gut Microbes 2023; 15:2172671. [PMID: 36740850 PMCID: PMC9904317 DOI: 10.1080/19490976.2023.2172671] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Changes in the composition of gut-associated microbial communities are associated with many human illnesses, but the factors driving dysbiosis remain incompletely understood. One factor governing the microbiota composition in the gut is bile. Bile acids shape the microbiota composition through their antimicrobial activity and by activating host signaling pathways that maintain gut homeostasis. Although bile acids are host-derived, their functions are integrally linked to bacterial metabolism, which shapes the composition of the intestinal bile acid pool. Conditions that change the size or composition of the bile acid pool can trigger alterations in the microbiota composition that exacerbate inflammation or favor infection with opportunistic pathogens. Therefore, manipulating the composition or size of the bile acid pool might be a promising strategy to remediate dysbiosis.
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Affiliation(s)
- Anaïs B. Larabi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Hugo L. P. Masson
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
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29
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Blair JMA, Siasat P, McNeil HE, Colclough A, Ricci V, Lawler AJ, Abdalaal H, Buckner MMC, Baylay A, Busby SJ, Piddock LJV. EnvR is a potent repressor of acrAB transcription in Salmonella. J Antimicrob Chemother 2022; 78:133-140. [PMID: 36308324 PMCID: PMC9780535 DOI: 10.1093/jac/dkac364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/06/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Resistance nodulation division (RND) family efflux pumps, including the major pump AcrAB-TolC, are important mediators of intrinsic and evolved antibiotic resistance. Expression of these pumps is carefully controlled by a network of regulators that respond to different environmental cues. EnvR is a TetR family transcriptional regulator encoded upstream of the RND efflux pump acrEF. METHODS Binding of EnvR protein upstream of acrAB was determined by electrophoretic mobility shift assays and the phenotypic consequence of envR overexpression on antimicrobial susceptibility, biofilm motility and invasion of eukaryotic cells in vitro was measured. Additionally, the global transcriptome of clinical Salmonella isolates overexpressing envR was determined by RNA-Seq. RESULTS EnvR bound to the promoter region upstream of the genes coding for the major efflux pump AcrAB in Salmonella, inhibiting transcription and preventing production of AcrAB protein. The phenotype conferred by overexpression of envR mimicked deletion of acrB as it conferred multidrug susceptibility, decreased motility and decreased invasion into intestinal cells in vitro. Importantly, we demonstrate the clinical relevance of this regulatory mechanism because RNA-Seq revealed that a drug-susceptible clinical isolate of Salmonella had low acrB expression even though expression of its major regulator RamA was very high; this was caused by very high EnvR expression. CONCLUSIONS In summary, we show that EnvR is a potent repressor of acrAB transcription in Salmonella, and can override binding by RamA so preventing MDR to clinically useful drugs. Finding novel tools to increase EnvR expression may form the basis of a new way to prevent or treat MDR infections.
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Affiliation(s)
- Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Helen E McNeil
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Abigail Colclough
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Vito Ricci
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Amelia J Lawler
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Hind Abdalaal
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Michelle M C Buckner
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Alison Baylay
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Stephen J Busby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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30
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TCA and SSRI Antidepressants Exert Selection Pressure for Efflux-Dependent Antibiotic Resistance Mechanisms in Escherichia coli. mBio 2022; 13:e0219122. [PMID: 36374097 PMCID: PMC9765716 DOI: 10.1128/mbio.02191-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microbial diversity is reduced in the gut microbiota of animals and humans treated with selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs). The mechanisms driving the changes in microbial composition, while largely unknown, is critical to understand considering that the gut microbiota plays important roles in drug metabolism and brain function. Using Escherichia coli, we show that the SSRI fluoxetine and the TCA amitriptyline exert strong selection pressure for enhanced efflux activity of the AcrAB-TolC pump, a member of the resistance-nodulation-cell division (RND) superfamily of transporters. Sequencing spontaneous fluoxetine- and amitriptyline-resistant mutants revealed mutations in marR and lon, negative regulators of AcrAB-TolC expression. In line with the broad specificity of AcrAB-TolC pumps these mutants conferred resistance to several classes of antibiotics. We show that the converse also occurs, as spontaneous chloramphenicol-resistant mutants displayed cross-resistance to SSRIs and TCAs. Chemical-genomic screens identified deletions in marR and lon, confirming the results observed for the spontaneous resistant mutants. In addition, deletions in 35 genes with no known role in drug resistance were identified that conferred cross-resistance to antibiotics and several displayed enhanced efflux activities. These results indicate that combinations of specific antidepressants and antibiotics may have important effects when both are used simultaneously or successively as they can impose selection for common mechanisms of resistance. Our work suggests that selection for enhanced efflux activities is an important factor to consider in understanding the microbial diversity changes associated with antidepressant treatments. IMPORTANCE Antidepressants are prescribed broadly for psychiatric conditions to alter neuronal levels of synaptic neurotransmitters such as serotonin and norepinephrine. Two categories of antidepressants are selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs); both are among the most prescribed drugs in the United States. While it is well-established that antidepressants inhibit reuptake of neurotransmitters there is evidence that they also impact microbial diversity in the gastrointestinal tract. However, the mechanisms and therefore biological and clinical effects remain obscure. We demonstrate antidepressants may influence microbial diversity through strong selection for mutant bacteria with increased AcrAB-TolC activity, an efflux pump that removes antibiotics from cells. Furthermore, we identify a new group of genes that contribute to cross-resistance between antidepressants and antibiotics, several act by regulating efflux activity, underscoring overlapping mechanisms. Overall, this work provides new insights into bacterial responses to antidepressants important for understanding antidepressant treatment effects.
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31
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Are Enterobacteriaceae and Enterococcus Isolated from Powdered Infant Formula a Hazard for Infants? A Genomic Analysis. Foods 2022; 11:foods11223556. [PMID: 36429148 PMCID: PMC9689349 DOI: 10.3390/foods11223556] [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: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
Powdered infant formulas (PIF) are the most used dietary substitutes that are used in order to supplement breastfeeding. However, PIF are not sterile and can be contaminated with different microorganisms. The objective of this study was to genomically characterize Enterobacteriaceae (ENT) and Enterococcus strains that were isolated from PIF. Strains were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and whole-genome sequencing (WGS). Genomic typing, detection of virulence, and resistance profiles and genes were performed with the Ridom SeqSphere+ software; the comprehensive antibiotic resistance database (CARD) platform; ResFinder and PlasmidFinder tools; and by the disk diffusion method. Nineteen isolates from PIF were analyzed, including ENT such as Kosakonia cowanii, Enterobacter hormaechei, Franconibacter helveticus, Mixta calida, and lactic acid bacteria such as Enterococcus faecium. The strains exhibited resistance to beta-lactams, cephalosporins, and macrolides. Resistance genes such as AcrAB-TolC, marA, msbA, knpEF, oqxAB, fosA, blaACT-7, blaACT-14,qacJ, oqxAB,aac(6')-Ii, and msr(C); and virulence genes such as astA, cheB, cheR, ompA ompX, terC, ironA, acm, and efaAfm, adem were also detected. All the analyzed strains possessed genes that produced heat-shock proteins, such as IbpA and ClpL. In PIF, the presence of ENT and Enterococcus that are multiresistant to antibiotics-together with resistance and virulence genes-pose a health risk for infants consuming these food products.
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32
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Wand ME, Sutton JM. Efflux-mediated tolerance to cationic biocides, a cause for concern? MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748532 DOI: 10.1099/mic.0.001263] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractWith an increase in the number of isolates resistant to multiple antibiotics, infection control has become increasingly important to help combat the spread of multi-drug-resistant pathogens. An important component of this is through the use of disinfectants and antiseptics (biocides). Antibiotic resistance has been well studied in bacteria, but little is known about potential biocide resistance genes and there have been few reported outbreaks in hospitals resulting from a breakdown in biocide effectiveness. Development of increased tolerance to biocides has been thought to be more difficult due to the mode of action of biocides which affect multiple cellular targets compared with antibiotics. Very few genes which contribute towards increased biocide tolerance have been identified. However, the majority of those that have are components or regulators of different efflux pumps or genes which modulate membrane function/modification. This review will examine the role of efflux in increased tolerance towards biocides, focusing on cationic biocides and heavy metals against Gram-negative bacteria. As many efflux pumps which are upregulated by biocide presence also contribute towards an antimicrobial resistance phenotype, the role of these efflux pumps in cross-resistance to both other biocides and antibiotics will be explored.
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Affiliation(s)
- Matthew E Wand
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - J Mark Sutton
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
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33
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Characterization and comparative transcriptome analyses of Salmonella enterica Enteritidis strains possessing different chlorine tolerance profiles. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Sebastiampillai S, Lacasse MJ, McCusker S, Campbell T, Nitz M, Zamble DB. Using a high-throughput, whole-cell hydrogenase assay to identify potential small molecule inhibitors of [NiFe]-hydrogenase. Metallomics 2022; 14:6747159. [DOI: 10.1093/mtomcs/mfac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
Abstract
Abstract
[NiFe]-hydrogenases are used by several human pathogens to catalyze the reversible conversion between molecular hydrogen and protons and electrons. Hydrogenases provide an increased metabolic flexibility for pathogens, such as Escherichia coli and Helicobacter pylori, by allowing the use of molecular hydrogen as an energy source to promote survival in anaerobic environments. With the rise of antimicrobial resistance and the desire for novel therapeutics, the [NiFe]-hydrogenases are alluring targets. Inhibiting the nickel insertion pathway of [NiFe]-hydrogenases is attractive as this pathway is required for the generation of functional enzymes and is orthogonal to human biochemistry. In this work, nickel availability for the production and function of E. coli [NiFe]-hydrogenase was explored through immunoblot and activity assays. Whole-cell hydrogenase activities were assayed in high throughput against a small molecule library of known bioactives. Iodoquinol was identified as a potential inhibitor of the nickel biosynthetic pathway of [NiFe]-hydrogenase through a two-step screening process, but further studies with immunoblot assays showed confounding effects dependent on the cell growth phase. This study highlights the significance of considering the growth phenotype for whole-cell based assays overall and its effects on various cellular processes influenced by metal trafficking and homeostasis.
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Affiliation(s)
| | - Michael J Lacasse
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6 , Canada
| | - Susan McCusker
- Centre for Microbial Chemical Biology , MDCL-2330, Hamilton, Ontario L8S 4K1 , Canada
| | - Tracey Campbell
- Centre for Microbial Chemical Biology , MDCL-2330, Hamilton, Ontario L8S 4K1 , Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6 , Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6 , Canada
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8 , Canada
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A genetic platform to investigate the functions of bacterial drug efflux pumps. Nat Chem Biol 2022; 18:1399-1409. [PMID: 36065018 DOI: 10.1038/s41589-022-01119-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
Efflux pumps are a serious challenge for the development of antibacterial agents. Overcoming efflux requires an in-depth understanding of efflux pump functions, specificities and the development of inhibitors. However, the complexities of efflux networks have limited such studies. To address these challenges, we generated Efflux KnockOut-35 (EKO-35), a highly susceptible Escherichia coli strain lacking 35 efflux pumps. We demonstrate the use of this strain by constructing an efflux platform comprising EKO-35 strains individually producing efflux pumps forming tripartite complexes with TolC. This platform was profiled against a curated diverse compound collection, which enabled us to define physicochemical properties that contribute to transport. We also show the E. coli drug efflux network is conditionally essential for growth, and that the platform can be used to investigate efflux pump inhibitor specificities and efflux pump interplay. We believe EKO-35 and the efflux platform will have widespread application for the study of drug efflux.
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Trampari E, Zhang C, Gotts K, Savva GM, Bavro VN, Webber M. Cefotaxime Exposure Selects Mutations within the CA-Domain of envZ Which Promote Antibiotic Resistance but Repress Biofilm Formation in Salmonella. Microbiol Spectr 2022; 10:e0214521. [PMID: 35475640 PMCID: PMC9241649 DOI: 10.1128/spectrum.02145-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Cephalosporins are important beta lactam antibiotics, but resistance can be mediated by various mechanisms including production of beta lactamase enzymes, changes in membrane permeability or active efflux. We used an evolution model to study how Salmonella adapts to subinhibitory concentrations of cefotaxime in planktonic and biofilm conditions and characterized the mechanisms underpinning this adaptation. We found that Salmonella rapidly adapts to subinhibitory concentrations of cefotaxime via selection of multiple mutations within the CA-domain region of EnvZ. We showed that changes in this domain affect the ATPase activity of the enzyme and in turn impact OmpC, OmpF porin expression and hence membrane permeability leading to increased tolerance to cefotaxime and low-level resistance to different classes of antibiotics. Adaptation to cefotaxime through EnvZ also resulted in a significant cost to biofilm formation due to downregulation of curli. We assessed the role of the mutations identified on the activity of EnvZ by genetic characterization, biochemistry and in silico analysis and confirmed that they are responsible for the observed phenotypes. We observed that sublethal cefotaxime exposure selected for heterogeneity in populations with only a subpopulation carrying mutations within EnvZ and being resistant to cefotaxime. Population structure and composition dynamically changed depending on the presence of the selection pressure, once selected, resistant subpopulations were maintained even in extended passage without drug. IMPORTANCE Understanding mechanisms of antibiotic resistance is crucial to guide how best to use antibiotics to minimize emergence of resistance. We used a laboratory evolution system to study how Salmonella responds to cefotaxime in both planktonic and biofilm conditions. In both contexts, we observed rapid selection of mutants within a single hot spot within envZ. The mutations selected altered EnvZ which in turn triggers changes in porin production at the outer membrane. Emergence of mutations within this region was repeatedly observed in parallel lineages in different conditions. We used a combination of genetics, biochemistry, phenotyping and structural analysis to understand the mechanisms. This data show that the changes we observe provide resistance to cefotaxime but come at a cost to biofilm formation and the fitness of mutants changes greatly depending on the presence or absence of a selective drug. Studying how resistance emerges can inform selective outcomes in the real world.
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Affiliation(s)
| | - Chuanzhen Zhang
- Quadram Institute Bioscience, Norwich, United Kingdom
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Drug Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Kathryn Gotts
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Vassiliy N. Bavro
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Mark Webber
- Quadram Institute Bioscience, Norwich, United Kingdom
- Medical School, University of East Anglia, Norfolk, United Kingdom
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Wan X, Li Q, Olsen RH, Meng H, Zhang Z, Wang J, Zheng H, Li L, Shi L. Engineering a CRISPR interference system targeting AcrAB-TolC efflux pump to prevent multidrug resistance development in Escherichia coli. J Antimicrob Chemother 2022; 77:2158-2166. [PMID: 35642356 DOI: 10.1093/jac/dkac166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES We engineered a CRISPR interference (CRISPRi) system targeting the AcrAB-TolC efflux pump to prevent MDR development in Escherichia coli. METHODS Nine specific single-guide RNAs (sgRNAs) were designed to target the components of the AcrAB-TolC efflux pump, namely AcrA, AcrB and TolC. A total of thirteen CRISPRi recombinant plasmids were constructed with single or clustered sgRNAs. The transcriptional levels of the target genes, MICs of multiple antibiotics and biofilm formation in each CRISPRi strain were tested. RESULTS The CRISPRi system expressing sgRNA clusters targeting acrB and tolC simultaneously exhibited the highest inhibitory effect on AcrAB-TolC efflux pump activity in E. coli HB101, with 78.3%, 90.0% and 65.4% inhibition rates on the transcriptional levels of acrA, acrB and tolC, respectively. The CRISPRi system resulted in ∼2-, ∼8- and 16-fold increased susceptibility to rifampicin, erythromycin and tetracycline, respectively. In addition, the constructed CRISPRi system reduced biofilm formation with inhibition rates in the range of 11.2% to 58.2%. CONCLUSIONS To the best of our knowledge, this is the first report on the construction of an inducible CRISPRi system targeting the AcrAB-TolC efflux pump to prevent MDR development in E. coli. This study provides insights for future regulation and manipulation of AcrAB-TolC activity and bacterial MDR by a CRISPRi system.
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Affiliation(s)
- Xiulin Wan
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingyang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Zhigang Zhang
- State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
| | - Junlin Wang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Hanyu Zheng
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China.,State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
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Virulence and DNA sequence analysis of Cronobacter spp. isolated from infant cereals. Int J Food Microbiol 2022; 376:109745. [DOI: 10.1016/j.ijfoodmicro.2022.109745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/20/2022]
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Wand ME, Darby EM, Blair JMA, Sutton JM. Contribution of the efflux pump AcrAB-TolC to the tolerance of chlorhexidine and other biocides in Klebsiella spp. J Med Microbiol 2022; 71. [PMID: 35324422 PMCID: PMC9176267 DOI: 10.1099/jmm.0.001496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Introduction. We are becoming increasingly reliant on the effectiveness of biocides to combat the spread of Gram-negative multi-drug-resistant (MDR) pathogens, including Klebsiella pneumoniae. It has been shown that chlorhexidine exposure can lead to mutations in the efflux pump repressor regulators SmvR and RamR, but the contribution of each individual efflux pump to biocide tolerance is unknown. Hypothesis. Multiple efflux pumps, including SmvA and AcrAB-TolC, are involved in increased tolerance to biocides. However, strains with upregulated AcrAB-TolC caused by biocide exposure are more problematic due to their increased MDR phenotype. Aim. To investigate the role of AcrAB-TolC in the tolerance to several biocides, including chlorhexidine, and the potential threat of cross-resistance to antibiotics through increased expression of this efflux pump. Methodology. Antimicrobial susceptibility testing was performed on K. pneumoniae isolates with ramR mutations selected for after exposure to chlorhexidine, as well as transposon mutants in components and regulators of AcrAB-TolC. RTPCR was used to detect the expression levels of this pump after biocide exposure. Strains from the globally important ST258 clade were compared for genetic differences in acrAB-TolC and its regulators and for phenotypic differences in antimicrobial susceptibility. Results. Cross-resistance to antimicrobials was observed following mutations in ramR. Exposure to chlorhexidine led to increased expression of acrA and its activator ramA, and transposon mutants in AcrAB-TolC have increased susceptibility to several biocides, including chlorhexidine. Variations in ramR within the ST258 clade led to an increase in tolerance to certain biocides, although this was strain dependent. One strain, MKP103, that had increased levels of biocide tolerance showed a unique mutation in ramR that was reflected in enhanced expression of acrA and ramA. MKP103 transposon variants were able to further enhance their tolerance to specific biocides with mutations affecting SmvA. Conclusions. Biocide tolerance in K. pneumoniae is dependent upon several components, with increased efflux through AcrAB-TolC being an important one.
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Affiliation(s)
- Matthew E Wand
- UK Health Security Agency, Research and Development, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Elizabeth M Darby
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jessica M A Blair
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - J Mark Sutton
- UK Health Security Agency, Research and Development, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
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Transcriptional Regulation and Functional Characterization of the Plasmid-Borne oqxAB Genes in Salmonella Typhimurium. Microbiol Spectr 2022; 10:e0217021. [PMID: 35315694 PMCID: PMC9045139 DOI: 10.1128/spectrum.02170-21] [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] [Indexed: 11/20/2022] Open
Abstract
Coexistence of oqxAB and aac(6')-Ib-cr is often associated with the expression of fluoroquinolone resistance in Salmonella. The actual role of the plasmid-borne oqxAB gene and its regulatory mechanism compared to its chromosomally encoded counterpart in Klebsiella pneumoniae remain unclear We found that cloning of oqxAB gene only or chromosomally encoded oqxABR (ABRc) locus did not lead to an increase of ciprofloxacin (CIP) minimum inhibitory concentration (MIC) in S. Typhimurium, while cloning of the plasmid-encoded oqxABR (ABRp) locus led to a 4-fold increase in CIP MIC, reaching 0.0065 μg/mL. The co-carriage of these constructs with aac(6')-Ib-cr further increased the CIP MIC to 0.25 μg/mL in S. Typhimurium carrying aac(6')-Ib-cr and ABRp. Analysis of the transcription start site sequences showed that the expression level of suppressor protein gene, oqxR, in strains carrying ABRp was lower than that of its chromosomal counterpart due to the truncated promoter region in ABRp. The lower expression of OqxR in ABRp led to the overexpression of OqxAB, which elevated CIP MIC and exhibited a synergistic antimicrobial effect with the aac(6')-Ib-cr gene product to confer intermediate CIP (MIC = 0.25 μg/mL) in S. Typhimurium. Global transcriptional regulators in S. Typhimurium did not seem to play a role in regulating the plasmid-borne oqxAB genes. In conclusion, findings in this work showed that neither aac(6')-Ib-cr nor oqxABRp, but the combination of both genes, could mediate intermediated resistance to fluoroquinolone in Salmonella. The truncated promoter region in the oqxR gene of the plasmid-encoded locus led to the constituted expression of oqxAB genes. IMPORTANCE The transferable mechanisms of quinolone resistance (TMQR) gene, oqxAB, has been widely detected in Salmonella and is commonly associated with aac(6')-Ib-cr. It is thought to be associated with fluoroquinolone resistance, while its ancestor gene from K. pneumoniae is not. This study evaluated the actual role of the plasmid-borne oqxAB genes in Salmonella and showed that it was not able to mediate intermediated resistance to fluoroquinolone and only did so when it coexisted with aac(6')-Ib-cr. Chromosomally encoded oqxABRc from K. pneumoniae was not able to mediate enhanced CIP MIC due to tight regulation by the suppressor oqxR. However, plasmid-encoded oqxABRp enabled oqxAB to be expressed constitutionally due to the truncated promoter region of oqxR, leading to lower expression of the suppressor oqxR. This study clarified the roles of oqxAB and aac(6')-Ib-cr in mediating fluoroquinolone resistance in Salmonella and provides insights into the regulation of plasmid-encoded TMQR determinant, oqxAB.
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Asakura H, Yamamoto S, Sasaki Y, Okada Y, Katabami S, Fujimori A, Munakata K, Shiraki Y, Nishibu H, Hisamoto C, Kawase J, Ojima Y, Kiyoshima A, Shiroma K. Bacterial Distribution and Community Structure in Beef Cattle Liver and Bile at Slaughter. J Food Prot 2022; 85:424-434. [PMID: 34818425 DOI: 10.4315/jfp-21-288] [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: 07/25/2021] [Accepted: 11/24/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT In this study, the distribution of hygienic indicator bacteria in cattle livers and bile was examined at slaughterhouses. One hundred twenty-seven cattle livers with gallbladders were carefully eviscerated from carcasses at 10 slaughterhouses. Microbiological examination revealed that nine bile samples (7.1% prevalence) and 19 liver parenchyma samples (15.0% prevalence) were positive for Enterobacteriaceae (EB) with means ± standard deviations of 3.68 ± 4.63 log CFU/mL and 1.59 ± 2.47 log CFU/g, respectively; thus, bacterial contamination was apparent even at the postevisceration stage. Subsequently, 70 cattle livers were obtained at the postprocessing and storage stage from 7 of the 10 slaughterhouses. Microbiological analysis revealed significantly higher levels of EB in the liver parenchyma (3.00 ± 3.89 log CFU/g, P = 0.011) than those at the postevisceration stage, suggesting that bacterial dissemination and/or replication occurred in the liver parenchyma during processing and storage. According to 16S rRNA ion semiconductor sequencing analysis of representative samples from 12 cattle, Proteobacteria, Firmicutes, and Actinobacteria were dominant in both the parenchyma and bile in which EB and Escherichia coli were predominant among livers with higher EB levels. These results suggest that bile plays a role as a vehicle for bacterial transmission to the liver parenchyma. This study is the first to evaluate bacterial distribution and community structure in the liver and biliary microecosystem of cattle at slaughter. Our data support the use of EB testing of bile to screen cattle livers contaminated with high levels of fecal indicator bacteria. HIGHLIGHTS
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Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Kanagawa, Japan
| | - Shiori Yamamoto
- Division of Biomedical Food Research, National Institute of Health Sciences, Kanagawa, Japan
| | - Yoshimasa Sasaki
- Division of Biomedical Food Research, National Institute of Health Sciences, Kanagawa, Japan
| | - Yumiko Okada
- Division of Biomedical Food Research, National Institute of Health Sciences, Kanagawa, Japan
| | - Sachiko Katabami
- Towada Meat Inspection Office of Aomori Prefecture, Aomori, Japan
| | - Akiko Fujimori
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Iwate, Japan
| | - Kanako Munakata
- Tou-sou Meat Inspection Office of Chiba Prefecture, Chiba, Japan
| | - Yutaka Shiraki
- Gifu Prefectural Research Institute for Health and Environmental Sciences, Gifu, Japan
| | | | - Chie Hisamoto
- Meat Inspection Center of Hyogo Prefecture, Hyogo, Japan
| | - Jun Kawase
- Shimane Prefectural Institute of Public Health and Environmental Science, Shimane, Japan
| | | | | | - Ken Shiroma
- Akune Meat Inspection Office of Kagoshima Prefecture, Kagoshima, Japan
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Marmion M, Macori G, Ferone M, Whyte P, Scannell A. Survive and thrive: Control mechanisms that facilitate bacterial adaptation to survive manufacturing-related stress. Int J Food Microbiol 2022; 368:109612. [DOI: 10.1016/j.ijfoodmicro.2022.109612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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Rinaldi MA, Ferraz CA, Scrutton NS. Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli. Nat Prod Rep 2022; 39:90-118. [PMID: 34231643 PMCID: PMC8791446 DOI: 10.1039/d1np00025j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.
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Affiliation(s)
- Mauro A Rinaldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Clara A Ferraz
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Seo S, Disney-McKeethen S, Prabhakar RG, Song X, Mehta HH, Shamoo Y. Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics. ACS Infect Dis 2022; 8:242-254. [PMID: 34962128 PMCID: PMC10022597 DOI: 10.1021/acsinfecdis.1c00564] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In vitro experimental evolution of pathogens to antibiotics is commonly used for the identification of clinical biomarkers associated with antibiotic resistance. Microdroplet emulsions allow exquisite control of spatial structure, species complexity, and selection microenvironments for such studies. We investigated the use of monodisperse microdroplets in experimental evolution. Using Escherichia coli adaptation to doxycycline, we examined how changes in environmental conditions such as droplet size, starting lambda value, selection strength, and incubation method affected evolutionary outcomes. We also examined the extent to which emulsions could reveal potentially new evolutionary trajectories and dynamics associated with antimicrobial resistance. Interestingly, we identified both expected and unexpected evolutionary trajectories including large-scale chromosomal rearrangements and amplification that were not observed in suspension culture methods. As microdroplet emulsions are well-suited for automation and provide exceptional control of conditions, they can provide a high-throughput approach for biomarker identification as well as preclinical evaluation of lead compounds.
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Affiliation(s)
- Seokju Seo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | | | | | - Xinhao Song
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Heer H Mehta
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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Liao W, Wang L, Zheng X, Zhang Y, Chen T, Zhou C, Xu Y, Chen L, Zhou T. Evolution of tet(A) Variant Mediating Tigecycline Resistance in KPC-2-Producing Klebsiella pneumoniae during Tigecycline Treatment. J Glob Antimicrob Resist 2022; 28:168-173. [PMID: 35038616 DOI: 10.1016/j.jgar.2022.01.007] [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: 08/20/2021] [Revised: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES This study investigated the underlying mechanisms of the evolution of tigecycline resistance in a patient infected with Klebsiella pneumoniae harboring blaKPC-2 during treatment. METHODS Totally 7 clonal K. pneumoniae strains were continuously isolated from a patient during the hospitalization period. Antibiotic resistance in the strains was detected by antimicrobial susceptibility testing. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to explore the homology of isolates. Whole Genome Shotgun (WGS) and Cloning were used to investigate the underlying mechanisms of the evolution of tigecycline resistance. RESULTS All the available isolates had a MIC of 4 μg/ml for tigecycline except strain FK6768, which had a MIC of 32 μg/ml. Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains (FK6614, FK6768 and FK6809) were consecutively isolated from the feces in different treatment periods. Antibiotic susceptibility testing indicated that tigecycline resistance increased in FK6768 and finally decreased in FK6809, which attracted our attention. Whole genome shotgun (WGS) and further bioinformatics analysis showed a homology for the three isolates of >99%. The carbapenemase gene blaKPC-2 and a tet(A) mutation were found in the tigecycline-resistant isolate FK6768. Subsequent cloning experiments confirmed the contribution of tet(A) variant to reducing tigecycline susceptibility. CONCLUSIONS This is a report on K. pneumoniae carrying both tet(A) mutation and blaKPC-2, which led to increased tigecycline resistance in K. pneumoniae during tigecycline treatment. This is the first report describing tigecycline resistance of K. pneumoniae first increasing and subsequently decreasing in vivo.
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Affiliation(s)
- Wenli Liao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Department of Laboratory, Yongzhou Central Hospital, Yongzhou, Hunan Province, China
| | - Lingbo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiangkuo Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Ying Zhang
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tao Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Ye Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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Ikehata Y, Doukyu N. Improving the organic solvent tolerance of Escherichia coli with vanillin, and the involvement of an AcrAB-TolC efflux pump in vanillin tolerance. J Biosci Bioeng 2022; 133:347-352. [DOI: 10.1016/j.jbiosc.2021.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 10/19/2022]
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Onishi R, Shigemura K, Osawa K, Yang YM, Maeda K, Fang SB, Sung SY, Onuma K, Uda A, Miyara T, Fujisawa M. The Antimicrobial Resistance Characteristics of Imipenem-Non-Susceptible, Imipenemase-6-Producing Escherichia coli. Antibiotics (Basel) 2021; 11:antibiotics11010032. [PMID: 35052909 PMCID: PMC8772982 DOI: 10.3390/antibiotics11010032] [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: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Imipenemase-6 (IMP-6) type carbapenemase-producing Enterobacteriaceae is regarded as dangerous due to its unique lack of antimicrobial susceptibility. It is resistant to meropenem (MEPM) but susceptible to imipenem (IPM). In addition to carbapenemase, outer membrane porins and efflux pumps also play roles in carbapenem resistance by reducing the antimicrobial concentration inside cells. Extended-spectrum β-lactamase (ESBL) is transmitted with IMP-6 by the plasmid and broadens the spectrum of antimicrobial resistance. We collected 42 strains of IMP-6-producing Escherichia coli and conducted a molecular analysis of carbapenemase, ESBL, porin, efflux, and epidemiological characteristics using plasmid replicon typing. Among the 42 isolates, 21 strains were susceptible to IPM (50.0%) and 1 (2.4%) to MEPM. Seventeen strains (40.5%) co-produced CTX-M-2 type ESBL. We found that the relative expression of ompC and ompF significantly correlated with the MIC of IPM (p = 0.01 and p = 0.03, respectively). Sixty-eight% of CTX-M-2-non-producing strains had IncI1, which was significantly different from CTX-M-2-producing strains (p < 0.001). In conclusion, 50.0% of our IMP-6-producing strains were non-susceptible to IPM, which is different from the typical pattern and can be attributed to decreased porin expression. Further studies investigating other types of carbapenemase are warranted.
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Affiliation(s)
- Reo Onishi
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan;
| | - Katsumi Shigemura
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan;
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
- Correspondence: ; Tel.: +81-78-382-6155
| | - Kayo Osawa
- Department of Medical Technology, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe 653-0838, Japan;
| | - Young-Min Yang
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
| | - Koki Maeda
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
| | - Shiuh-Bin Fang
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, Taipei Medical University, 291 Jhong Jheng Road, Jhong Ho District, New Taipei City 23561, Taiwan;
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Shian-Ying Sung
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Kenichiro Onuma
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (K.O.); (A.U.); (T.M.)
| | - Atsushi Uda
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (K.O.); (A.U.); (T.M.)
| | - Takayuki Miyara
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (K.O.); (A.U.); (T.M.)
| | - Masato Fujisawa
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.-M.Y.); (K.M.); (M.F.)
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Reducing the Periplasmic Glutathione Content Makes Escherichia coli Resistant to Trimethoprim and Other Antimicrobial Drugs. Microbiol Spectr 2021; 9:e0074321. [PMID: 34908461 PMCID: PMC8672908 DOI: 10.1128/spectrum.00743-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Although glutathione (GSH) has been shown to influence the antimicrobial effects of many kinds of antibiotics, little is known about its role in relation to trimethoprim (TMP), a widely used antifolate. In this study, several genes related to glutathione metabolism were deleted in different Escherichia coli strains (i.e., O157:H7 and ATCC 25922), and their effects on susceptibility to TMP were tested. The results showed that deleting gshA, gshB, grxA, and cydD caused TMP resistance, and deleting cydD also caused resistance to other drugs. Meanwhile, deleting gshA, grxA, and cydD resulted in a significant decrease of the periplasmic glutathione content. Supplementing exogenous GSH or further deleting glutathione importer genes (gsiB and ggt) restored TMP sensitivity to ΔcydD. Subsequently, the results of quantitative-reverse transcription PCR experiments showed that expression levels of acrA, acrB, and tolC were significantly upregulated in both ΔgrxA and ΔcydD. Correspondingly, deleting cydD led to a decreased accumulation of TMP within bacterial cells, and further deleting acrA, acrB, or tolC restored TMP sensitivity to ΔcydD. Inactivation of CpxR and SoxS, two transcriptional factors that modulate the transcription of acrAB-tolC, restored TMP sensitivity to ΔcydD. Furthermore, mutations of gshA, gshB, grxA, cydC, and cydD are highly prevalent in E. coli clinical strains. Collectively, these data suggest that reducing the periplasmic glutathione content of E. coli leads to increased expression of acrAB-tolC with the involvement of CpxR and SoxS, ultimately causing drug resistance. To the best of our knowledge, this is the first report showing a linkage between periplasmic GSH and drug resistance in bacteria. IMPORTANCE After being used extensively for decades, trimethoprim still remains one of the key accessible antimicrobials recommended by the World Health Organization. A better understanding of the mechanisms of resistance would be beneficial for the future utilization of this drug. It has been shown that the AcrAB-TolC efflux pump is associated with trimethoprim resistance in E. coli clinical strains. In this study, we show that E. coli can sense the periplasmic glutathione content with the involvement of the CpxAR two-component system. As a result, reducing the periplasmic glutathione content leads to increased expression of acrA, acrB, and tolC via CpxR and SoxS, causing resistance to antimicrobials, including trimethoprim. Meanwhile, mutations in the genes responsible for periplasmic glutathione content maintenance are highly prevalent in E. coli clinical isolates, indicating a potential correlation of the periplasmic glutathione content and clinical antimicrobial resistance, which merits further investigation.
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Research on the drug resistance mechanism of foodborne pathogens. Microb Pathog 2021; 162:105306. [PMID: 34822970 DOI: 10.1016/j.micpath.2021.105306] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/08/2021] [Accepted: 11/19/2021] [Indexed: 12/30/2022]
Abstract
Foodborne diseases caused by foodborne pathogens are one of the main problems threatening human health and safety. The emergence of multi-drug resistant strains due to the abuse of antibiotics has increased the difficulty of clinical treatment. Research on the drug resistance mechanism of foodborne pathogens has become an effective method to solve multi-drug resistant strains. In this paper, the four main drug resistance mechanisms, including reduced cell membrane permeability, efflux pump mechanism, target site mutation mechanism, and enzymatic hydrolysis, were used to systematically analyze the drug resistance of Salmonella, Listeria monocytogenes, and Escherichia coli. And the new methods were discussed that may be used to solve the drug resistance of foodborne pathogens such as CRISPR and bacteriophages. This review provided a certain theoretical basis for the treatment of foodborne diseases.
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50
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Flavonoids as Inhibitors of Bacterial Efflux Pumps. Molecules 2021; 26:molecules26226904. [PMID: 34833994 PMCID: PMC8625893 DOI: 10.3390/molecules26226904] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Flavonoids are widely occurring secondary plant constituents, and are abundant in vegetable and fruit diets as well as herbal medicines. Therapeutic treatment options for bacterial infections are limited due to the spread of antimicrobial resistances. Hence, in a number of studies during the last few years, different classes of plant secondary metabolites as resistance-modifying agents have been carried out. In this review, we present the role of flavonoids as inhibitors of bacterial efflux pumps. Active compounds could be identified in the subclasses of chalcones, flavan-3-ols, flavanones, flavones, flavonols, flavonolignans and isoflavones; by far the majority of compounds were aglycones, although some glycosides like kaempferol glycosides with p-coumaroyl acylation showed remarkable results. Staphylococcus aureus NorA pump was the focus of many studies, followed by mycobacteria, whereas Gram-negative bacteria are still under-investigated.
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