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Sreekumaran S, V K P, Premnath M, P R P, M N A, Mathew J, K J, E K R. Novel in-genome based analysis demonstrates the evolution of OmpK37, antimicrobial resistance gene from a potentially pathogenic pandrug resistant Klebsiella pneumoniae MS1 isolated from healthy broiler feces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172713. [PMID: 38657814 DOI: 10.1016/j.scitotenv.2024.172713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Antimicrobial resistance transmission from farm animals to humans is a critical health concern and hence a detailed molecular surveillance is essential for tracking the spread and consequent evolution of antimicrobial resistance. In this study, a pan-drug resistant Klebsiella pneumoniae MS1 strain was isolated from a healthy broiler farm and studied. From the results of the study, MS1 was found to be is resistant to 18 tested antibiotics and has a high-risk to be pathogenic to humans with a probability of 0.80. The whole genome sequencing data of MS1 was used to predict the presence of antimicrobial resistance genes and pathogenicity. The genome analysis has revealed MS1 to have 34 AMR genes. Out of these, the AMR gene OmpK37 codes for an important protein involved in cell permeability and hence in antibiotic resistance. Further analysis was carried out by using an in-genome analysis method to understand the evolution of OmpK37 and the underlying reason for the emergence of resistance. From the detailed analysis, the current study could demonstrate for the first time the evolution of OmpK37 from OmpC. Though structurally OmpK37 was very similar to other porins present in MS1, it was found to have higher mutability as a distinguishing feature which makes it an important protein in monitoring the evolving resistances in microorganisms.
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Affiliation(s)
- Sreejith Sreekumaran
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Priya V K
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Manjusha Premnath
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Prathiush P R
- State Institute of Animal Diseases, Thiruvananthapuram, Kerala 695563, India
| | - Anisha M N
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Jyothis Mathew
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Jayachandran K
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India
| | - Radhakrishnan E K
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686 560, India.
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2
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Gauthier J, Kukavica-Ibrulj I, Cockenpot L, Mohit V, Bernier J, Brisson C, Levesque RC. Complete genome sequence of multidrug-resistant Enterobacter roggenkampii 0-E. Microbiol Resour Announc 2024; 13:e0114923. [PMID: 38299819 DOI: 10.1128/mra.01149-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Here, we present the complete 4.77 Mb genome of Enterobacter roggenkampii 0-E assembled with Oxford Nanopore long reads. This genome harbors 19 antimicrobial resistance genes, including ramA and marA decreasing permeability to carbapenems. This genome adds novel knowledge on emerging multidrug resistance in the Enterobacter cloacae species complex.
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Affiliation(s)
- Jeff Gauthier
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Canada
| | - Laure Cockenpot
- Direction Générale de la coordination scientifique et du Centre d'expertise en analyse environnementale du Québec (DGCSCEAEQ); Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, Canada
| | - Vani Mohit
- Direction Générale de la coordination scientifique et du Centre d'expertise en analyse environnementale du Québec (DGCSCEAEQ); Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, Canada
| | - Jimmy Bernier
- Direction Générale de la coordination scientifique et du Centre d'expertise en analyse environnementale du Québec (DGCSCEAEQ); Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, Canada
| | - Chantal Brisson
- Direction Générale de la coordination scientifique et du Centre d'expertise en analyse environnementale du Québec (DGCSCEAEQ); Ministère de l'Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP), Québec, Canada
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Faculté de médecine, Université Laval, Québec, Canada
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3
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Verma T, Nandini SS, Singh V, Raghavan A, Annappa H, Bhaskarla C, Dubey AK, Nandi D. Divergent Roles of Escherichia Coli Encoded Lon Protease in Imparting Resistance to Uncouplers of Oxidative Phosphorylation: Roles of marA, rob, soxS and acrB. Curr Microbiol 2024; 81:98. [PMID: 38372817 DOI: 10.1007/s00284-024-03632-w] [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: 09/19/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024]
Abstract
Uncouplers of oxidative phosphorylation dissipate the proton gradient, causing lower ATP production. Bacteria encounter several non-classical uncouplers in the environment, leading to stress-induced adaptations. Here, we addressed the molecular mechanisms responsible for the effects of uncouplers in Escherichia coli. The expression and functions of genes involved in phenotypic antibiotic resistance were studied using three compounds: two strong uncouplers, i.e., Carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and 2,4-Dinitrophenol (DNP), and one moderate uncoupler, i.e., Sodium salicylate (NaSal). Quantitative expression studies demonstrated induction of transcripts encoding marA, soxS and acrB with NaSal and DNP, but not CCCP. Since MarA and SoxS are degraded by the Lon protease, we investigated the roles of Lon using a lon-deficient strain (Δlon). Compared to the wild-type strain, Δlon shows compromised growth upon exposure to NaSal or 2, 4-DNP. This sensitivity is dependent on marA but not rob and soxS. On the other hand, the Δlon strain shows enhanced growth in the presence of CCCP, which is dependent on acrB. Interestingly, NaSal and 2,4-DNP, but not CCCP, induce resistance to antibiotics, such as ciprofloxacin and tetracycline. This study addresses the effects of uncouplers and the roles of genes involved during bacterial growth and phenotypic antibiotic resistance. Strong uncouplers are often used to treat wastewater, and these results shed light on the possible mechanisms by which bacteria respond to uncouplers. Also, the rampant usage of some uncouplers to treat wastewater may lead to the development of antibiotic resistance.
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Affiliation(s)
- Taru Verma
- Department of Bioengineering, Indian Institute of Science, Bengaluru, 560012, India
| | - Santhi Sanil Nandini
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Varsha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Abinaya Raghavan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Harshita Annappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Chetana Bhaskarla
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India
| | - Ashim Kumar Dubey
- Undergraduate program, Indian Institute of Science, Bengaluru, 560012, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bengaluru, 560012, India.
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Ghosh D, Pal A, Mohapatra S, Raj S, Vivekanandan P. Distinct epigenetic signatures of classical and hypervirulent Klebsiella pneumoniae. mSphere 2024; 9:e0046423. [PMID: 38112443 PMCID: PMC10826340 DOI: 10.1128/msphere.00464-23] [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: 08/15/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
Emergence and spread of the hypervirulent pathotype of Klebsiella pneumoniae have significantly increased infection rates in community as well as healthcare settings. There is an increasing interest to identify discriminating features between classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) to facilitate our understanding of the rapid emergence and dissemination of the hypervirulent pathotype. Here, we sought to identify unique epigenetic signatures of hvKp pathotype that differ from its classical counterpart using single-base resolution methylome analysis of native DNA sequencing on the Oxford Nanopore Technologies platform. The overall global adenine methylation in GATC motifs (i.e., Dam methylation motif) and cytosine methylation in CCWGG motifs (i.e., Dcm methylation motif) were significantly higher in hvKp isolates compared to that in cKp isolates, irrespective of their position in chromosomes or putative extra-chromosomal genetic elements. Notably, we observed significant enrichment of hypermethylated GATC and CCWGG motifs in the virulome of hvKp compared to hvKp genes not directly associated with virulence. We also observed increased methylation of GATC and CCWGG motifs in the capsule synthesis locus of hvKp isolates compared to cKp isolates. Furthermore, we identified several differentially methylated genes (DMGs) between the two pathotypes; interestingly, these DMGs include metal ion transporters, multidrug efflux pumps, transcriptional regulators of stress response, and genes associated with biofilm formation. Our results highlight hypermethylation of GATC and CCWGG motifs as unique epigenetic signatures of hvKp isolates.IMPORTANCEHypervirulent Klebsiella pneumoniae (hvKp) is a more virulent and rapidly evolving hypermucoviscous pathotype of classical K. pneumoniae (cKp). The hypervirulent pathotype is a major public health concern and is associated with high infection rates in community as well as hospital settings. With the recent emergence of multidrug-resistant hvKp, it has become imperative to investigate non-classical mechanisms such as epigenetics in addition to canonical biochemical and genetic mechanisms that delineate and differentiate the hypervirulent pathotype from its classical counterpart. Here, we identify genome-wide differences in adenine and cytosine methylation marks at well-characterized motifs between the two pathotypes. Overall, significantly higher levels of methylation were observed across chromosomal DNA and extrachromosomal elements in hvKp compared to cKp. Among hvKp isolates, the genes associated with virulence are particularly enriched for methylation marks. Our findings shed light on how epigenetic signatures may help distinguish the pathogenic potential of bacteria.
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Affiliation(s)
- Dipannita Ghosh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Arijit Pal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Sarita Mohapatra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Stephen Raj
- Department of Microbiology, PGIMER, Chandigarh, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 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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Zhang SP, Ye YP, Hou J, Ye ZR, Wang ZS, Yu XQ, Guo DD, Wang Y, He YX. Antitoxin MqsA decreases antibiotic susceptibility through the global regulator AgtR in Pseudomonas fluorescens. Antimicrob Agents Chemother 2023; 67:e0081223. [PMID: 37877694 PMCID: PMC10649091 DOI: 10.1128/aac.00812-23] [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: 06/20/2023] [Accepted: 08/31/2023] [Indexed: 10/26/2023] Open
Abstract
Type II toxin-antitoxin systems are highly prevalent in bacterial genomes and play crucial roles in the general stress response. Previously, we demonstrated that the type II antitoxin PfMqsA regulates biofilm formation through the global regulator AgtR in Pseudomonas fluorescens. Here, we found that both the C-terminal DNA-binding domain of PfMqsA and AgtR are involved in bacterial antibiotic susceptibility. Electrophoretic mobility shift assay (EMSA) analyses revealed that AgtR, rather than PfMqsA, binds to the intergenic region of emhABC-emhR, in which emhABC encodes an resistance-nodulation-cell division efflux pump and emhR encodes a repressor. Through quantitative real-time reverse-transcription PCR and EMSA analysis, we showed that AgtR directly activates the expression of the emhR by binding to the DNA motif [5´-CTAAGAAATATACTTAC-3´], leading to repression of the emhABC. Furthermore, we demonstrated that PfMqsA modulates the expression of EmhABC and EmhR. These findings enhance our understanding of the mechanism by which antitoxin PfMqsA contributes to antibiotic susceptibility.
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Affiliation(s)
- Si-Ping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yi-Ping Ye
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Jun Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Zi-Rui Ye
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Zhi-Song Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Xiao-Quan Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ding-Ding Guo
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Yong Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
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Ding Y, Hao J, Xiao W, Ye C, Xiao X, Jian C, Tang M, Li G, Liu J, Zeng Z. Role of efflux pumps, their inhibitors, and regulators in colistin resistance. Front Microbiol 2023; 14:1207441. [PMID: 37601369 PMCID: PMC10436536 DOI: 10.3389/fmicb.2023.1207441] [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: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
Colistin is highly promising against multidrug-resistant and extensively drug-resistant bacteria clinically. Bacteria are resistant to colistin mainly through mcr and chromosome-mediated lipopolysaccharide (LPS) synthesis-related locus variation. However, the current understanding cannot fully explain the resistance mechanism in mcr-negative colistin-resistant strains. Significantly, the contribution of efflux pumps to colistin resistance remains to be clarified. This review aims to discuss the contribution of efflux pumps and their related transcriptional regulators to colistin resistance in various bacteria and the reversal effect of efflux pump inhibitors on colistin resistance. Previous studies suggested a complex regulatory relationship between the efflux pumps and their transcriptional regulators and LPS synthesis, transport, and modification. Carbonyl cyanide 3-chlorophenylhydrazone (CCCP), 1-(1-naphthylmethyl)-piperazine (NMP), and Phe-Arg-β-naphthylamide (PAβN) all achieved the reversal of colistin resistance, highlighting the role of efflux pumps in colistin resistance and their potential for adjuvant development. The contribution of the efflux pumps to colistin resistance might also be related to specific genetic backgrounds. They can participate in colistin tolerance and heterogeneous resistance to affect the treatment efficacy of colistin. These findings help understand the development of resistance in mcr-negative colistin-resistant strains.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jinbo Liu
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, the Affiliated Hospital of Southwest Medical University, Luzhou, China
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8
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Nucci A, Rocha EPC, Rendueles O. Latent evolution of biofilm formation depends on life-history and genetic background. NPJ Biofilms Microbiomes 2023; 9:53. [PMID: 37537176 PMCID: PMC10400614 DOI: 10.1038/s41522-023-00422-3] [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: 04/07/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptation to one environment can often generate phenotypic and genotypic changes which impact the future ability of an organism to thrive in other environmental conditions. In the context of host-microbe interactions, biofilm formation can increase survival rates in vivo upon exposure to stresses, like the host's immune system or antibiotic therapy. However, how the generic process of adaptation impacts the ability to form biofilm and how it may change through time has seldomly been studied. To do so, we used a previous evolution experiment with three strains of the Klebsiella pneumoniae species complex, in which we specifically did not select for biofilm formation. We observed that changes in the ability to form biofilm happened very fast at first and afterwards reverted to ancestral levels in many populations. Biofilm changes were associated to changes in population yield and surface polysaccharide production. Genotypically, mutations in the tip adhesin of type III fimbriae (mrkD) or the fim switch of type I fimbriae were shaped by nutrient availability during evolution, and their impact on biofilm formation was dependent on capsule production. Analyses of natural isolates revealed similar mutations in mrkD, suggesting that such mutations also play an important role in adaptation outside the laboratory. Our work reveals that the latent evolution of biofilm formation, and its temporal dynamics, depend on nutrient availability, the genetic background and other intertwined phenotypic and genotypic changes. Ultimately, it suggests that small differences in the environment can alter an organism's fate in more complex niches like the host.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France.
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Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk. Int J Mol Sci 2023; 24:ijms24065135. [PMID: 36982209 PMCID: PMC10048834 DOI: 10.3390/ijms24065135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.
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Alnahhas RN, Dunlop MJ. Advances in linking single-cell bacterial stress response to population-level survival. Curr Opin Biotechnol 2023; 79:102885. [PMID: 36641904 PMCID: PMC9899315 DOI: 10.1016/j.copbio.2022.102885] [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: 11/04/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023]
Abstract
Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.
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Affiliation(s)
- Razan N Alnahhas
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Biological Design Center, Boston University, Boston, MA 02215, United States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States; Biological Design Center, Boston University, Boston, MA 02215, United States.
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11
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Holden ER, Yasir M, Turner AK, Wain J, Charles IG, Webber MA. Genome-wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36745554 DOI: 10.1099/mic.0.001296] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The incidence of multidrug-resistant bacteria is increasing globally, with efflux pumps being a fundamental platform limiting drug access and synergizing with other mechanisms of resistance. Increased expression of efflux pumps is a key feature of most cells that are resistant to multiple antibiotics. Whilst expression of efflux genes can confer benefits, production of complex efflux systems is energetically costly and the expression of efflux is highly regulated, with cells balancing benefits against costs. This study used TraDIS-Xpress, a genome-wide transposon mutagenesis technology, to identify genes in Escherichia coli and Salmonella Typhimurium involved in drug efflux and its regulation. We exposed mutant libraries to the canonical efflux substrate acriflavine in the presence and absence of the efflux inhibitor phenylalanine-arginine β-naphthylamide. Comparisons between conditions identified efflux-specific and drug-specific responses. Known efflux-associated genes were easily identified, including acrAB, tolC, marRA, ramRA and soxRS, confirming the specificity of the response. Further genes encoding cell envelope maintenance enzymes and products involved with stringent response activation, DNA housekeeping, respiration and glutathione biosynthesis were also identified as affecting efflux activity in both species. This demonstrates the deep relationship between efflux regulation and other cellular regulatory networks. We identified a conserved set of pathways crucial for efflux activity in these experimental conditions, which expands the list of genes known to impact on efflux efficacy. Responses in both species were similar and we propose that these common results represent a core set of genes likely to be relevant to efflux control across the Enterobacteriaceae.
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Affiliation(s)
- Emma R Holden
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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12
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Antidepressants can induce mutation and enhance persistence toward multiple antibiotics. Proc Natl Acad Sci U S A 2023; 120:e2208344120. [PMID: 36689653 PMCID: PMC9945972 DOI: 10.1073/pnas.2208344120] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Antibiotic resistance is an urgent threat to global health. Antidepressants are consumed in large quantities, with a similar pharmaceutical market share (4.8%) to antibiotics (5%). While antibiotics are acknowledged as the major driver of increasing antibiotic resistance, little attention is paid to the contribution of antidepressants in this process. Here, we demonstrate that antidepressants at clinically relevant concentrations induce resistance to multiple antibiotics, even following short periods of exposure. Antibiotic persistence was also enhanced. Phenotypic and genotypic analyses revealed the enhanced production of reactive oxygen species following exposure to antidepressants was directly associated with increased resistance. An enhanced stress signature response and stimulation of efflux pump expression were also associated with increased resistance and persistence. Mathematical modeling also predicted that antidepressants would accelerate the emergence of antibiotic-resistant bacteria, and persister cells would help to maintain the resistance. Overall, our findings highlight the antibiotic resistance risk caused by antidepressants.
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13
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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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14
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Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W. Structural basis of three different transcription activation strategies adopted by a single regulator SoxS. Nucleic Acids Res 2022; 50:11359-11373. [PMID: 36243985 PMCID: PMC9638938 DOI: 10.1093/nar/gkac898] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Transcription activation is established through extensive protein–protein and protein–DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription activator, diversely regulates subsets of stress response genes with different promoters, but the detailed SoxS-dependent transcription initiation mechanisms remain obscure. Here, we report cryo-EM structures of three SoxS-dependent transcription activation complexes (SoxS-TACI, SoxS-TACII and SoxS-TACIII) comprising of Escherichia coli RNA polymerase (RNAP), SoxS protein and three representative classes of SoxS-regulated promoters. The structures reveal that SoxS monomer orchestrates transcription initiation through specific interactions with the promoter DNA and different conserved domains of RNAP. In particular, SoxS is positioned in the opposite orientation in SoxS-TACIII to that in SoxS-TACI and SoxS-TACII, unveiling a novel mode of transcription activation. Strikingly, two universally conserved C-terminal domains of alpha subunit (αCTD) of RNAP associate with each other, bridging SoxS and region 4 of σ70. We show that SoxS interacts with RNAP directly and independently from DNA, remodeling the enzyme to activate transcription from cognate SoxS promoters while repressing transcription from UP-element containing promoters. Our data provide a comprehensive summary of SoxS-dependent promoter architectures and offer new insights into the αCTD contribution to transcription control in bacteria.
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Affiliation(s)
- Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lu Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, 510631 Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, 510631 Guangzhou, Guangdong, China.,Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China
| | - Libing Yu
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621900, China
| | - Fangfang Li
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuanling Jin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhenzhen Feng
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jiacong Li
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yujiao Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fei Gao
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Zhang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China.,Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210023, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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15
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Klanschnig M, Cserjan-Puschmann M, Striedner G, Grabherr R. CRISPRactivation-SMS, a message for PAM sequence independent gene up-regulation in Escherichia coli. Nucleic Acids Res 2022; 50:10772-10784. [PMID: 36134715 PMCID: PMC9561276 DOI: 10.1093/nar/gkac804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/10/2022] [Accepted: 09/08/2022] [Indexed: 12/26/2022] Open
Abstract
Governance of the endogenous gene regulatory network enables the navigation of cells towards beneficial traits for recombinant protein production. CRISPRactivation and interference provides the basis for gene expression modulation but is primarily applied in eukaryotes. Particularly the lack of wide-ranging prokaryotic CRISPRa studies might be attributed to intrinsic limitations of bacterial activators and Cas9 proteins. While bacterial activators need accurate spatial orientation and distancing towards the target promoter to be functional, Cas9-based CRISPR tools only bind sites adjacent to NGG PAM sequences. These circumstances hampered Cas9-guided activators from mediating the up-regulation of endogenous genes at precise positions in bacteria. We could overcome this limitation by combining the PAM independent Cas9 variant SpRY and a CRISPRa construct using phage protein MCP fused to transcriptional activator SoxS. This CRISPRa construct, referred to as SMS, was compared with previously reported CRISPRa constructs and showed up-regulation of a reporter gene library independent of its PAM sequence in Escherichia coli. We also demonstrated down-regulation and multi-gene expression control with SMS at non-NGG PAM sites. Furthermore, we successfully applied SMS to up-regulate endogenous genes, and transgenes at non-NGG PAM sites, which was impossible with the previous CRISPRa construct.
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Affiliation(s)
- Marco Klanschnig
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
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16
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Mathematical Modelling Highlights the Potential for Genetic Manipulation as an Adjuvant to Counter Efflux-Mediated MDR in Salmonella. Bull Math Biol 2022; 84:56. [PMID: 35380320 PMCID: PMC8983579 DOI: 10.1007/s11538-022-01011-9] [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: 07/06/2021] [Accepted: 03/02/2022] [Indexed: 11/18/2022]
Abstract
Bacteria have developed resistance to antibiotics by various mechanisms, notable amongst these is the use of permeation barriers and the expulsion of antibiotics via efflux pumps. The resistance-nodulation-division (RND) family of efflux pumps is found in Gram-negative bacteria and a major contributor to multidrug resistance (MDR). In particular, Salmonella encodes five RND efflux pump systems: AcrAB, AcrAD, AcrEF, MdsAB and MdtAB which have different substrate ranges including many antibiotics. We produce a spatial partial differential equation (PDE) model governing the diffusion and efflux of antibiotic in Salmonella, via these RND efflux pumps. Using parameter fitting techniques on experimental data, we are able to establish the behaviour of multiple wild-type and efflux mutant Salmonella strains, which enables us to produce efflux profiles for each individual efflux pump system. By combining the model with a gene regulatory network (GRN) model of efflux regulation, we simulate how the bacteria respond to their environment. Finally, performing a parameter sensitivity analysis, we look into various different targets to inhibit the efflux pumps. The model provides an in silico framework with which to test these potential adjuvants to counter MDR.
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17
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Di Pilato V, Henrici De Angelis L, Aiezza N, Baccani I, Niccolai C, Parisio EM, Giordano C, Camarlinghi G, Barnini S, Forni S, Righi L, Mechi MT, Giani T, Antonelli A, Rossolini GM. Resistome and virulome accretion in an NDM-1-producing ST147 sublineage of Klebsiella pneumoniae associated with an outbreak in Tuscany, Italy: a genotypic and phenotypic characterisation. THE LANCET MICROBE 2022; 3:e224-e234. [DOI: 10.1016/s2666-5247(21)00268-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 08/26/2021] [Accepted: 09/23/2021] [Indexed: 10/24/2022] Open
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18
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Holden ER, Yasir M, Turner AK, Wain J, Charles IG, Webber MA. Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli. Microb Genom 2021; 7. [PMID: 34783647 PMCID: PMC8743551 DOI: 10.1099/mgen.0.000673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biofilms complete a life cycle where cells aggregate, grow and produce a structured community before dispersing to colonize new environments. Progression through this life cycle requires temporally controlled gene expression to maximize fitness at each stage. Previous studies have largely focused on identifying genes essential for the formation of a mature biofilm; here, we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress, a massively parallel transposon mutagenesis approach using transposon-located promoters to assay the impact of disruption or altered expression of all genes in the genome on biofilm formation. We identified 48 genes that affected the fitness of cells growing in a biofilm, including genes with known roles and those not previously implicated in biofilm formation. Regulation of type 1 fimbriae and motility were important at all time points, adhesion and motility were important for the early biofilm, whereas matrix production and purine biosynthesis were only important as the biofilm matured. We found strong temporal contributions to biofilm fitness for some genes, including some where expression changed between being beneficial or detrimental depending on the stage at which they are expressed, including dksA and dsbA. Novel genes implicated in biofilm formation included zapE and truA involved in cell division, maoP in chromosome organization, and yigZ and ykgJ of unknown function. This work provides new insights into the requirements for successful biofilm formation through the biofilm life cycle and demonstrates the importance of understanding expression and fitness through time.
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Affiliation(s)
- Emma R Holden
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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19
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Casalone E, Vignolini T, Braconi L, Gardini L, Capitanio M, Pavone FS, Giovannelli L, Dei S, Teodori E. Characterization of substituted piperazines able to reverse MDR in Escherichia coli strains overexpressing resistance-nodulation-cell division (RND) efflux pumps. J Antimicrob Chemother 2021; 77:413-424. [PMID: 34747445 DOI: 10.1093/jac/dkab388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/28/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND MDR in bacteria is threatening to public health. Overexpression of efflux pumps is an important cause of MDR. The co-administration of antimicrobial drugs and efflux pump inhibitors (EPIs) is a promising approach to address the problem of MDR. OBJECTIVES To identify new putative EPIs and to characterize their mechanisms of action. METHODS The effects of four selected piperazine derivatives on resistance-nodulation-cell division (RND) pumps was evaluated in Escherichia coli strains overexpressing or not expressing RND pumps by assays aimed at evaluating antibiotic potentiation, membrane functionality, ethidium bromide accumulation and AcrB expression. The cytotoxicity of selected piperazines towards primary cultures of human dermal fibroblasts was also investigated. RESULTS Four molecules enhanced levofloxacin activity against strains overexpressing RND efflux pumps (AcrAB-TolC and AcrEF-TolC), but not against RND pump-deficient strains. They had little effects on membrane potential. Molecule 4 decreased, whereas the other three increased, membrane permeability compared with untreated control cells. The four molecules showed differences in the specificity of interaction with RND efflux pumps, by inactivating the transport of one or more antibiotics, and in the levels of ethidium bromide accumulation and of acrB expression inhibition. CONCLUSIONS Piperazine derivatives are good candidates as inhibitors of RND efflux pumps. They decreased the activity of RND pumps by mixed mechanisms of action. Small structural differences among the molecules can be critical in defining their behaviour.
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Affiliation(s)
- Enrico Casalone
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tiziano Vignolini
- LENS-European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Laura Braconi
- Department of Neurosciences, Psychology, Drug Research and Child's Health-Section of Pharmaceutical and Nutraceutical Sciences, Via U. Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Gardini
- LENS-European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy
| | - Marco Capitanio
- LENS-European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Francesco S Pavone
- LENS-European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Lisa Giovannelli
- Department of Neurosciences, Psychology, Drug Research and Child's Health-Section of Pharmacology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
| | - Silvia Dei
- Department of Neurosciences, Psychology, Drug Research and Child's Health-Section of Pharmaceutical and Nutraceutical Sciences, Via U. Schiff 6, 50019 Sesto Fiorentino, Italy
| | - Elisabetta Teodori
- Department of Neurosciences, Psychology, Drug Research and Child's Health-Section of Pharmaceutical and Nutraceutical Sciences, Via U. Schiff 6, 50019 Sesto Fiorentino, Italy
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20
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Clinical Status of Efflux Resistance Mechanisms in Gram-Negative Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10091117. [PMID: 34572699 PMCID: PMC8467137 DOI: 10.3390/antibiotics10091117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/05/2021] [Accepted: 09/15/2021] [Indexed: 01/25/2023] Open
Abstract
Antibiotic efflux is a mechanism that is well-documented in the phenotype of multidrug resistance in bacteria. Efflux is considered as an early facilitating mechanism in the bacterial adaptation face to the concentration of antibiotics at the infectious site, which is involved in the acquirement of complementary efficient mechanisms, such as enzymatic resistance or target mutation. Various efflux pumps have been described in the Gram-negative bacteria most often encountered in infectious diseases and, in healthcare-associated infections. Some are more often involved than others and expel virtually all families of antibiotics and antibacterials. Numerous studies report the contribution of these pumps in resistant strains previously identified from their phenotypes. The authors characterize the pumps involved, the facilitating antibiotics and those mainly concerned by the efflux. However, today no study describes a process for the real-time quantification of efflux in resistant clinical strains. It is currently necessary to have at hospital level a reliable and easy method to quantify the efflux in routine and contribute to a rational choice of antibiotics. This review provides a recent overview of the prevalence of the main efflux pumps observed in clinical practice and provides an idea of the prevalence of this mechanism in the multidrug resistant Gram-negative bacteria. The development of a routine diagnostic tool is now an emergency need for the proper application of current recommendations regarding a rational use of antibiotics.
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21
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Cross ER, Coulter SM, Pentlavalli S, Laverty G. Unravelling the antimicrobial activity of peptide hydrogel systems: current and future perspectives. SOFT MATTER 2021; 17:8001-8021. [PMID: 34525154 PMCID: PMC8442837 DOI: 10.1039/d1sm00839k] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/19/2021] [Indexed: 05/05/2023]
Abstract
The use of hydrogels has garnered significant interest as biomaterial and drug delivery platforms for anti-infective applications. For decades antimicrobial peptides have been heralded as a much needed new class of antimicrobial drugs. Self-assembling peptide hydrogels with inherent antimicrobial ability have recently come to the fore. However, their fundamental antimicrobial properties, selectivity and mechanism of action are relatively undefined. This review attempts to establish a link between antimicrobial efficacy; the self-assembly process; peptide-membrane interactions and mechanical properties by studying several reported peptide systems: β-hairpin/β-loop peptides; multidomain peptides; amphiphilic surfactant-like peptides and ultrashort/low molecular weight peptides. We also explore their role in the formation of amyloid plaques and the potential for an infection etiology in diseases such as Alzheimer's. We look briefly at innovative methods of gel characterization. These may provide useful tools for future studies within this increasingly important field.
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Affiliation(s)
- Emily R Cross
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
| | - Sophie M Coulter
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
| | - Sreekanth Pentlavalli
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
| | - Garry Laverty
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, N. Ireland, BT9 7BL, UK.
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