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Tuo Y, Tang Y, Yang R, Zhao X, Luo M, Zhou X, Wang Y. Virtual screening and biological activity evaluation of novel efflux pump inhibitors targeting AdeB. Int J Biol Macromol 2023; 250:126109. [PMID: 37544561 DOI: 10.1016/j.ijbiomac.2023.126109] [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: 05/15/2023] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
The AdeABC efflux pump is an important mechanism causing multidrug resistance in Acinetobacter baumannii, and its main component AdeB can recognize carbapenems, aminoglycosides, and other multi-class antibiotics and efflux them intracellularly, which is an ideal target for the development of anti-multidrug resistant bacteria drugs. Here, we combined multiple computer-aided drug design methods to target AdeB to identify promising novel structural inhibitors. Virtual screening was performed by molecular docking and molecular dynamics simulation (MD) and 12 potential compounds were identified from the databases. Meanwhile, their biological activities were validated by in vitro activity assays, and ChemDiv L676-2179 (γ-IFN), ChemDiv L676-1461, and Chembridge 53717615 were confirmed to suppress efflux effects and restore antibiotic susceptibility of resistant bacteria, which are expected to be developed as adjuvant drugs for the treatment of multi-drug resistant Acinetobacter baumannii clinical infections.
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Affiliation(s)
- Yan Tuo
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China; Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yuelu Tang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China; Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Ran Yang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - XueMin Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Minghe Luo
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xing Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China; Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China; Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing 400054, China.
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Chandal N, Tambat R, Kalia R, Kumar G, Mahey N, Jachak S, Nandanwar H. Efflux pump inhibitory potential of indole derivatives as an arsenal against norA over-expressing Staphylococcus aureus. Microbiol Spectr 2023; 11:e0487622. [PMID: 37754560 PMCID: PMC10581058 DOI: 10.1128/spectrum.04876-22] [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: 11/28/2022] [Accepted: 07/11/2023] [Indexed: 09/28/2023] Open
Abstract
NorA, an extensively studied efflux pump in Staphylococcus aureus, has been connected to fluoroquinolone, antiseptic, and disinfection resistance. Several studies have also emphasized how efflux pumps, including NorA, function as the first line of defense of S. aureus against antibiotics. In this study, we have screened some chemically synthesized indole derivatives for their activity as efflux pump inhibitors (EPIs). The derivative SMJ-5 was found to be a potent NorA efflux pump inhibitor among the screened indole derivatives, owing to increased ethidium bromide and norfloxacin accumulation in norA over-expressing S. aureus. The combination of SMJ-5 and ciprofloxacin demonstrated the eradication of S. aureus biofilm and prolonged the post-antibiotic effect more than ciprofloxacin alone. SMJ-5 was able to inhibit staphyloxanthin virulence. In in vitro time-kill trials and in vivo efficacy investigations, the combination enhanced the bactericidal activity of ciprofloxacin against S. aureus. Additionally, reverse transcription PCR results revealed that SMJ-5 also inhibits the NorA efflux pump indirectly at the transcriptional level. IMPORTANCE The NorA efflux pump is the most effective resistance mechanism in S. aureus. The clinical importance of NorA efflux pumps is demonstrated by the expression of pump genes in S. aureus strains in response to fluoroquinolones and biocides. Along with the repercussions of decreased fluoroquinolone sensitivity, increasing expression of efflux pump genes by their substrate necessitates the importance of efflux pump inhibitors. Reserpine and verapamil are clinically used to treat ailments and have proven NorA inhibitors, but, unfortunately, the concentration needed for these drugs to inhibit the pump is not safe in clinical settings. In the current study, we have screened some indole derivatives, and among them, SMJ-5 was reported to potentiate norfloxacin and ciprofloxacin at their sub-inhibitory concentration by inhibiting the norA gene transcriptionally. Here we highlight the promising points of this study, which could serve as a model to design a therapeutic EPI candidate against norA over-expressing S. aureus.
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Affiliation(s)
- Nishtha Chandal
- Clinical Microbiology and Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Rushikesh Tambat
- Clinical Microbiology and Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ritu Kalia
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Mohali, Punjab, India
| | - Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research- Hyderabad, Balanagar, Telangana, India
| | - Nisha Mahey
- Clinical Microbiology and Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sanjay Jachak
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Mohali, Punjab, India
| | - Hemraj Nandanwar
- Clinical Microbiology and Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Cai W, Lu M, Dai W. Novel antibiotic susceptibility of an RNA polymerase α-subunit mutant in Pseudomonas aeruginosa. J Antimicrob Chemother 2023; 78:2162-2169. [PMID: 37428003 DOI: 10.1093/jac/dkad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
BACKGROUND RNA polymerase (RNAP) is highly conserved and essential for prokaryotic housekeeping activities, making it an important target for the development of new antibiotics. The rpoB gene, encoding a β-subunit of bacterial RNAP, has a well-known association with rifampicin resistance. However, the roles of other RNAP component genes such as rpoA, encoding an α-subunit of RNAP, in antibiotic resistance remain unexplored. OBJECTIVES To characterize the antibiotic resistance-related role of RpoA. METHODS We measured the expression of the MexEF-OprN efflux pump in an RpoA mutant using a transcriptional reporter. The MICs of various antibiotics for this RpoA mutant were determined. RESULTS We uncover a novel role of antibiotic susceptibility for an RpoA mutant in Pseudomonas aeruginosa. We found that a single amino acid substitution in RpoA resulted in reduced activity of the MexEF-OprN efflux pump, which is responsible for the exportation of various antibiotics, including ciprofloxacin, chloramphenicol, ofloxacin and norfloxacin. This attenuated efflux pump activity, caused by the RpoA mutation, conferred the bacteria further susceptibility to antibiotics regulated by MexEF-OprN. Our work further revealed that certain clinical P. aeruginosa isolates also contained the same RpoA mutation, providing clinical relevance to our findings. Our results elucidate why this new antibiotic-susceptible function of RpoA mutants would have remained undetected in conventional screens for mutants involving antibiotic resistance. CONCLUSIONS The discovery of antibiotic susceptibility in an RpoA mutant implicates a new therapeutic approach for treating clinical isolates of P. aeruginosa with RpoA mutations, using specific antibiotics regulated by MexEF-OprN. More generally, our work suggests that RpoA could serve as a promising candidate target for anti-pathogen therapeutic purposes.
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Affiliation(s)
- Wenjie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Mingqi Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
- College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
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Qumar S, Majid M, Qaria MA, Mendem SK, Ahmed N. Functional molecular characterization and the assessment of the transmission route of multidrug-resistant Helicobacter pullorum isolates from free-range and broiler chickens. Microb Pathog 2023; 182:106253. [PMID: 37463609 DOI: 10.1016/j.micpath.2023.106253] [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: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Some of the life-threatening, food-borne, and zoonotic infections are transmitted through poultry birds. Inappropriate and irrational use of antimicrobials in the livestock industry has resulted in an increased incidence of multi-drug resistant bacteria of epidemic potentials. MATERIALS AND METHODS The adhesion and invasion properties of 11 free-range and broiler chicken derived Helicobacterpullorum isolates were evaluated. To examine the biofilm formation of H. pullorum isolates, crystal violet assay was performed. A quantitative assay of invasion-associated genes was carried out after infecting HepG2 cells with two different representative (broiler and free-range chicken) H. pullorum isolates, using RT-PCR assay. Furthermore, we investigated the prevalence of H. pullorum, Campylobacter jejuni and Salmonella spp. in chicken caeca and oviducts to determine the possibility of trans-ovarian transmission. RESULTS All H. pullorum isolates adhered to HepG2 cells significantly but a notable difference towards their invasion potential was observed between free-range and broiler chicken isolates wherein broiler isolates were found to be more invasive compared to free-range isolates. Furthermore, cdtB, flhA and flaB genes of H. pullorum were upregulated post infection of HepG2 cells, in broiler chicken isolates compared to free-range chicken isolates. Moreover, all isolates of H. pullorum were found to form biofilm on the liquid-air interface of the glass coverslips and sidewalls of the wells with similar propensities. Despite presence of H. pullorum and C. jejuni in high concentrations in the caecum, they were completely absent in oviduct samples, thus ruling out the possibility of vertical transmission of these bacterial species. In contrast, Salmonella spp. was found to be present in a significant proportion in the oviduct samples of egg-laying hens suggesting its vertical transmission. CONCLUSIONS Our findings suggest that H. pullorum, an emerging multi-drug resistant (MDR) pathogen could be transmitted from poultry sources to humans. In addition to this, its strong functional similarity with C. jejuni provides a firm basis for H. pullorum to be an emerging food-associated, MDR pathogenic bacterium that could pose risk to public health.
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Affiliation(s)
- Shamsul Qumar
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India; GeneStore India Pvt. Ltd, Sector 14, Gurugram, Haryana, 122001, India.
| | - Mohammad Majid
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India; Central Food Laboratory, Ministry of Public Health, Doha, Qatar
| | - Majjid A Qaria
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Suresh Kumar Mendem
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India.
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Verma H, Rawat M, Verma R, Gandham R, Tiwari AK, Khan RIN, Praharaj MR, Smith E. First report of whole genome sequence of septicemic Pasteurella multocida serovar B:2 'Soron' strain isolated from swine. Braz J Microbiol 2023; 54:2445-2460. [PMID: 37191868 PMCID: PMC10484883 DOI: 10.1007/s42770-023-00995-3] [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: 01/23/2022] [Accepted: 10/04/2022] [Indexed: 05/17/2023] Open
Abstract
Pig pasteurellosis, caused by Pasteurella multocida, is an acute infection that also has economic implications for pig farmers. We report the complete genome sequence of a P. multocida, serovar B:2 'Soron' strain isolated from the blood of a pig that had died of pasteurellosis in India. The isolate was not found to be haemorrhagic septicaemia (HS) specific B:2 by the PCR assay. The genome of 'Soron' strain is a single circular chromosome of 2,272,124 base pairs in length and contains 2014 predicted coding regions, 4 ribosomal RNA operons, and 52 tRNAs. It has 1812 protein-coding genes that were also found in reference sequence PmP52Vac. Phylogenetic analysis revealed that Pm_P52VAc and P. multocida 'Soron' serovar B:2 were clustered in different clades. Pasteurella multocida 'Soron' serovar B:2 was found to cluster with the same ancestor of Pm70, which is of avian origin. The genome was found to contain regions that encode proteins which may confer resistance to various antibiotics including cephalosporin, which is used to treat pasteurellosis. The isolate was also found to harbour a phage region. This strain represents a novel multi-locus sequence type (MLST) that has not been previously identified, as all of the alleles used for MLST were found, but did not match any of the alleles in the database with 100% nucleotide identity. The most closely related ST was ST221. This is the first whole-genome sequence from P. multocida serovar B:2 of pig origin.
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Affiliation(s)
- Harshit Verma
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Mayank Rawat
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Rishendra Verma
- ICAR-Indian Veterinary Research Institute, Izatnagar, India.
| | - Ravi Gandham
- ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | | | | | | | - Emily Smith
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, MN, USA
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Alshehri WA, Abulfaraj AA, Alqahtani MD, Alomran MM, Alotaibi NM, Alwutayd K, Aloufi AS, Alshehrei FM, Alabbosh KF, Alshareef SA, Ashy RA, Refai MY, Jalal RS. Abundant resistome determinants in rhizosphere soil of the wild plant Abutilon fruticosum. AMB Express 2023; 13:92. [PMID: 37646836 PMCID: PMC10469157 DOI: 10.1186/s13568-023-01597-w] [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: 05/30/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
A metagenomic whole genome shotgun sequencing approach was used for rhizospheric soil micribiome of the wild plant Abutilon fruticosum in order to detect antibiotic resistance genes (ARGs) along with their antibiotic resistance mechanisms and to detect potential risk of these ARGs to human health upon transfer to clinical isolates. The study emphasized the potential risk to human health of such human pathogenic or commensal bacteria, being transferred via food chain or horizontally transferred to human clinical isolates. The top highly abundant rhizospheric soil non-redundant ARGs that are prevalent in bacterial human pathogens or colonizers (commensal) included mtrA, soxR, vanRO, golS, rbpA, kdpE, rpoB2, arr-1, efrA and ileS genes. Human pathogenic/colonizer bacteria existing in this soil rhizosphere included members of genera Mycobacterium, Vibrio, Klebsiella, Stenotrophomonas, Pseudomonas, Nocardia, Salmonella, Escherichia, Citrobacter, Serratia, Shigella, Cronobacter and Bifidobacterium. These bacteria belong to phyla Actinobacteria and Proteobacteria. The most highly abundant resistance mechanisms included antibiotic efflux pump, antibiotic target alteration, antibiotic target protection and antibiotic inactivation. antimicrobial resistance (AMR) families of the resistance mechanism of antibiotic efflux pump included resistance-nodulation-cell division (RND) antibiotic efflux pump (for mtrA, soxR and golS genes), major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration included glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection included bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation included rifampin ADP-ribosyltransferase (for arr-1 gene). Better agricultural and food transport practices are required especially for edible plant parts or those used in folkloric medicine.
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Affiliation(s)
- Wafa A Alshehri
- Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, 21911, Rabigh, Saudi Arabia
| | - Mashael D Alqahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Maryam M Alomran
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Khairiah Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Abeer S Aloufi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia
| | - Fatimah M Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, 21955, Makkah, Saudi Arabia
| | - Khulood F Alabbosh
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Sahar A Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, 21921, Jeddah, Saudi Arabia
| | - Ruba A Ashy
- Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia
| | - Mohammed Y Refai
- Department of Biochemistry, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
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Zhang Z, Lizer N, Wu Z, Morgan CE, Yan Y, Zhang Q, Yu EW. Cryo-Electron Microscopy Structures of a Campylobacter Multidrug Efflux Pump Reveal a Novel Mechanism of Drug Recognition and Resistance. Microbiol Spectr 2023; 11:e0119723. [PMID: 37289051 PMCID: PMC10434076 DOI: 10.1128/spectrum.01197-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
Campylobacter jejuni is a bacterium that is commonly present in the intestinal tracts of animals. It is also a major foodborne pathogen that causes gastroenteritis in humans. The most predominant and clinically important multidrug efflux system in C. jejuni is the CmeABC (Campylobacter multidrug efflux) pump, a tripartite system that includes an inner membrane transporter (CmeB), a periplasmic fusion protein (CmeA), and an outer membrane channel protein (CmeC). This efflux protein machinery mediates resistance to a number of structurally diverse antimicrobial agents. A recently identified CmeB variant, termed resistance enhancing CmeB (RE-CmeB), can increase its multidrug efflux pump activity, likely by influencing antimicrobial recognition and extrusion. Here, we report structures of RE-CmeB in its apo form as well as in the presence of four different drugs by using single-particle cryo-electron microscopy (cryo-EM). Coupled with mutagenesis and functional studies, this structural information allows us to identify critical amino acids that are important for drug resistance. We also report that RE-CmeB utilizes a somewhat unique subset of residues to bind different drugs, thereby optimizing its ability to accommodate different compounds with distinct scaffolds. These findings provide insights into the structure-function relationship of this newly emerged antibiotic efflux transporter variant in Campylobacter. IMPORTANCE Campylobacter jejuni has emerged as one of the most problematic and highly antibiotic-resistant pathogens, worldwide. The Centers for Disease Control and Prevention have designated antibiotic-resistant C. jejuni as a serious antibiotic resistance threat in the United States. We recently identified a C. jejuni resistance enhancing CmeB (RE-CmeB) variant that can increase its multidrug efflux pump activity and confers an exceedingly high-level of resistance to fluoroquinolones. Here, we report the cryo-EM structures of this prevalent and clinically important C. jejuni RE-CmeB multidrug efflux pump in both the absence and presence of four antibiotics. These structures allow us to understand the action mechanism for multidrug recognition in this pump. Our studies will ultimately inform an era in structure-guided drug design to combat multidrug resistance in these Gram-negative pathogens.
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Affiliation(s)
- Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Nicholas Lizer
- Department of Veterinary Microbiology, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Zuowei Wu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Yuqi Yan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Majumder P, Ahmed S, Ahuja P, Athreya A, Ranjan R, Penmatsa A. Cryo-EM structure of antibacterial efflux transporter QacA from Staphylococcus aureus reveals a novel extracellular loop with allosteric role. EMBO J 2023; 42:e113418. [PMID: 37458117 PMCID: PMC10425836 DOI: 10.15252/embj.2023113418] [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: 01/01/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
Efflux of antibacterial compounds is a major mechanism for developing antimicrobial resistance. In the Gram-positive pathogen Staphylococcus aureus, QacA, a 14 transmembrane helix containing major facilitator superfamily antiporter, mediates proton-coupled efflux of mono and divalent cationic antibacterial compounds. In this study, we report the cryo-EM structure of QacA, with a single mutation D411N that improves homogeneity and retains efflux activity against divalent cationic compounds like dequalinium and chlorhexidine. The structure of substrate-free QacA, complexed to two single-domain camelid antibodies, was elucidated to a resolution of 3.6 Å. The structure displays an outward-open conformation with an extracellular helical hairpin loop (EL7) between transmembrane helices 13 and 14, which is conserved in a subset of DHA2 transporters. Removal of the EL7 hairpin loop or disrupting the interface formed between EL7 and EL1 compromises efflux activity. Chimeric constructs of QacA with a helical hairpin and EL1 grafted from other DHA2 members, LfrA and SmvA, restore activity in the EL7 deleted QacA revealing the allosteric and vital role of EL7 hairpin in antibacterial efflux in QacA and related members.
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Affiliation(s)
- Puja Majumder
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
- Present address:
Memorial‐Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Shahbaz Ahmed
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
- Present address:
St. Jude Children's Research HospitalMemphisTNUSA
| | - Pragya Ahuja
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | - Arunabh Athreya
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | - Rakesh Ranjan
- ICAR‐National Research Centre on CamelJorbeerBikanerIndia
| | - Aravind Penmatsa
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
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Avakh A, Grant GD, Cheesman MJ, Kalkundri T, Hall S. The Art of War with Pseudomonas aeruginosa: Targeting Mex Efflux Pumps Directly to Strategically Enhance Antipseudomonal Drug Efficacy. Antibiotics (Basel) 2023; 12:1304. [PMID: 37627724 PMCID: PMC10451789 DOI: 10.3390/antibiotics12081304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) poses a grave clinical challenge due to its multidrug resistance (MDR) phenotype, leading to severe and life-threatening infections. This bacterium exhibits both intrinsic resistance to various antipseudomonal agents and acquired resistance against nearly all available antibiotics, contributing to its MDR phenotype. Multiple mechanisms, including enzyme production, loss of outer membrane proteins, target mutations, and multidrug efflux systems, contribute to its antimicrobial resistance. The clinical importance of addressing MDR in P. aeruginosa is paramount, and one pivotal determinant is the resistance-nodulation-division (RND) family of drug/proton antiporters, notably the Mex efflux pumps. These pumps function as crucial defenders, reinforcing the emergence of extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains, which underscores the urgency of the situation. Overcoming this challenge necessitates the exploration and development of potent efflux pump inhibitors (EPIs) to restore the efficacy of existing antipseudomonal drugs. By effectively countering or bypassing efflux activities, EPIs hold tremendous potential for restoring the antibacterial activity against P. aeruginosa and other Gram-negative pathogens. This review focuses on concurrent MDR, highlighting the clinical significance of efflux pumps, particularly the Mex efflux pumps, in driving MDR. It explores promising EPIs and delves into the structural characteristics of the MexB subunit and its substrate binding sites.
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Affiliation(s)
| | | | | | | | - Susan Hall
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD 4222, Australia; (A.A.); (G.D.G.); (M.J.C.); (T.K.)
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Tabor W, Katsogiannou A, Karta D, Andrianopoulou E, Berlicki Ł, Vassiliou S, Grabowiecka A. Exploration of Thiourea-Based Scaffolds for the Construction of Bacterial Ureases Inhibitors. ACS OMEGA 2023; 8:28783-28796. [PMID: 37576686 PMCID: PMC10413841 DOI: 10.1021/acsomega.3c03702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023]
Abstract
A series of 32 thiourea-based urease inhibitors were synthesized and evaluated against native bacterial enzyme and whole cells of Sporosarcina pasteurii and Proteus mirabilis strains. The proposed inhibitors represented structurally diverse thiosemicarbazones and thiocarbohydrazones, benzyl-substituted thiazolyl thioureas, 1H-pyrazole-1-carbothioamides, and dihydropirimidine-2(1H)-thiones. Kinetic characteristics with purified S. pasteurii enzyme determined low micromolar inhibitors within each structural group. (E)-2-(1-Phenylethylidene)hydrazine-1-carbothioamide 19 (Ki = 0.39 ± 0.01 μM), (E)-2-(4-methylbenzylidene)hydrazine-1-carbothioamide 16 (Ki = 0.99 ± 0.04 μM), and N'-((1E,2E)-1,3-diphenylallylidene)hydrazinecarbothiohydrazide 29 (Ki = 2.23 ± 0.19 μM) were used in modeling studies that revealed sulfur ion coordination of the active site nickel ion and hydrogen bonds between the amide group and the side chain of Asp363 and Ala366 carbonyl moiety. Whole-cell studies proved the activity of compounds in Gram-positive and Gram-negative microorganisms. Ureolysis control observed in P. mirabilis PCM 543 (e.g., IC50 = 304 ± 14 μM for 1-benzyl-3-(4-(4-hydroxyphenyl)thiazol-2-yl)thiourea 52) is a valuable achievement, as urease is recognized as a major virulence factor of this urinary tract pathogen.
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Affiliation(s)
- Wojciech Tabor
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Aikaterini Katsogiannou
- Laboratory
of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Danai Karta
- Laboratory
of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Evgenia Andrianopoulou
- Laboratory
of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Łukasz Berlicki
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Stamatia Vassiliou
- Laboratory
of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Agnieszka Grabowiecka
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
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61
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Riseh RS, Vazvani MG, Hajabdollahi N, Thakur VK. Bioremediation of Heavy Metals by Rhizobacteria. Appl Biochem Biotechnol 2023; 195:4689-4711. [PMID: 36287331 PMCID: PMC10354140 DOI: 10.1007/s12010-022-04177-z] [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] [Accepted: 09/28/2022] [Indexed: 11/02/2022]
Abstract
Heavy elements accumulate rapidly in the soil due to industrial activities and the industrial revolution, which significantly impact the morphology, physiology, and yield of crops. Heavy metal contamination will eventually affect the plant tolerance threshold and cause changes in the plant genome and genetic structure. Changes in the plant genome lead to changes in encoded proteins and protein sequences. Consuming these mutated products can seriously affect human and animal health. Bioremediation is a process that can be applied to reduce the adverse effects of heavy metals in the soil. In this regard, bioremediation using plant growth-promoting rhizobacteria (PGPRs) as beneficial living agents can help to neutralize the negative interaction between the plant and the heavy metals. PGPRs suppress the adverse effects of heavy metals and the negative interaction of plant-heavy elements by different mechanisms such as biological adsorption and entrapment of heavy elements in extracellular capsules, reduction of metal ion concentration, and formation of complexes with metal ions inside the cell.
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Affiliation(s)
- Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-E-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan, 7718897111 Iran
| | - Mozhgan Gholizadeh Vazvani
- Department of Plant Protection, Faculty of Agriculture, Vali-E-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan, 7718897111 Iran
| | - Najmeh Hajabdollahi
- Department of Plant Protection, Faculty of Agriculture, Vali-E-Asr University of Rafsanjan, Imam Khomeini Square, Rafsanjan, 7718897111 Iran
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Center, Scotland’s Rural College (SRUC), Edinburgh, EH9 3JG UK
- School of Engineering, University of Petroleum & Energy Studies (UPES), Dehradun, 248007 India
- Centre for Research and Development, Chandigarh University, Mohali, 140413 Punjab India
- Department of Biotechnology, Graphic Era Deemed to Be University, Dehradun, 248002 Uttarakhand India
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62
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Kelbrick M, Hesse E, O' Brien S. Cultivating antimicrobial resistance: how intensive agriculture ploughs the way for antibiotic resistance. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001384. [PMID: 37606636 PMCID: PMC10482381 DOI: 10.1099/mic.0.001384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
Antimicrobial resistance (AMR) is a growing threat to public health, global food security and animal welfare. Despite efforts in antibiotic stewardship, AMR continues to rise worldwide. Anthropogenic activities, particularly intensive agriculture, play an integral role in the dissemination of AMR genes within natural microbial communities - which current antibiotic stewardship typically overlooks. In this review, we examine the impact of anthropogenically induced temperature fluctuations, increased soil salinity, soil fertility loss, and contaminants such as metals and pesticides on the de novo evolution and dissemination of AMR in the environment. These stressors can select for AMR - even in the absence of antibiotics - via mechanisms such as cross-resistance, co-resistance and co-regulation. Moreover, anthropogenic stressors can prime bacterial physiology against stress, potentially widening the window of opportunity for the de novo evolution of AMR. However, research to date is typically limited to the study of single isolated bacterial species - we lack data on how intensive agricultural practices drive AMR over evolutionary timescales in more complex microbial communities. Furthermore, a multidisciplinary approach to fighting AMR is urgently needed, as it is clear that the drivers of AMR extend far beyond the clinical environment.
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Affiliation(s)
- Matthew Kelbrick
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Elze Hesse
- College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Siobhán O' Brien
- Department of Microbiology, Moyne Institute for Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Republic of Ireland
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Kumari K, Sharma PK, Shikha S, Singh RP. Molecular characterization and in-depth genome analysis of Enterobacter sp. S-16. Funct Integr Genomics 2023; 23:245. [PMID: 37460717 DOI: 10.1007/s10142-023-01161-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/20/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Shweta Shikha
- Shyama Prasad Mukherjee University, Ranchi, Jharkhand, India
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, Pin 835215, India.
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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64
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Long GS, Hider J, Duggan AT, Klunk J, Eaton K, Karpinski E, Giuffra V, Ventura L, Prowse TL, Fornaciari A, Fornaciari G, Holmes EC, Golding GB, Poinar HN. A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathog 2023; 19:e1011538. [PMID: 37523413 PMCID: PMC10414615 DOI: 10.1371/journal.ppat.1011538] [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: 02/12/2023] [Revised: 08/10/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.
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Affiliation(s)
- George S. Long
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Jessica Hider
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Daicel Arbor Biosciences, Ann Arbor, Michigan, United States of America
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Emil Karpinski
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Division of Pathology, San Salvatore Hospital, Coppito, Italy
| | - Tracy L. Prowse
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- CIFAR Humans and the Microbiome Program, Toronto, Canada
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Wang Y, Su J, Zhou Z, Yang J, Liu W, Zhang Y, Zhang P, Guo T, Li G. Baicalein Resensitizes Multidrug-Resistant Gram-Negative Pathogens to Doxycycline. Microbiol Spectr 2023; 11:e0470222. [PMID: 37070985 PMCID: PMC10269726 DOI: 10.1128/spectrum.04702-22] [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: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
As multidrug-resistant pathogens emerge and spread rapidly, novel antibiotics urgently need to be discovered. With a dwindling antibiotic pipeline, antibiotic adjuvants might be used to revitalize existing antibiotics. In recent decades, traditional Chinese medicine has occupied an essential position in adjuvants of antibiotics. This study found that baicalein potentiates doxycycline against multidrug-resistant Gram-negative pathogens. Mechanism studies have shown that baicalein causes membrane disruption by attaching to phospholipids on the Gram-negative bacterial cytoplasmic membrane and lipopolysaccharides on the outer membrane. This process facilitates the entry of doxycycline into bacteria. Through collaborative strategies, baicalein can also increase the production of reactive oxygen species and inhibit the activities of multidrug efflux pumps and biofilm formation to potentiate antibiotic efficacy. Additionally, baicalein attenuates the lipopolysaccharide-induced inflammatory response in vitro. Finally, baicalein can significantly improve doxycycline efficacy in mouse lung infection models. The present study showed that baicalein might be considered a lead compound, and it should be further optimized and developed as an adjuvant that helps combat antibiotic resistance. IMPORTANCE Doxycycline is an important broad-spectrum tetracycline antibiotic used for treating multiple human infections, but its resistance rates are recently rising globally. Thus, new agents capable of boosting the effectiveness of doxycycline need to be discovered. In this study, it was found that baicalein potentiates doxycycline against multidrug-resistant Gram-negative pathogens in vitro and in vivo. Due to its low cytotoxicity and resistance, the combination of baicalein and doxycycline provides a valuable clinical reference for selecting more effective therapeutic strategies for treating infections caused by multidrug-resistant Gram-negative clinical isolates.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, People’s Republic of China
| | - Junfeng Su
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
| | - Ziyan Zhou
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, People’s Republic of China
| | - Jie Yang
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Wenjuan Liu
- Laboratory Department, Affiliated Hospital of Yangzhou University, Yangzhou, People’s Republic of China
| | - Yafen Zhang
- Laboratory Department, Affiliated Hospital of Yangzhou University, Yangzhou, People’s Republic of China
| | - Pengyu Zhang
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, People’s Republic of China
| | - Tingting Guo
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Guocai Li
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, People’s Republic of China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
- Laboratory Department, Affiliated Hospital of Yangzhou University, Yangzhou, People’s Republic of China
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Soares GG, Campanini EB, Ferreira RL, Damas MSF, Rodrigues SH, Campos LC, Galvão JD, Fuentes ASDC, Freire CCDM, Malavazi I, Pitondo-Silva A, da Cunha AF, Pranchevicius MCDS. Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil. Microbiol Spectr 2023; 11:e0441522. [PMID: 37067439 PMCID: PMC10269605 DOI: 10.1128/spectrum.04415-22] [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: 11/03/2022] [Accepted: 02/17/2023] [Indexed: 04/18/2023] Open
Abstract
To increase knowledge on Brevundimonas pathogens, we conducted in-depth genomic and phenotypic characterization of a Brevundimonas strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus Brevundimonas based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. In silico analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to β-lactams (penP, blaTEM-16, and blaBKC-1) and aminoglycosides [strA, strB, aac(6')-Ib, and aac(6')-Il]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in qseC and/or phoP and GyrA/GyrB, respectively. The Brevundimonas brasiliensis sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn3-type and IS3, IS6, IS5, and IS1380 families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR Brevundimonas and highlight the need for monitoring and identifying new bacterial species in hospital environments. IMPORTANCE Brevundimonas species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of Brevundimonas in clinical settings. Hence, we identified a novel pathogenic bacterium, Brevundimonas brasiliensis sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR Brevundimonas.
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Affiliation(s)
- Gabriela Guerrera Soares
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Saulo Henrique Rodrigues
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Caio César de Melo Freire
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - André Pitondo-Silva
- Programas de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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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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68
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Kumawat M, Nabi B, Daswani M, Viquar I, Pal N, Sharma P, Tiwari S, Sarma DK, Shubham S, Kumar M. Role of bacterial efflux pump proteins in antibiotic resistance across microbial species. Microb Pathog 2023:106182. [PMID: 37263448 DOI: 10.1016/j.micpath.2023.106182] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Efflux proteins are transporter molecules that actively pump out a variety of substrates, including antibiotics, from cells to the environment. They are found in both Gram-positive and Gram-negative bacteria and eukaryotic cells. Based on their protein sequence homology, energy source, and overall structure, efflux proteins can be divided into seven groups. Multidrug efflux pumps are transmembrane proteins produced by microbes to enhance their survival in harsh environments and contribute to antibiotic resistance. These pumps are present in all bacterial genomes studied, indicating their ancestral origins. Many bacterial genes encoding efflux pumps are involved in transport, a significant contributor to antibiotic resistance in microbes. Efflux pumps are widely implicated in the extrusion of clinically relevant antibiotics from cells to the extracellular environment and, as such, represent a significant challenge to antimicrobial therapy. This review aims to provide an overview of the structures and mechanisms of action, substrate profiles, regulation, and possible inhibition of clinically relevant efflux pumps. Additionally, recent advances in research and the pharmacological exploitation of efflux pump inhibitors as a promising intervention for combating drug resistance will be discussed.
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Affiliation(s)
- Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Muskan Daswani
- Department of Biotechnology, SantHirdaram Girls College, Bhopal, 462030, India
| | - Iqra Viquar
- Department of Biotechnology, SantHirdaram Girls College, Bhopal, 462030, India
| | - Namrata Pal
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Poonam Sharma
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Shikha Tiwari
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Devojit Kumar Sarma
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Swasti Shubham
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India
| | - Manoj Kumar
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
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Wekesa C, Kiprotich K, Okoth P, Asudi GO, Muoma JO, Furch ACU, Oelmüller R. Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans. Int J Mol Sci 2023; 24:ijms24119509. [PMID: 37298462 DOI: 10.3390/ijms24119509] [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: 05/01/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.
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Affiliation(s)
- Clabe Wekesa
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Kelvin Kiprotich
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Patrick Okoth
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - George O Asudi
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844, Nairobi 00100, Kenya
| | - John O Muoma
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Alexandra C U Furch
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
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De Gaetano GV, Lentini G, Famà A, Coppolino F, Beninati C. Antimicrobial Resistance: Two-Component Regulatory Systems and Multidrug Efflux Pumps. Antibiotics (Basel) 2023; 12:965. [PMID: 37370284 DOI: 10.3390/antibiotics12060965] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The number of multidrug-resistant bacteria is rapidly spreading worldwide. Among the various mechanisms determining resistance to antimicrobial agents, multidrug efflux pumps play a noteworthy role because they export extraneous and noxious substrates from the inside to the outside environment of the bacterial cell contributing to multidrug resistance (MDR) and, consequently, to the failure of anti-infective therapies. The expression of multidrug efflux pumps can be under the control of transcriptional regulators and two-component systems (TCS). TCS are a major mechanism by which microorganisms sense and reply to external and/or intramembrane stimuli by coordinating the expression of genes involved not only in pathogenic pathways but also in antibiotic resistance. In this review, we describe the influence of TCS on multidrug efflux pump expression and activity in some Gram-negative and Gram-positive bacteria. Taking into account the strict correlation between TCS and multidrug efflux pumps, the development of drugs targeting TCS, alone or together with already discovered efflux pump inhibitors, may represent a beneficial strategy to contribute to the fight against growing antibiotic resistance.
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Affiliation(s)
| | - Germana Lentini
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Agata Famà
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
| | - Francesco Coppolino
- Department of Biomedical, Dental and Imaging Sciences, University of Messina, 98124 Messina, Italy
| | - Concetta Beninati
- Department of Human Pathology, University of Messina, 98124 Messina, Italy
- Scylla Biotech Srl, 98124 Messina, Italy
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Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [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: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
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Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
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Bina XR, Bina JE. Vibrio cholerae RND efflux systems: mediators of stress responses, colonization and pathogenesis. Front Cell Infect Microbiol 2023; 13:1203487. [PMID: 37256112 PMCID: PMC10225521 DOI: 10.3389/fcimb.2023.1203487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023] Open
Abstract
Resistance Nodulation Division (RND) efflux systems are ubiquitous transporters in gram-negative bacteria that provide protection against antimicrobial agents and thereby enhance survival in virtually all environments these prokaryotes inhabit. Vibrio cholerae is a dual lifestyle enteric pathogen that spends much of its existence in aquatic environments. An unwitting encounter with a human host can lead to V. cholerae intestinal colonization by strains that encode cholera toxin and toxin co-regulated pilus virulence factors leading to potentially fatal cholera diarrhea and dissemination in the environment. Adaptive response mechanisms to host factors encountered by these pathogens are therefore critical both to engage survival mechanisms such as RND-mediated transporters and to induce timely expression of virulence factors. Sensing of cues encountered in the host may therefore activate more than protective responses such as efflux systems, but also be coordinated to initiate expression of virulence factors. This review summarizes recent advances that contribute towards the understanding of RND efflux physiological functions and how the transport systems interface with the regulation of virulence factor production in V. cholerae.
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Affiliation(s)
| | - James E. Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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Trampari E, Prischi F, Vargiu AV, Abi-Assaf J, Bavro VN, Webber MA. Functionally distinct mutations within AcrB underpin antibiotic resistance in different lifestyles. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:2. [PMID: 38686215 PMCID: PMC11057200 DOI: 10.1038/s44259-023-00001-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2024]
Abstract
Antibiotic resistance is a pressing healthcare challenge and is mediated by various mechanisms, including the active export of drugs via multidrug efflux systems, which prevent drug accumulation within the cell. Here, we studied how Salmonella evolved resistance to two key antibiotics, cefotaxime and azithromycin, when grown planktonically or as a biofilm. Resistance to both drugs emerged in both conditions and was associated with different substitutions within the efflux-associated transporter, AcrB. Azithromycin exposure selected for an R717L substitution, while cefotaxime for Q176K. Additional mutations in ramR or envZ accumulated concurrently with the R717L or Q176K substitutions respectively, resulting in clinical resistance to the selective antibiotics and cross-resistance to other drugs. Structural, genetic, and phenotypic analysis showed the two AcrB substitutions confer their benefits in profoundly different ways. R717L reduces steric barriers associated with transit through the substrate channel 2 of AcrB. Q176K increases binding energy for cefotaxime, improving recognition in the distal binding pocket, resulting in increased efflux efficiency. Finally, we show the R717 substitution is present in isolates recovered around the world.
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Affiliation(s)
- Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, S. P. 8, km. 0.700, 09042 Monserrato, Italy
| | - Justin Abi-Assaf
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
| | - Vassiliy N. Bavro
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ UK
- Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7UA UK
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Pun M, Khazanov N, Galsurker O, Kerem Z, Senderowitz H, Yedidia I. Inhibition of AcrAB-TolC enhances antimicrobial activity of phytochemicals in Pectobacterium brasiliense. FRONTIERS IN PLANT SCIENCE 2023; 14:1161702. [PMID: 37229130 PMCID: PMC10203483 DOI: 10.3389/fpls.2023.1161702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023]
Abstract
Introduction The eons-long co-evolvement of plants and bacteria led to a plethora of interactions between the two kingdoms, in which bacterial pathogenicity is counteracted by plant-derived antimicrobial defense molecules. In return, efflux pumps (EP) form part of the resistance mechanism employed by bacteria to permit their survival in this hostile chemical environment. In this work we study the effect of combinations of efflux pump inhibitors (EPIs) and plant-derived phytochemicals on bacterial activity using Pectobacteriun brasiliense 1692 (Pb1692) as a model system. Methods We measured the minimal inhibitory concentration (MIC) of two phytochemicals, phloretin (Pht) and naringenin (Nar), and of one common antibiotic ciprofloxacin (Cip), either alone or in combinations with two known inhibitors of the AcrB EP of Escherichia coli, a close homolog of the AcrAB-TolC EP of Pb1692. In addition, we also measured the expression of genes encoding for the EP, under similar conditions. Results Using the FICI equation, we observed synergism between the EPIs and the phytochemicals, but not between the EPIs and the antibiotic, suggesting that EP inhibition potentiated the antimicrobial activity of the plant derived compounds, but not of Cip. Docking simulations were successfully used to rationalize these experimental results. Discussion Our findings suggest that AcrAB-TolC plays an important role in survival and fitness of Pb1692 in the plant environment and that its inhibition is a viable strategy for controlling bacterial pathogenicity.
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Affiliation(s)
- Manoj Pun
- The Institute of Plant Sciences, Volcani Center, Agricultural Research Organization (ARO), Rishon Lezion, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Ortal Galsurker
- The Institute of Plant Sciences, Volcani Center, Agricultural Research Organization (ARO), Rishon Lezion, Israel
| | - Zohar Kerem
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Iris Yedidia
- The Institute of Plant Sciences, Volcani Center, Agricultural Research Organization (ARO), Rishon Lezion, Israel
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Gaurav A, Bakht P, Saini M, Pandey S, Pathania R. Role of bacterial efflux pumps in antibiotic resistance, virulence, and strategies to discover novel efflux pump inhibitors. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37224055 DOI: 10.1099/mic.0.001333] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The problem of antibiotic resistance among pathogenic bacteria has reached a crisis level. The treatment options against infections caused by multiple drug-resistant bacteria are shrinking gradually. The current pace of the discovery of new antibacterial entities is lagging behind the rate of development of new resistance. Efflux pumps play a central role in making a bacterium resistant to multiple antibiotics due to their ability to expel a wide range of structurally diverse compounds. Besides providing an escape from antibacterial compounds, efflux pumps are also involved in bacterial stress response, virulence, biofilm formation, and altering host physiology. Efflux pumps are unique yet challenging targets for the discovery of novel efflux pump inhibitors (EPIs). EPIs could help rejuvenate our currently dried pipeline of antibacterial drug discovery. The current article highlights the recent developments in the field of efflux pumps, challenges faced during the development of EPIs and potential approaches for their development. Additionally, this review highlights the utility of resources such as natural products and machine learning to expand our EPIs arsenal using these latest technologies.
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Affiliation(s)
- Amit Gaurav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Perwez Bakht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Mahak Saini
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Shivam Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Recent advances in nanoparticle-mediated antibacterial applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Verdial C, Serrano I, Tavares L, Gil S, Oliveira M. Mechanisms of Antibiotic and Biocide Resistance That Contribute to Pseudomonas aeruginosa Persistence in the Hospital Environment. Biomedicines 2023; 11:biomedicines11041221. [PMID: 37189839 DOI: 10.3390/biomedicines11041221] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen responsible for multiple hospital- and community-acquired infections, both in human and veterinary medicine. P. aeruginosa persistence in clinical settings is worrisome and is a result of its remarkable flexibility and adaptability. This species exhibits several characteristics that allow it to thrive under different environmental conditions, including the ability to colonize inert materials such as medical equipment and hospital surfaces. P. aeruginosa presents several intrinsic mechanisms of defense that allow it to survive external aggressions, but it is also able to develop strategies and evolve into multiple phenotypes to persevere, which include antimicrobial-tolerant strains, persister cells, and biofilms. Currently, these emergent pathogenic strains are a worldwide problem and a major concern. Biocides are frequently used as a complementary/combination strategy to control the dissemination of P. aeruginosa-resistant strains; however, tolerance to commonly used biocides has also already been reported, representing an impediment to the effective elimination of this important pathogen from clinical settings. This review focuses on the characteristics of P. aeruginosa responsible for its persistence in hospital environments, including those associated with its antibiotic and biocide resistance ability.
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Affiliation(s)
- Cláudia Verdial
- Gato Escondido-Veterinary Clinic, Av. Bombeiros Voluntários n°22B, 2950-209 Palmela, Portugal
| | - Isa Serrano
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Luís Tavares
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Solange Gil
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Manuela Oliveira
- CIISA-Center for Interdisciplinary Research in Animal Health, Faculty of Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisboa, Portugal
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Wei H, Wu D, Zheng M, Wang W, Wang D. Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131443. [PMID: 37094440 DOI: 10.1016/j.jhazmat.2023.131443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.
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Affiliation(s)
- Huawei Wei
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China; Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| | - Dong Wu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Mingying Zheng
- Guizhou Province Bureau of Geology and Mineral Exploration and Development, Guiyang 550004, PR China
| | - Wanjin Wang
- Guizhou Province Bureau of Geology and Mineral Exploration and Development, Guiyang 550004, PR China
| | - Dapeng Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China; Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
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Duan C, Yu M, Xu J, Li BY, Zhao Y, Kankala RK. Overcoming Cancer Multi-drug Resistance (MDR): Reasons, mechanisms, nanotherapeutic solutions, and challenges. Biomed Pharmacother 2023; 162:114643. [PMID: 37031496 DOI: 10.1016/j.biopha.2023.114643] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Multi-drug resistance (MDR) in cancer cells, either intrinsic or acquired through various mechanisms, significantly hinders the therapeutic efficacy of drugs. Typically, the reduced therapeutic performance of various drugs is predominantly due to the inherent over expression of ATP-binding cassette (ABC) transporter proteins on the cell membrane, resulting in the deprived uptake of drugs, augmenting drug detoxification, and DNA repair. In addition to various physiological abnormalities and extensive blood flow, MDR cancer phenotypes exhibit improved apoptotic threshold and drug efflux efficiency. These severe consequences have substantially directed researchers in the fabrication of various advanced therapeutic strategies, such as co-delivery of drugs along with various generations of MDR inhibitors, augmented dosage regimens and frequency of administration, as well as combinatorial treatment options, among others. In this review, we emphasize different reasons and mechanisms responsible for MDR in cancer, including but not limited to the known drug efflux mechanisms mediated by permeability glycoprotein (P-gp) and other pumps, reduced drug uptake, altered DNA repair, and drug targets, among others. Further, an emphasis on specific cancers that share pathogenesis in executing MDR and effluxed drugs in common is provided. Then, the aspects related to various nanomaterials-based supramolecular programmable designs (organic- and inorganic-based materials), as well as physical approaches (light- and ultrasound-based therapies), are discussed, highlighting the unsolved issues and future advancements. Finally, we summarize the review with interesting perspectives and future trends, exploring further opportunities to overcome MDR.
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Affiliation(s)
- Chunyan Duan
- School of New Energy and Environmental Protection Engineering, Foshan Polytechnic, Foshan 528137, PR China.
| | - Mingjia Yu
- School of New Energy and Environmental Protection Engineering, Foshan Polytechnic, Foshan 528137, PR China
| | - Jiyuan Xu
- School of New Energy and Environmental Protection Engineering, Foshan Polytechnic, Foshan 528137, PR China
| | - Bo-Yi Li
- Institute of Biomaterials and Tissue Engineering, College of Chemical Engineering, Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, PR China
| | - Ying Zhao
- Institute of Biomaterials and Tissue Engineering, College of Chemical Engineering, Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, PR China
| | - Ranjith Kumar Kankala
- Institute of Biomaterials and Tissue Engineering, College of Chemical Engineering, Fujian Provincial Key Laboratory of Biochemical Technology, Huaqiao University, Xiamen 361021, PR China.
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Bonn CM, Rafiqullah IM, Crawford JA, Qian YM, Guthrie JL, Matuszewska M, Robinson DA, McGavin MJ. Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0074922. [PMID: 36744906 PMCID: PMC10019231 DOI: 10.1128/aac.00749-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent in vitro selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that in vivo selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarRH121Y from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. Of these, FarRE160G and FarRE93EE were exclusive to CC5, while FarRC116Y, FarRP165L, and FarRG166D also occurred in nonrelated CCs, primarily from bovine hosts. Within CC5, FarRC116Y and FarRG166D strains were polyphyletic, each exhibiting two emergence events. FarRC116Y and FarRE160G were individually sufficient to confer increased expression of FarE and enhanced resistance to linoleic acid (LA). Isolates with FarRE93EE were most closely related to S. aureus N315 MRSA and exhibited increased resistance independently of FarRE93EE. Accumulation of pseudogenes and additional polymorphisms in FarRE93EE strains contributed to a multiresistance phenotype which included fosfomycin and fusidic acid resistance in addition to increased linoleic acid resistance. These findings underscore the remarkable adaptive capacity of CC5 MRSA, which includes the polyphyletic USA100 lineage of HA-MRSA that is endemic in the Western hemisphere and known for the acquisition of multiple resistance phenotypes.
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Affiliation(s)
- Camryn M. Bonn
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - John A. Crawford
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yi Meng Qian
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Jennifer L. Guthrie
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Marta Matuszewska
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Martin J. McGavin
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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81
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Qiu L, Wang Y, Du W, Ai F, Yin Y, Guo H. Efflux pumps activation caused by mercury contamination prompts antibiotic resistance and pathogen's virulence under ambient and elevated CO 2 concentration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160831. [PMID: 36526183 DOI: 10.1016/j.scitotenv.2022.160831] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The occurrence and development of antibiotic resistance genes (ARGs) in pathogens poses serious threatens to global health. Agricultural soils provide reservoirs for pathogens and ARGs, closely related to public health and food safety. Especially, metals stress provides more long-standing selection pressure for ARGs, and climate change is a "threat multiplier" for the spread of ARGs. However, little is known about the impact of metals contamination on pathogens and ARGs in agricultural soils and their sensitivity to ongoing climate changes. To fill this gap, a pot experiment was conducted in open-top chambers (OTCs) to investigate the influence of mercury (Hg) contamination on the distribution of soil pathogens and ARGs under ambient and elevated CO2 concentration. Results showed that the relative abundance of common plant and human pathogens increased significantly in Hg-contaminated soil under two CO2 concentrations. Hg contamination was a positive effector of the activation of efflux pumps and offensive virulence factors (adhere and secretion system) under two CO2 levels. Activation of efflux pumps caused by Hg contamination might contribute to changes of virulence or fitness of certain pathogens. Overall, our study emphasizes the critical role of efflux pumps as an intersection of antibiotic resistance and pathogen's virulence under Hg stress.
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Affiliation(s)
- Linlin Qiu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yabo Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wenchao Du
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Fuxun Ai
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China; Joint International Research Centre for Critical Zone Science-University of Leeds and Nanjing University, Nanjing University, Nanjing 210023, China.
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82
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Athar M, Gervasoni S, Catte A, Basciu A, Malloci G, Ruggerone P, Vargiu AV. Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies? MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972322 DOI: 10.1099/mic.0.001307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Bacterial resistance to antibiotics has been long recognized as a priority to address for human health. Among all micro-organisms, the so-called multi-drug resistant (MDR) bacteria, which are resistant to most, if not all drugs in our current arsenal, are particularly worrisome. The World Health Organization has prioritized the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) pathogens, which include four Gram-negative bacterial species. In these bacteria, active extrusion of antimicrobial compounds out of the cell by means of 'molecular guns' known as efflux pumps is a main determinant of MDR phenotypes. The resistance-nodulation-cell division (RND) superfamily of efflux pumps connecting the inner and outer membrane in Gram-negative bacteria is crucial to the onset of MDR and virulence, as well as biofilm formation. Thus, understanding the molecular basis of the interaction of antibiotics and inhibitors with these pumps is key to the design of more effective therapeutics. With the aim to contribute to this challenge, and complement and inspire experimental research, in silico studies on RND efflux pumps have flourished in recent decades. Here, we review a selection of such investigations addressing the main determinants behind the polyspecificity of these pumps, the mechanisms of substrate recognition, transport and inhibition, as well as the relevance of their assembly for proper functioning, and the role of protein-lipid interactions. The journey will end with a perspective on the role of computer simulations in addressing the challenges posed by these beautifully complex machineries and in supporting the fight against the spread of MDR bacteria.
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Affiliation(s)
- Mohd Athar
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Silvia Gervasoni
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Andrea Catte
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Andrea Basciu
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Giuliano Malloci
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Paolo Ruggerone
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Attilio Vittorio Vargiu
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
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83
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Cryo-EM Structures of AcrD Illuminate a Mechanism for Capturing Aminoglycosides from Its Central Cavity. mBio 2023; 14:e0338322. [PMID: 36625574 PMCID: PMC9973356 DOI: 10.1128/mbio.03383-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Escherichia coli acriflavine resistance protein D (AcrD) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. Its primary function is to provide resistance to aminoglycoside-based drugs by actively extruding these noxious compounds out of E. coli cells. AcrD can also mediate resistance to a limited range of other amphiphilic agents, including bile acids, novobiocin, and fusidic acids. As there is no structural information available for any aminoglycoside-specific RND pump, here we describe cryo-electron microscopy (cryo-EM) structures of AcrD in the absence and presence of bound gentamicin. These structures provide new information about the RND superfamily of efflux pumps, specifically, that three negatively charged residues central to the aminoglycoside-binding site are located within the ceiling of the central cavity of the AcrD trimer. Thus, it is likely that AcrD is capable of picking up aminoglycosides via this central cavity. Through the combination of cryo-EM structural determination, mutagenesis analysis, and molecular simulation, we show that charged residues are critically important for this pump to shuttle drugs directly from the central cavity to the funnel of the AcrD trimer for extrusion. IMPORTANCE Here, we report cryo-EM structures of the AcrD aminoglycoside efflux pump in the absence and presence of bound gentamicin, posing the possibility that this pump is capable of capturing aminoglycosides from the central cavity of the AcrD trimer. The results indicate that AcrD utilizes charged residues to bind and export drugs, mediating resistance to these antibiotics.
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84
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Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens. Commun Biol 2023; 6:195. [PMID: 36807602 PMCID: PMC9938908 DOI: 10.1038/s42003-023-04412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 01/03/2023] [Indexed: 02/20/2023] Open
Abstract
Type IA topoisomerases maintain DNA topology by cleaving ssDNA and relaxing negative supercoils. The inhibition of its activity in bacteria prevents the relaxation of negative supercoils, which in turn impedes DNA metabolic processes leading to cell death. Using this hypothesis, two bisbenzimidazoles, PPEF and BPVF are synthesized, selectively inhibiting bacterial TopoIA and TopoIII. PPEF stabilizes the topoisomerase and topoisomerase-ssDNA complex, acts as an interfacial inhibitor. PPEF display high efficacy against ~455 multi-drug resistant gram positive and negative bacteria. To understand molecular mechanism of inhibition of TopoIA and PPEF, accelerated MD simulation is carried out, and results suggested that PPEF binds, stabilizes the closed conformation of TopoIA with -6Kcal/mol binding energy and destabilizes the binding of ssDNA. The TopoIA gate dynamics model can be used as a tool to screen TopoIA inhibitors as therapeutic candidates. PPEF and BPVF cause cellular filamentation and DNA fragmentation leading to bacterial cell death. PPEF and BPVF show potent efficacy against systemic and neutropenic mouse models harboring E. coli, VRSA, and MRSA infection without cellular toxicity.
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85
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Yee JX, Kim J, Yeom J. Membrane Proteins as a Regulator for Antibiotic Persistence in Gram-Negative Bacteria. J Microbiol 2023; 61:331-341. [PMID: 36800168 DOI: 10.1007/s12275-023-00024-w] [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: 01/03/2023] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/18/2023]
Abstract
Antibiotic treatment failure threatens our ability to control bacterial infections that can cause chronic diseases. Persister bacteria are a subpopulation of physiological variants that becomes highly tolerant to antibiotics. Membrane proteins play crucial roles in all living organisms to regulate cellular physiology. Although a diverse membrane component involved in persistence can result in antibiotic treatment failure, the regulations of antibiotic persistence by membrane proteins has not been fully understood. In this review, we summarize the recent advances in our understanding with regards to membrane proteins in Gram-negative bacteria as a regulator for antibiotic persistence, highlighting various physiological mechanisms in bacteria.
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Affiliation(s)
- Jia Xin Yee
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Juhyun Kim
- School of Life Science, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Jinki Yeom
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore. .,Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. .,Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. .,Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea.
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86
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Fanelli G, Pasqua M, Prosseda G, Grossi M, Colonna B. AcrAB efflux pump impacts on the survival of adherent-invasive Escherichia coli strain LF82 inside macrophages. Sci Rep 2023; 13:2692. [PMID: 36792672 PMCID: PMC9931695 DOI: 10.1038/s41598-023-29817-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The tripartite complex AcrAB-TolC is the major RND pump in Escherichia coli and other Enterobacteriaceae. It consists of the AcrB transporter, which is embedded in the inner membrane, the AcrA adapter located in the periplasm, and the channel protein TolC responsible for the transport of substrates towards the extracellular environment. Besides conferring resistance to many classes of antibiotics, AcrAB plays a role in the pathogenesis and virulence of several bacterial pathogens. Here we report that the AcrAB pump heavily affects the infection process of the LF82 strain, the prototype of Adherent-Invasive Escherichia coli (AIEC) which are highly abundant in the ileal mucosa of Chron disease patients. We found that the deletion of genes encoding AcrA and/or AcrB leads to decreased survival of LF82 within macrophages. Ectopic AcrAB expression in a acrAB defective mutant restores the wild type condition. Furthermore, we demonstrate that inhibition of AcrB and replacement of the transporter with an unfunctional AcrB also interfere with bacterial viability inside macrophages. Overall, these data suggest a pivotal role of the AcrAB efflux pump in bacteria-host cell interactions also in AIEC.
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Affiliation(s)
- Giulia Fanelli
- grid.7841.aDepartment of Biology and Biotechnology “C. Darwin”, Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Martina Pasqua
- grid.7841.aDepartment of Biology and Biotechnology “C. Darwin”, Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Gianni Prosseda
- grid.7841.aDepartment of Biology and Biotechnology “C. Darwin”, Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy
| | - Milena Grossi
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy.
| | - Bianca Colonna
- Department of Biology and Biotechnology "C. Darwin", Istituto Pasteur Italia, Sapienza Università di Roma, Rome, Italy.
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87
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Pham DN, Wu Q, Li M. Global profiling of antibiotic resistomes in maize rhizospheres. Arch Microbiol 2023; 205:89. [PMID: 36781495 DOI: 10.1007/s00203-023-03424-z] [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: 11/21/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.
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Affiliation(s)
- Dung Ngoc Pham
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Qiong Wu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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88
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Bhowmik P, Bharatham N, Murakami S, Ramachandran V, Datta S. Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis. Res Microbiol 2023; 174:104039. [PMID: 36738814 DOI: 10.1016/j.resmic.2023.104039] [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: 11/17/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both, hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.
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Affiliation(s)
- Purnendu Bhowmik
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Bengaluru, Karnataka 560064.
| | - Nagakumar Bharatham
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Bengaluru, Karnataka 560064.
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, 259 Nagatsuta-cho, 1, Midori Ward, Yokohama, Kanagawa 226-8501, Japan.
| | - Vasanthi Ramachandran
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Bengaluru, Karnataka 560064.
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India.
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Rayane Correia de Oliveira M, Gabriely de Lima Silva M, Datiane de Morais Oliveira-Tintino C, Relison Tintino S, Esmeraldo Rocha J, Ernani Alves Magalhães F, Henrique Sousa da Costa R, Torres Pessoa R, Sousa Alcântara I, Oliveira Brito Pereira Bezerra Martins A, Douglas Melo Coutinho H, Raposo A, Carrascosa C, Raduan Jaber J, Aquino Saraiva R, Rose Alencar de Menezes I. Antibacterial effect, efflux pump inhibitory (NorA, TetK and MepA) of Staphylococcus aureus and in silico prediction of α, β and δ-damascone compounds. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2022.104482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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90
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Bai H, He LY, Gao FZ, Wu DL, Yao KS, Zhang M, Jia WL, He LX, Zou HY, Yao MS, Ying GG. Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic. ENVIRONMENT INTERNATIONAL 2023; 172:107784. [PMID: 36731187 PMCID: PMC9884615 DOI: 10.1016/j.envint.2023.107784] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/22/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Antimicrobial resistance is recognized as one of the greatest public health concerns. It is becoming an increasingly threat during the COVID-19 pandemic due to increasing usage of antimicrobials, such as antibiotics and disinfectants, in healthcare facilities or public spaces. To explore the characteristics of airborne antibiotic resistome in public transport systems, we assessed distribution and health risks of airborne antibiotic resistome and microbiome in railway stations before and after the pandemic outbreak by culture-independent and culture-dependent metagenomic analysis. Results showed that the diversity of airborne antibiotic resistance genes (ARGs) decreased following the pandemic, while the relative abundance of core ARGs increased. A total of 159 horizontally acquired ARGs, predominantly confering resistance to macrolides and aminoglycosides, were identified in the airborne bacteria and dust samples. Meanwhile, the abundance of horizontally acquired ARGs hosted by pathogens increased during the pandemic. A bloom of clinically important antibiotic (tigecycline and meropenem) resistant bacteria was found following the pandemic outbreak. 251 high-quality metagenome-assembled genomes (MAGs) were recovered from 27 metagenomes, and 86 genera and 125 species were classified. Relative abundance of ARG-carrying MAGs, taxonomically assigned to genus of Bacillus, Pseudomonas, Acinetobacter, and Staphylococcus, was found increased during the pandemic. Bayesian source tracking estimated that human skin and anthropogenic activities were presumptive resistome sources for the public transit air. Moreover, risk assessment based on resistome and microbiome data revealed elevated airborne health risks during the pandemic.
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Affiliation(s)
- Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Dai-Ling Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China; Aquatic Ecology and Water Quality Management group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Kai-Sheng Yao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China; Aquatic Ecology and Water Quality Management group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Wei-Li Jia
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Hai-Yan Zou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Mao-Sheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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91
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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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92
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Grézal G, Spohn R, Méhi O, Dunai A, Lázár V, Bálint B, Nagy I, Pál C, Papp B. Plasticity and Stereotypic Rewiring of the Transcriptome Upon Bacterial Evolution of Antibiotic Resistance. Mol Biol Evol 2023; 40:7013728. [PMID: 36718533 PMCID: PMC9927579 DOI: 10.1093/molbev/msad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 12/01/2022] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Bacterial evolution of antibiotic resistance frequently has deleterious side effects on microbial growth, virulence, and susceptibility to other antimicrobial agents. However, it is unclear how these trade-offs could be utilized for manipulating antibiotic resistance in the clinic, not least because the underlying molecular mechanisms are poorly understood. Using laboratory evolution, we demonstrate that clinically relevant resistance mutations in Escherichia coli constitutively rewire a large fraction of the transcriptome in a repeatable and stereotypic manner. Strikingly, lineages adapted to functionally distinct antibiotics and having no resistance mutations in common show a wide range of parallel gene expression changes that alter oxidative stress response, iron homeostasis, and the composition of the bacterial outer membrane and cell surface. These common physiological alterations are associated with changes in cell morphology and enhanced sensitivity to antimicrobial peptides. Finally, the constitutive transcriptomic changes induced by resistance mutations are largely distinct from those induced by antibiotic stresses in the wild type. This indicates a limited role for genetic assimilation of the induced antibiotic stress response during resistance evolution. Our work suggests that diverse resistance mutations converge on similar global transcriptomic states that shape genetic susceptibility to antimicrobial compounds.
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Affiliation(s)
- Gábor Grézal
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary,Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Réka Spohn
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,HCEMM-BRC Translational Microbiology Research Lab, Szeged, Hungary
| | - Anett Dunai
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,HCEMM-BRC Pharmacodynamic Drug Interaction Research Group, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,SeqOmics Biotechnology Ltd., Mórahalom, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary,Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary,National Laboratory of Biotechnology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
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93
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Kim H, Kim ES, Cho JH, Song M, Cho JH, Kim S, Keum GB, Kwak J, Doo H, Pandey S, Park SH, Lee JH, Jung H, Hur TY, Kim JK, Oh KK, Kim HB, Lee JH. Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing. J Microbiol Biotechnol 2023; 33:51-60. [PMID: 36517072 PMCID: PMC9896000 DOI: 10.4014/jmb.2209.09013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/17/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.
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Affiliation(s)
- Hyeri Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jin Ho Cho
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Minho Song
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Republic of Korea
| | - Jae Hyoung Cho
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sheena Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Gi Beom Keum
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jinok Kwak
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Hyunok Doo
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Hyunjung Jung
- Animal Nutrition & Physiology Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Tai Young Hur
- Animal Diseases & Health Division, National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang Kyo Oh
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea,Corresponding authors H.B. Kim Phone: +82-41-550-3653 E-mail:
| | - Ju-Hoon Lee
- Department of Food Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea,J.H. Lee Phone: +82-2-880-4854 E-mail:
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94
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Miao YB, Zhao W, Renchi G, Gong Y, Shi Y. Customizing delivery nano-vehicles for precise brain tumor therapy. J Nanobiotechnology 2023; 21:32. [PMID: 36707835 PMCID: PMC9883977 DOI: 10.1186/s12951-023-01775-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/09/2023] [Indexed: 01/29/2023] Open
Abstract
Although some tumor has become a curable disease for many patients, involvement of the central nervous system (CNS) is still a major concern. The blood-brain barrier (BBB), a special structure in the CNS, protects the brain from bloodborne pathogens via its excellent barrier properties and hinders new drug development for brain tumor. Recent breakthroughs in nanotechnology have resulted in various nanovehicless (NPs) as drug carriers to cross the BBB by different strategys. Here, the complex compositions and special characteristics of causes of brain tumor formation and BBB are elucidated exhaustively. Additionally, versatile drug nanovehicles with their recent applications and their pathways on different drug delivery strategies to overcome the BBB obstacle for anti-brain tumor are briefly discussed. Customizing nanoparticles for brain tumor treatments is proposed to improve the efficacy of brain tumor treatments via drug delivery from the gut to the brain. This review provides a broad perspective on customizing delivery nano-vehicles characteristics facilitate drug distribution across the brain and pave the way for the creation of innovative nanotechnology-based nanomaterials for brain tumor treatments.
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Affiliation(s)
- Yang-Bao Miao
- grid.410646.10000 0004 1808 0950Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu, 610000 China ,Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, 610072 Sichuan China
| | - Wang Zhao
- grid.410646.10000 0004 1808 0950Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu, 610000 China ,Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, 610072 Sichuan China
| | - Gao Renchi
- grid.410646.10000 0004 1808 0950Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu, 610000 China ,Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, 610072 Sichuan China
| | - Ying Gong
- grid.263901.f0000 0004 1791 7667School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031 People’s Republic of China
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, 610072 Sichuan China ,grid.9227.e0000000119573309Natural Products Research Center, Institute of Chengdu Biology, Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, 610072 Sichuan China ,grid.410646.10000 0004 1808 0950Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, 610072 Sichuan China
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95
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Ma K, Wang H, Lv Z, Hu Y, Wang H, Shu F, Zhu C, Xue T. The Two-Component System CpxRA Affects Antibiotic Susceptibility and Biofilm Formation in Avian Pathogenic Escherichia coli. Animals (Basel) 2023; 13:ani13030383. [PMID: 36766272 PMCID: PMC9913434 DOI: 10.3390/ani13030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the common extraintestinal infectious disease pathogens in chickens, geese, and other birds. It can cause a variety of infections, and even the death of poultry, causing enormous economic losses. However, the misuse and abuse of antibiotics in the poultry industry have led to the development of drug resistance in the gut microbes, posing a challenge for the treatment of APEC infections. It has been reported that the CpxRA two-component system has an effect on bacterial drug resistance, but the specific regulatory mechanism remains unclear. In this study, the regulatory mechanism of CpxRA on APEC biofilm formation and EmrKY efflux pump was investigated. The cpxRA knockout strain of E. coli APEC40 was constructed, and the molecular regulatory mechanism of CpxR on biofilms and efflux pump-coding genes were identified by biofilm formation assays, drug susceptibility test, real-time reverse transcription quantitative PCR, and electrophoretic mobility shift assay (EMSA). The results indicated that CpxR can directly bind to the promoter region of emrKY and negatively regulate the sensitivity of bacteria to ofloxacin and erythromycin. These results confirm the important regulatory role of the CpxRA two-component system under antibiotic stress in APEC.
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96
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Liu S, Liu J, Fu N, Kornmatitsuk B, Yan Z, Luo J. Phenylalanine-arginine β-naphthylamide could enhance neomycin-sensitivity on Riemerella anatipestifer in vitro and in vivo. Front Microbiol 2023; 13:985789. [PMID: 36713163 PMCID: PMC9873997 DOI: 10.3389/fmicb.2022.985789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Riemerella anatipestifer is an important duck pathogen responsible for septicemia and infectious serositis, which has caused great economic losses to the duck industry. Phenylalanine-arginine β-naphthylamide (PAβN) is an efflux pump inhibitor, which mainly reduces the efflux effect by competing with antibiotics for efflux pump channels. Here, we found that R. anatipestifer strain GD2019 showed resistances to gentamicin, amikacin, kanamycin, and neomycin. Notably, PAβN could significantly reduce the Minimal inhibitory concentrations (MICs) of neomycin on the GD2019 strain. Moreover, PAβN combined with neomycin significantly decreased bacterial loads, relieved pathological injury and increase survival rate (p < 0.05) for the ducks lethally challenged by the GD2019 strain. Therefore, our results suggested, in vitro and in vivo, PAβN could reduce neomycin-resistant of R. anatipestifer. Importantly, finding of this study provide a new approach for treating antibiotic-resistant R. anatipestifer infection.
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Affiliation(s)
- Shiqi Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China,Jinzhai County Agriculture and Rural Bureau, Jinzhai, Anhui, China
| | - Junfa Liu
- Wen's Group Academy, Xinxing, Guangdong, China
| | - Ning Fu
- Chifeng Institute of Agricultural Sciences, Chifeng, China
| | - Bunlue Kornmatitsuk
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | | | - Junrong Luo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China,*Correspondence: Junrong Luo, ✉
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97
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Zhao Y, Wei HM, Yuan JL, Xu L, Sun JQ. A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains. Front Microbiol 2023; 14:1177951. [PMID: 37138596 PMCID: PMC10149724 DOI: 10.3389/fmicb.2023.1177951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Hua-Mei Wei
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jia-Li Yuan
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- *Correspondence: Ji-Quan Sun,
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98
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Chaudhari R, Singh K, Kodgire P. Biochemical and molecular mechanisms of antibiotic resistance in Salmonella spp. Res Microbiol 2023; 174:103985. [PMID: 35944794 DOI: 10.1016/j.resmic.2022.103985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 01/11/2023]
Abstract
Salmonella is a diverse Gram-negative bacterium that represents the major disease burden worldwide. According to WHO, Salmonella is one of the fourth global causes of diarrhoeal disease. Antibiotic resistance is a worldwide health concern, and Salmonella spp. is one of the microorganisms that can evade the toxicity of antimicrobials via antibiotic resistance. This review aims to deliver in-depth knowledge of the molecular mechanisms and the underlying biochemical alterations perceived in antibiotic resistance in Salmonella. This information will help understand and mitigate the impact of antibiotic-resistant bacteria on humans and contribute to the state-of-the-art research developing newer and more potent antibiotics.
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Affiliation(s)
- Rahul Chaudhari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Kanika Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Simrol, Khandwa Road, Indore 453552, India.
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99
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Chetri S. The culmination of multidrug-resistant efflux pumps vs. meager antibiotic arsenal era: Urgent need for an improved new generation of EPIs. Front Microbiol 2023; 14:1149418. [PMID: 37138605 PMCID: PMC10149990 DOI: 10.3389/fmicb.2023.1149418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
Efflux pumps function as an advanced defense system against antimicrobials by reducing the concentration of drugs inside the bacteria and extruding the substances outside. Various extraneous substances, including antimicrobials, toxic heavy metals, dyes, and detergents, have been removed by this protective barrier composed of diverse transporter proteins found in between the cell membrane and the periplasm within the bacterial cell. In this review, multiple efflux pump families have been analytically and widely outlined, and their potential applications have been discussed in detail. Additionally, this review also discusses a variety of biological functions of efflux pumps, including their role in the formation of biofilms, quorum sensing, their survivability, and the virulence in bacteria, and the genes/proteins associated with efflux pumps have also been explored for their potential relevance to antimicrobial resistance and antibiotic residue detection. A final discussion centers around efflux pump inhibitors, particularly those derived from plants.
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100
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Liao M, Gong H, Quan X, Wang Z, Hu X, Chen Z, Li Z, Liu H, Zhang L, McBain AJ, Waigh TA, Zhou J, Lu JR. Intramembrane Nanoaggregates of Antimicrobial Peptides Play a Vital Role in Bacterial Killing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204428. [PMID: 36417574 DOI: 10.1002/smll.202204428] [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: 07/18/2022] [Revised: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Recent developments in antimicrobial peptides (AMPs) have focused on the rational design of short sequences with less than 20 amino acids due to their relatively low synthesis costs and ease of correlation of the structure-function relationship. However, gaps remain in the understanding of how short cationic AMPs interact with the bacterial outer and inner membranes to affect their antimicrobial efficacy and dynamic killing. The membrane-lytic actions of two designed AMPs, G(IIKK)3 I-NH2 (G3 ) and G(IIKK)4 I-NH2 (G4 ), and previously-studied controls GLLDLLKLLLKAAG-NH2 (LDKA, biomimetic) and GIGAVLKVLTTGLPALISWIKRKR-NH2 (Melittin, natural) are examined. The mechanistic processes of membrane damage and the disruption strength of the four AMPs are characterized by molecular dynamics simulations and experimental measurements including neutron reflection and scattering. The results from the combined studies are characterized with distinctly different intramembrane nanoaggregates formed upon AMP-specific binding, reflecting clear influences of AMP sequence, charge and the chemistry of the inner and outer membranes. G3 and G4 display different nanoaggregation with the outer and inner membranes, and the smaller sizes and further extent of insertion of the intramembrane nanoaggregates into bacterial membranes correlate well with their greater antimicrobial efficacy and faster dynamic killing. This work demonstrates the crucial roles of intramembrane nanoaggregates in optimizing antimicrobial efficacy and dynamic killing.
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Affiliation(s)
- Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, China
| | - Ziwei Wang
- National Graphene Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Xuzhi Hu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Zheng Chen
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, China
| | - Zongyi Li
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Huayang Liu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Lin Zhang
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Andrew J McBain
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thomas A Waigh
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, China
| | - Jian Ren Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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