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Wang Y, Hu H, Shi Q, Zhang P, Zhao D, Jiang Y, Yu Y. Prevalence and characteristics of ertapenem-mono-resistant isolates among carbapenem-resistant Enterobacterales in China. Emerg Microbes Infect 2024; 13:2332658. [PMID: 38517707 PMCID: PMC10993752 DOI: 10.1080/22221751.2024.2332658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/14/2024] [Indexed: 03/24/2024]
Abstract
Carbapenem-resistant Enterobacterales (CRE), specifically those resistant to only ertapenem among carbapenems (ETP-mono-resistant), are increasingly reported, while the optimal therapy options remain uncertain. To investigate the prevalence and characteristics of ETP-mono-resistant CRE, CRE strains were systematically collected from 102 hospitals across China between 2018 and 2021. A 1:1 randomized matching study was conducted with ETP-mono-resistant strains to meropenem- and/or imipenem-resistant (MEM/IPM-resistant) strains. Antimicrobial susceptibility testing, whole-genome sequencing, carbapenem-hydrolysing activity and the expression of carbapenemase genes were determined. In total, 18.8% of CRE strains were ETP-mono-resistant, with relatively low ertapenem MIC values. ETP-mono-resistant strains exhibited enhanced susceptibility to β-lactams, β-lactam/β-lactamase inhibitor combinations, levofloxacin, fosfomycin, amikacin and polymyxin than MEM/IPM-resistant strains (P < 0.05). Phylogenetic analysis revealed high genetic diversity among ETP-mono-resistant strains. Extended-spectrum β-lactamases (ESBLs) and/or AmpC, as well as porin mutations, were identified as potential major mechanisms mediating ETP-mono-resistance, while the presence of carbapenemases was found to be the key factor distinguishing the carbapenem-resistant phenotypes between the two groups (P < 0.001). Compared with the MEM/IPM-resistant group, limited carbapenemase-producing CRE (CP-CRE) strains in the ETP-mono-resistant group showed a significantly lower prevalence of ESBLs and porin mutations, along with reduced expression of carbapenemase. Remarkably, spot assays combined with modified carbapenem inactivation method indicated that ETP-mono-resistant CP-CRE isolates grew at meropenem concentrations eightfold above their corresponding MIC values, accompanied by rapidly enhanced carbapenem-hydrolysing ability. These findings illustrate that ETP-mono-resistant CRE strains are relatively prevalent and that caution should be exercised when using meropenem alone for treatment. The detection of carbapenemase should be prioritized.
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Affiliation(s)
- Yinping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Huangdu Hu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Ping Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
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Ganjo AR, Balaky STJ, Mawlood AH, Smail SB, Shabila NP. Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection. BMC Microbiol 2024; 24:122. [PMID: 38600509 PMCID: PMC11005145 DOI: 10.1186/s12866-024-03283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is a multidrug resistant opportunistic pathogen that can cause secondary bacterial infections in patients with COVID-19. This study aimed to determine the antimicrobial resistance profile of E. coli as a secondary bacterial infection in patients with COVID-19 and to assess the prevalence and characterization of genes related to efflux pumps and porin. METHODS A total of 50 nonduplicate E. coli isolates were collected as secondary bacterial infections in COVID-19 patients. The isolates were cultured from sputum samples. Confirmation and antibiotic susceptibility testing were conducted by Vitek 2. PCR was used to assess the prevalence of the efflux pump and porin-related genes in the isolates. The phenotypic and genotypic evolution of antibiotic resistance genes related to the efflux pump was evaluated. RESULTS The E. coli isolates demonstrated high resistance to ampicillin (100%), cefixime (62%), cefepime (62%), amoxicillin-clavulanic acid (60%), cefuroxime (60%), and ceftriaxone (58%). The susceptibility of E. coli to ertapenem was greatest (92%), followed by imipenem (88%), meropenem (86%), tigecycline (80%), and levofloxacin (76%). Regarding efflux pump gene combinations, there was a significant association between the acrA gene and increased resistance to levofloxacin, between the acrB gene and decreased resistance to meropenem and increased resistance to levofloxacin, and between the ompF and ompC genes and increased resistance to gentamicin. CONCLUSIONS The antibiotics ertapenem, imipenem, meropenem, tigecycline, and levofloxacin were effective against E. coli in patients with COVID-19. Genes encoding efflux pumps and porins, such as acrA, acrB, and outer membrane porins, were highly distributed among all the isolates. Efflux pump inhibitors could be alternative antibiotics for restoring tetracycline activity in E. coli isolates.
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Affiliation(s)
- Aryan R Ganjo
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Iraq
| | - Salah Tofik Jalal Balaky
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Iraq.
- Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Kurdistan Region, Iraq.
| | - Ahang Hasan Mawlood
- Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Kurdistan Region, Iraq
- Department of Medical Laboratory Technique, College of Medical Technology, AL-Kitab University, Kirkuk, Iraq
| | | | - Nazar P Shabila
- College of Health Sciences, Catholic University in Erbil, Erbil, Kurdistan Region, Iraq
- Department of Community Medicine, College of Medicine, Hawler Medical University, Erbil, Iraq
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3
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Luo XW, Li PL, Zhai YJ, Pan YS, Hu GZ, He DD. Upregulation of outer membrane porin gene ompC contributed to enhancement of azithromycin susceptibility in multidrug-resistant Escherichia coli. Microbiol Spectr 2024; 12:e0391823. [PMID: 38441474 DOI: 10.1128/spectrum.03918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/24/2024] [Indexed: 04/06/2024] Open
Abstract
The outer membrane (OM) in gram-negative bacteria contains proteins that regulate the passive or active uptake of small molecules for growth and cell function, as well as mediate the emergence of antibiotic resistance. This study aims to explore the potential mechanisms for restoring bacteria to azithromycin susceptibility based on transcriptome analysis of bacterial membrane-related genes. Transcriptome sequencing was performed by treating multidrug-resistant Escherichia coli T28R with azithromycin or in combination with colistin and confirmed by reverse transcription-quantitative PCR (RT-qPCR). Azithromycin enzyme-linked immunosorbent assay (ELISA) test, ompC gene overexpression, and molecular docking were utilized to conduct the confirmatory research of the potential mechanisms. We found that colistin combined with azithromycin led to 48 differentially expressed genes, compared to azithromycin alone, such as downregulation of tolA, eptB, lpxP, and opgE and upregulation of ompC gene. Interestingly, the addition of colistin to azithromycin differentially downregulated the mph(A) gene mediating azithromycin resistance, facilitating the intracellular accumulation of azithromycin. Also, overexpression of the ompC elevated azithromycin susceptibility, and colistin contributed to further suppression of the Mph(A) activity in the presence of azithromycin. These findings suggested that colistin firstly enhanced the permeability of bacterial OM, causing intracellular drug accumulation, and then had a repressive effect on the Mph(A) activity along with azithromycin. Our study provides a novel perspective that the improvement of azithromycin susceptibility is related not only to the downregulation of the mph(A) gene and conformational remodeling of the Mph(A) protein but also the upregulation of the membrane porin gene ompC.IMPORTANCEUsually, active efflux via efflux pumps is an important mechanism of antimicrobial resistance, such as the AcrAB-TolC complex and MdtEF. Also, bacterial porins exhibited a substantial fraction of the total number of outer membrane proteins in Enterobacteriaceae, which are involved in mediating the development of the resistance. We found that the upregulation or overexpression of the ompC gene contributed to the enhancement of resistant bacteria to azithromycin susceptibility, probably due to the augment of drug uptakes caused and the opportunity of Mph(A) function suppressed by azithromycin with colistin. Under the combination of colistin and azithromycin treatment, OmpC exhibited an increased selectivity for cationic molecules and played a key role in the restoral of the antibiotic susceptibility. Investigations on the regulation of porin expression that mediated drug resistance would be important in clinical isolates treated with antibiotics.
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Affiliation(s)
- Xing-Wei Luo
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Peng-Liang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ya-Jun Zhai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yu-Shan Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gong-Zheng Hu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dan-Dan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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Pavlenok M, Nair RR, Hendrickson RC, Niederweis M. The C-terminus is essential for the stability of the mycobacterial channel protein MspA. Protein Sci 2024; 33:e4912. [PMID: 38358254 PMCID: PMC10868439 DOI: 10.1002/pro.4912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Outer membrane proteins perform essential functions in uptake and secretion processes in bacteria. MspA is an octameric channel protein in the outer membrane of Mycobacterium smegmatis and is structurally distinct from any other known outer membrane protein. MspA is the founding member of a family with more than 3000 homologs and is one of the most widely used proteins in nanotechnological applications due to its advantageous pore structure and extraordinary stability. While a conserved C-terminal signal sequence is essential for folding and protein assembly in the outer membrane of Gram-negative bacteria, the molecular determinants of these processes are unknown for MspA. In this study, we show that mutation and deletion of methionine 183 in the highly conserved C-terminus of MspA and mutation of the conserved tryptophan 40 lead to a complete loss of protein in heat extracts of M. smegmatis. Swapping these residues partially restores the heat stability of MspA indicating that methionine 183 and tryptophan 40 form a conserved sulfur-π electron interaction, which stabilizes the MspA monomer. Flow cytometry showed that all MspA mutants are surface-accessible demonstrating that oligomerization and membrane integration in M. smegmatis are not affected. Thus, the conserved C-terminus of MspA is essential for its thermal stability, but it is not required for protein assembly in its native membrane, indicating that this process is mediated by a mechanism distinct from that in Gram-negative bacteria. These findings will benefit the rational design of MspA-like pores to tailor their properties in current and future applications.
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Affiliation(s)
- Mikhail Pavlenok
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | | | | | - Michael Niederweis
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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Zhao X, Wang W, Zeng X, Xu R, Yuan B, Yu W, Wang M, Jia R, Chen S, Zhu D, Liu M, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Cheng A. Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. J Biol Chem 2024; 300:105694. [PMID: 38301890 PMCID: PMC10906532 DOI: 10.1016/j.jbc.2024.105694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriocins, which have narrow-spectrum activity and limited adverse effects, are promising alternatives to antibiotics. In this study, we identified klebicin E (KlebE), a small bacteriocin derived from Klebsiella pneumoniae. KlebE exhibited strong efficacy against multidrug-resistant K. pneumoniae isolates and conferred a significant growth advantage to the producing strain during intraspecies competition. A giant unilamellar vesicle leakage assay demonstrated the unique membrane permeabilization effect of KlebE, suggesting that it is a pore-forming toxin. In addition to a C-terminal toxic domain, KlebE also has a disordered N-terminal domain and a globular central domain. Pulldown assays and soft agar overlay experiments revealed the essential role of the outer membrane porin OmpC and the Ton system in KlebE recognition and cytotoxicity. Strong binding between KlebE and both OmpC and TonB was observed. The TonB-box, a crucial component of the toxin-TonB interaction, was identified as the 7-amino acid sequence (E3ETLTVV9) located in the N-terminal region. Further studies showed that a region near the bottom of the central domain of KlebE plays a primary role in recognizing OmpC, with eight residues surrounding this region identified as essential for KlebE toxicity. Finally, based on the discrepancies in OmpC sequences between the KlebE-resistant and sensitive strains, it was found that the 91st residue of OmpC, an aspartic acid residue, is a key determinant of KlebE toxicity. The identification and characterization of this toxin will facilitate the development of bacteriocin-based therapies targeting multidrug-resistant K. pneumoniae infections.
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Affiliation(s)
- Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Wenyu Wang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Zeng
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rong Xu
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Wenyao Yu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
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Dhara L, Tripathi A. Contribution of genetic factors towards cefotaxime and ciprofloxacin resistance development among Extended spectrum beta-lactamase producing-Quinolone resistant pathogenic Enterobacteriaceae. Gene 2024; 893:147921. [PMID: 37884102 DOI: 10.1016/j.gene.2023.147921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
β-lactams and quinolones are widely utilised to treat pathogenic Enterobacterial isolates worldwide. Due to improper use of these antibiotics, both ESBL producing and quinolone resistant (ESBL-QR) pathogenic bacteria have emerged. Nature of contribution of beta-lactamase (bla)/quinolone resistant (QR) genes, efflux pumps (AcrAB-TolC) over-expression and outer membrane proteins (OMPs) /porin loss/reduction and their combinations towards development of this phenotype were explored in this study. Kirby-Bauer disc diffusion method was used for phenotypic characterization of these bacteria and minimum inhibitory concentration of cefotaxime and ciprofloxacin was determined by broth micro dilution assay. Presence of bla, QR, gyrA/B genes was examined by PCR; acrB upregulation by real-time quantitative PCR and porin loss/reduction by SDS-PAGE. Based on antibiogram, phenotypic categorization of 715 non-duplicate clinical isolates was: ESBL+QR+ (n = 265), ESBL+QR- (n = 6), ESBL-QR+ (n = 346) and ESBL-QR-(n = 11). Increased OmpF/K35 and OmpC/K36 reduction, acrB up-regulation, prevalence of bla, QR genes and gyrA/B mutation was observed among the groups in following order: ESBL+QR+> ESBL-QR+> ESBL+QR-> ESBL-QR-. Presence of bla gene alone or combined porin loss and efflux pump upregulation or their combination contributed most for development of a highest level of cefotaxime resistance of ESBL+QR+ isolates. Similarly, combined presence of QR genes, porin loss/reduction, efflux pump upregulation and gyrA/B mutation contributed towards highest ciprofloxacin resistance development of these isolates.
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Affiliation(s)
- Lena Dhara
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata 700073, India
| | - Anusri Tripathi
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata 700073, India.
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Bianchi M, Winterhalter M, Harbig TA, Hörömpöli D, Ghai I, Nieselt K, Brötz-Oesterhelt H, Mayer C, Borisova-Mayer M. Fosfomycin Uptake in Escherichia coli Is Mediated by the Outer-Membrane Porins OmpF, OmpC, and LamB. ACS Infect Dis 2024; 10:127-137. [PMID: 38104323 PMCID: PMC10789261 DOI: 10.1021/acsinfecdis.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
The antibiotic fosfomycin (FOS) is widely recognized for the treatment of lower urinary tract infections with Escherichia coli and has lately gained importance as a therapeutic option to combat multidrug-resistant bacteria. However, resistance to FOS frequently develops through mutations reducing its uptake. Although the inner-membrane transport of FOS has been extensively studied in E. coli, its outer-membrane (OM) transport remains insufficiently understood. While evaluating minimal inhibitory concentrations in OM porin-deficient mutants, we observed that the E. coli ΔompFΔompC strain is four times more resistant to FOS than the wild type and the respective single mutants. Continuous monitoring of FOS-induced lysis of porin-deficient strains additionally highlighted the importance of LamB. The relevance of OmpF, OmpC, and LamB to FOS uptake was confirmed by electrophysiological and transcriptional analysis. Our study gives for the first time in-depth insight into the transport of FOS through the OM in E. coli.
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Affiliation(s)
- Martina Bianchi
- Department
of Organismic Interactions, Interfaculty Institute of Microbiology
and Infection Medicine (IMIT), University
of Tübingen, 72076 Tübingen, Germany
| | - Mathias Winterhalter
- Department
of Life Sciences and Chemistry, Constructor
University, 28759 Bremen, Germany
| | - Theresa Anisja Harbig
- Institute
for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
| | - Daniel Hörömpöli
- Department
of Microbial Bioactive Compounds, IMIT, University of Tübingen, 72076 Tübingen, Germany
| | - Ishan Ghai
- Department
of Life Sciences and Chemistry, Constructor
University, 28759 Bremen, Germany
| | - Kay Nieselt
- Institute
for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- Cluster
of Excellence “Controlling Microbes to Fight Infections”
University of Tübingen, 72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department
of Microbial Bioactive Compounds, IMIT, University of Tübingen, 72076 Tübingen, Germany
- Cluster
of Excellence “Controlling Microbes to Fight Infections”
University of Tübingen, 72076 Tübingen, Germany
| | - Christoph Mayer
- Department
of Organismic Interactions, Interfaculty Institute of Microbiology
and Infection Medicine (IMIT), University
of Tübingen, 72076 Tübingen, Germany
- Cluster
of Excellence “Controlling Microbes to Fight Infections”
University of Tübingen, 72076 Tübingen, Germany
| | - Marina Borisova-Mayer
- Department
of Organismic Interactions, Interfaculty Institute of Microbiology
and Infection Medicine (IMIT), University
of Tübingen, 72076 Tübingen, Germany
- Cluster
of Excellence “Controlling Microbes to Fight Infections”
University of Tübingen, 72076 Tübingen, Germany
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Ortiz-Velez AN, Sukumaran J, Rouzbehani R, Kelley ST. AutoPhy: Automated phylogenetic identification of novel protein subfamilies. PLoS One 2024; 19:e0291801. [PMID: 38206953 PMCID: PMC10783759 DOI: 10.1371/journal.pone.0291801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/06/2023] [Indexed: 01/13/2024] Open
Abstract
Phylogenetic analysis of protein sequences provides a powerful means of identifying novel protein functions and subfamilies, and for identifying and resolving annotation errors. However, automation of functional clustering based on phylogenetic trees has been challenging and most of it is done manually. Clustering phylogenetic trees usually requires the delineation of tree-based thresholds (e.g., distances), leading to an ad hoc problem. We propose a new phylogenetic clustering approach that identifies clusters without using ad hoc distances or other pre-defined values. Our workflow combines uniform manifold approximation and projection (UMAP) with Gaussian mixture models as a k-means like procedure to automatically group sequences into clusters. We then apply a "second pass" clade identification algorithm to resolve non-monophyletic groups. We tested our approach with several well-curated protein families (outer membrane porins, acyltransferase, and nuclear receptors) and showed our automated methods recapitulated known subfamilies. We also applied our methods to a broad range of different protein families from multiple databases, including Pfam, PANTHER, and UniProt, and to alignments of RNA viral genomes. Our results showed that AutoPhy rapidly generated monophyletic clusters (subfamilies) within phylogenetic trees evolving at very different rates both within and among phylogenies. The phylogenetic clusters generated by AutoPhy resolved misannotations and identified new protein functional groups and novel viral strains.
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Affiliation(s)
- Adrian N Ortiz-Velez
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Jeet Sukumaran
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Ryin Rouzbehani
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
| | - Scott T Kelley
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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Seddon C, Frankel G, Beis K. Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae. Acta Crystallogr F Struct Biol Commun 2024; 80:22-27. [PMID: 38206593 PMCID: PMC10833342 DOI: 10.1107/s2053230x23010579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops.
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Affiliation(s)
- Chloe Seddon
- Department of Life Sciences, Imperial College, London, United Kingdom
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Gad Frankel
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College, London, United Kingdom
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
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10
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Yang F, Wang H, Zhao C, Zhang L, Liu X, Park H, Yuan Y, Ye JW, Wu Q, Chen GQ. Metabolic engineering of Halomonas bluephagenesis for production of five carbon molecular chemicals derived from L-lysine. Metab Eng 2024; 81:227-237. [PMID: 38072357 DOI: 10.1016/j.ymben.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/28/2023] [Accepted: 12/01/2023] [Indexed: 12/31/2023]
Abstract
5-Aminovaleric acid (5-AVA), 5-hydroxyvalerate (5HV), copolymer P(3HB-co-5HV) of 3-hydroxybutyrate (3HB) and 5HV were produced from L-lysine as a substrate by recombinant Halomonas bluephagenesis constructed based on codon optimization, deletions of competitive pathway and L-lysine export protein, and three copies of davBA genes encoding L-lysine monooxygenase (DavB) and 5-aminovaleramide amidohydrolase (DavA) inserted into its genome to form H. bluephagenesis YF117ΔgabT1+2, which produced 16.4 g L-1 and 67.4 g L-1 5-AVA in flask cultures and in 7 L bioreactor, respectively. It was able to de novo synthesize 5-AVA from glucose by L-lysine-overproducing H. bluephagenesis TD226. Corn steep liquor was used instead of yeast extract for cost reduction during the 5-AVA production. Using promoter engineering based on Pporin mutant library for downstream genes, H. bluephagenesis YF117 harboring pSEVA341-Pporin42-yqhDEC produced 6 g L-1 5HV in shake flask growth, while H. bluephagenesis YF117 harboring pSEVA341-Pporin42-yqhDEC-Pporin278-phaCRE-abfT synthesized 42 wt% P(3HB-co-4.8 mol% 5HV) under the same condition. Thus, H. bluephagenesis was successfully engineered to produce 5-AVA and 5HV in supernatant and intracellular P(3HB-co-5HV) utilizing L-lysine as the substrate.
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Affiliation(s)
- Fang Yang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, Beijing, 101309, China
| | - Helen Park
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yiping Yuan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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11
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Di Pilato V, Codda G, Niccolai C, Willison E, Wong JLC, Coppo E, Frankel G, Marchese A, Rossolini GM. Functional features of KPC-109, a novel 270-loop KPC-3 mutant mediating resistance to avibactam-based β-lactamase inhibitor combinations and cefiderocol. Int J Antimicrob Agents 2024; 63:107030. [PMID: 37931849 DOI: 10.1016/j.ijantimicag.2023.107030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/02/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
OBJECTIVES To investigate a ceftazidime/avibactam (CZA)-resistant Klebsiella pneumoniae (NE368), isolated from a patient exposed to CZA, expressing a novel K. pneumoniae carbapenemase (KPC)-3 variant (KPC-109). METHODS Antimicrobial susceptibility testing was performed by reference broth microdilution. Whole-genome sequencing (WGS) analysis of NE368 was performed combining a short- and long-reads approach (Illumina and Oxford Nanopore Technologies). Functional characterization of KPC-109 was performed to investigate the impact of KPC-109 production on the β-lactam resistance phenotype of various Escherichia coli and Klebsiella pneumoniae strains, including derivatives of K. pneumoniae with OmpK35 and OmpK36 porin alterations. Horizontal transfer of the KPC-109-encoding plasmid was investigated by conjugation and transformation experiments. RESULTS K. pneumoniae NE368 was isolated from a patient after repeated CZA exposure, and showed resistance to CZA, fluoroquinolones, piperacillin/tazobactam, expanded-spectrum cephalosporins, amikacin, carbapenems and cefiderocol. WGS revealed the presence of a large chimeric plasmid of original structure (pKPN-NE368), encoding a novel 270-loop mutated KPC-3 variant (KPC-109; ins_270_KYNKDD). KPC-109 production mediated resistance/decreased susceptibility to avibactam-based combinations (with ceftazidime, cefepime and aztreonam) and cefiderocol, with a trade-off on carbapenem resistance. However, in the presence of porin alterations commonly encountered in high-risk clonal lineages of K. pneumoniae, KPC-109 was also able to confer clinical-level resistance to carbapenems. Resistance of NE368 to cefiderocol was likely contributed by KPC-109 production acting in concert with a mutated EnvZ sensor kinase. The KPC-109-encoding plasmid did not appear to be conjugative. CONCLUSIONS These findings expand current knowledge about the diversity of emerging KPC enzyme variants with 270-loop alterations that can be encountered in the clinical setting.
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Affiliation(s)
- Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy.
| | - Giulia Codda
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Edward Willison
- Microbiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Joshua L C Wong
- Department of Life Sciences, Imperial College London, London, UK
| | - Erika Coppo
- Microbiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gad Frankel
- Department of Life Sciences, Imperial College London, London, UK
| | - Anna Marchese
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy; Microbiology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
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Hsu PC, Wang YW, Chen BH, Hong YP, Teng RH, Liu PY, Chiou CS. Carbapenem resistance in extensively drug-resistant Salmonella enterica serovar Agona and AmpC β-lactamase-producing S. Infantis. Microbiol Spectr 2023; 11:e0292223. [PMID: 37787563 PMCID: PMC10714929 DOI: 10.1128/spectrum.02922-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Carbapenem resistance arising from the loss of porins is commonly observed in extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase-producing strains of certain Enterobacteriaceae genera, including Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa. However, this resistance mechanism is rarely reported in the Salmonella genus. To address this knowledge gap, our study offers genetic evidence demonstrating that the loss of two specific porins (OmpC_378 and OmpD) is crucial for the development of carbapenem resistance in Salmonella ESBL and AmpC β-lactamase-producing strains. Furthermore, our findings reveal that most Salmonella serovars carry seven porin parathologs, with OmpC_378 and OmpD being the key porins involved in the development of carbapenem resistance in Salmonella strains.
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Affiliation(s)
- Ping-Chun Hsu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - You-Wun Wang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
| | - Bo-Han Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
| | - Yu-Ping Hong
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
| | - Ru-Hsiou Teng
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chien-Shun Chiou
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan
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13
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Shallom SJ, Tettelin H, Chandrasekaran P, Park IK, Agrawal S, Arora K, Sadzewicz L, Milestone AM, Aitken ML, Brown-Elliott BA, Wallace RJ, Sampaio EP, Niederweis M, Olivier KN, Holland SM, Zelazny AM. Evolution of Mycobacterium abscessus in the human lung: Cumulative mutations and genomic rearrangement of porin genes in patient isolates. Virulence 2023; 14:2215602. [PMID: 37221835 PMCID: PMC10243398 DOI: 10.1080/21505594.2023.2215602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/01/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Mycobacterium abscessus subspecies massiliense (M. massiliense) is increasingly recognized as an emerging bacterial pathogen, particularly in cystic fibrosis (CF) patients and CF centres' respiratory outbreaks. We characterized genomic and phenotypic changes in 15 serial isolates from two CF patients (1S and 2B) with chronic pulmonary M. massiliense infection leading to death, as well as four isolates from a CF centre outbreak in which patient 2B was the index case. RESULTS Comparative genomic analysis revealed the mutations affecting growth rate, metabolism, transport, lipids (loss of glycopeptidolipids), antibiotic susceptibility (macrolides and aminoglycosides resistance), and virulence factors. Mutations in 23S rRNA, mmpL4, porin locus and tetR genes occurred in isolates from both CF patients. Interestingly, we identified two different spontaneous mutation events at the mycobacterial porin locus: a fusion of two tandem porin paralogs in patient 1S and a partial deletion of the first porin paralog in patient 2B. These genomic changes correlated with reduced porin protein expression, diminished 14C-glucose uptake, slower bacterial growth rates, and enhanced TNF-α induction in mycobacteria-infected THP-1 human cells. Porin gene complementation of porin mutants partly restored 14C-glucose uptake, growth rate and TNF-α levels to those of intact porin strains. CONCLUSIONS We hypothesize that specific mutations accumulated and maintained over time in M. massiliense, including mutations shared among transmissible strains, collectively lead to more virulent, host adapted lineages in CF patients and other susceptible hosts.
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Affiliation(s)
- Shamira J. Shallom
- Microbiology Service, Department of Laboratory Medicine (DLM), Clinical Center, NIH, Bethesda, MD, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Prabha Chandrasekaran
- Laboratory of Clinical Infectious Diseases (LCID), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - In Kwon Park
- Laboratory of Clinical Infectious Diseases (LCID), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Sonia Agrawal
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kriti Arora
- Laboratory of Clinical Infectious Diseases (LCID), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aaron M. Milestone
- Pediatric Infectious Diseases, Johns Hopkins University, Baltimore, MD, USA
| | - Moira L. Aitken
- Division of Pulmonary and Critical Care Medicine, University of Washington Medical Center, Seattle, WA, USA
| | | | - Richard J. Wallace
- Mycobacteria/Nocardia Laboratory, University of Texas Health Science Center, Tyler, TX, USA
| | - Elizabeth P. Sampaio
- Laboratory of Clinical Infectious Diseases (LCID), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | | | - Kenneth N. Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart Lung and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Steven M. Holland
- Laboratory of Clinical Infectious Diseases (LCID), National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Adrian M. Zelazny
- Microbiology Service, Department of Laboratory Medicine (DLM), Clinical Center, NIH, Bethesda, MD, USA
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14
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Gong G, Chen Q, Luo J, Wang Y, Li X, Zhang F, Zhang Z, Cheng J, Xiong X, Hu R, Zhou Y. Characteristics of a ceftadine/avibatam resistance KPC-33-producing Klebsiella Pneumoniae strain with capsular serotype K19 belonging to ST15. J Glob Antimicrob Resist 2023; 35:159-162. [PMID: 37751846 DOI: 10.1016/j.jgar.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/13/2023] [Accepted: 09/16/2023] [Indexed: 09/28/2023] Open
Abstract
OBJECTIVES The aim of this study was to characterize the blaKPC-33 in a ST15-K19 ceftazidime-avibactam (CAZ-AVI)-resistant Klebsiella pneumoniae strain after the antibiotic CAZ-AVI was approved for use in Wuxi No. 2 People's Hospital, China. METHODS Antimicrobial susceptibility testing was performed by the microdilution broth method. Whole genome sequencing (WGS) was performed using PacBio II and MiSeq sequencers. High-quality reads were assembled using the SOAPdenovo and GapCloser v1.12, and genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Genomic characteristics were analysed by using bioinformatics methods. RESULTS K. pneumoniae strain KPHRJ showed resistance to CAZ-AVI. WGS analysis showed that strain KPHRJ had one 5 536 506 bp chromosome (57.25% G+C content) and one plasmid (133 451 bp, G+C 54.29%). KPHRJ was classified as ST15 and K19 serotype. Resistome analysis showed that KPHRJ carries seven antimicrobial resistance genes (ARGs). WGS analysis and conjugation experiments demonstrated that the blaKPC-33 gene was carried by plasmid pKPHRJ, flanked by two copies of IS26 mobile elements (IS26-ISKpn27-blaKPC-33-ISKpn6-korC-TnAs1-tetR-tetA-Tn3-IS26). Besides these acquired resistance genes, mutations in porin protein-coding genes, such as OmpK36 and OmpK37, which may reduce susceptibility to the CAZ-AVI, were also identified from the genome. CONCLUSION Here, we present the WGS of a CAZ-AVI resistant K. pneumoniae isolate, strain KPHRJ, with capsular serotype K19 and belonging to ST15. CAZ-AVI resistance is likely conferred by a KPC-2 variant, blaKPC-33 and mutations in porin-coding genes. We speculate that the approval of the CAZ-AVI in hospital could contribute to the emergence of these genomic features by providing a selective pressure leading to the emergence of CAZ-AVI resistant bacteria.
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Affiliation(s)
- Guozhong Gong
- Department of Clinical Laboratory, Suining First People's Hospital, Suining, China
| | - Qiao Chen
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Jinjing Luo
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Ying Wang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Xingming Li
- The First People's Hospital of Neijiang, Neijiang, China
| | - Feiyang Zhang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Zhikun Zhang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Jialiang Cheng
- Department of Clinical Laboratory, Suining First People's Hospital, Suining, China
| | - Xia Xiong
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Renjing Hu
- Department of Laboratory Medicine, Jiangnan University Medical Center, Wuxi, China.
| | - Yingshun Zhou
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China.
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15
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Okasha H, Dahroug H, Gouda AE, Shemis MA. A novel antibacterial approach of Cecropin-B peptide loaded on chitosan nanoparticles against MDR Klebsiella pneumoniae isolates. Amino Acids 2023; 55:1965-1980. [PMID: 37966500 PMCID: PMC10724327 DOI: 10.1007/s00726-023-03356-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/28/2023] [Indexed: 11/16/2023]
Abstract
Egypt has witnessed the emergence of multidrug-resistant (MDR) Klebsiella pneumoniae, which has posed a serious healthcare challenge. The proper treatment choice for MDR-KP infections is not well determined which renders the problem more complicated, thus making the control of such infections a serious challenge for healthcare professionals. This study aims to encapsulate the cationic antimicrobial peptide; Cecropin-B (Cec-B), to increase its lifetime, drug targeting, and efficacy and study the antimicrobial effect of free and encapsulated recombinant rCec-B peptide on multidrug-resistant K. pneumoniae (MDR-KP) isolates. Fifty isolates were collected from different clinical departments at Theodore Bilharz Research Institute. Minimal inhibitory concentrations (MICs) of rCec-B against MDR-KP isolates were determined by the broth microdilution test. In addition, encapsulation of rCec-B peptide into chitosan nanoparticles and studying its bactericidal effect against MDR-KP isolates were also performed. The relative expression of efflux pump and porin coding genes (ArcrB, TolC, mtdK, and Ompk35) was detected by quantitative PCR in treated MDR-KP bacterial isolates compared to untreated isolates. Out of 60 clinical MDR isolates, 50 were MDR-KP. 60% of the isolates were XDR while 40% were MDR. rCec-B were bactericidal on 21 isolates, then these isolates were subjected to treatment using free nanocapsule in addition to the encapsulated peptide. Free capsules showed a mild cytotoxic effect on MDR-KP at the highest concentration. MIC of encapsulated rCec-B was higher than the free peptide. The expression level of genes encoding efflux and porin (ArcrB, TolC, mtdK, and Ompk35) was downregulated after treatment with encapsulated rCec-B. These findings indicate that encapsulated rCec-B is a promising candidate with potent antibacterial activities against drug-resistant K. pneumoniae.
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Affiliation(s)
- Hend Okasha
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt.
| | - Heba Dahroug
- Microbiology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Abdullah E Gouda
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Mohamed Abbas Shemis
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt
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16
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Liu B, Gao J, Liu XF, Rao G, Luo J, Han P, Hu W, Zhang Z, Zhao Q, Han L, Jiang Z, Zhou M. Direct prediction of carbapenem resistance in Pseudomonas aeruginosa by whole genome sequencing and metagenomic sequencing. J Clin Microbiol 2023; 61:e0061723. [PMID: 37823665 PMCID: PMC10662344 DOI: 10.1128/jcm.00617-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/17/2023] [Indexed: 10/13/2023] Open
Abstract
Carbapenem resistance is a major concern in the management of antibiotic-resistant Pseudomonas aeruginosa infections. The direct prediction of carbapenem-resistant phenotype from genotype in P. aeruginosa isolates and clinical samples would promote timely antibiotic therapy. The complex carbapenem resistance mechanism and the high prevalence of variant-driven carbapenem resistance in P. aeruginosa make it challenging to predict the carbapenem-resistant phenotype through the genotype. In this study, using whole genome sequencing (WGS) data of 1,622 P. aeruginosa isolates followed by machine learning, we screened 16 and 31 key gene features associated with imipenem (IPM) and meropenem (MEM) resistance in P. aeruginosa, including oprD(HIGH), and constructed the resistance prediction models. The areas under the curves of the IPM and MEM resistance prediction models were 0.906 and 0.925, respectively. For the direct prediction of carbapenem resistance in P. aeruginosa from clinical samples by the key gene features selected and prediction models constructed, 72 P. aeruginosa-positive sputum samples were collected and sequenced by metagenomic sequencing (MGS) based on next-generation sequencing (NGS) or Oxford Nanopore Technology (ONT). The prediction applicability of MGS based on NGS outperformed that of MGS based on ONT. In 72 P. aeruginosa-positive sputum samples, 65.0% (26/40) of IPM-insensitive and 63.2% (24/38) of MEM-insensitive P. aeruginosa were directly predicted by NGS-based MGS with positive predictive values of 0.897 and 0.889, respectively. By the direct detection of the key gene features associated with carbapenem resistance of P. aeruginosa, the carbapenem resistance of P. aeruginosa could be directly predicted from cultured isolates by WGS or from clinical samples by NGS-based MGS, which could assist the timely treatment and surveillance of carbapenem-resistant P. aeruginosa.
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Affiliation(s)
- Bing Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Jianpeng Gao
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Xue Fei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Guanhua Rao
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Jiajie Luo
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Weiting Hu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Ze Zhang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Qianqian Zhao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology,, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Jiang
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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17
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Dhar R, Bowman AM, Hatungimana B, Sg Slusky J. Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. J Mol Biol 2023; 435:168292. [PMID: 37769963 DOI: 10.1016/j.jmb.2023.168292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
In protein evolution, diversification is generally driven by genetic duplication. The hallmarks of this mechanism are visible in the repeating topology of various proteins. In outer membrane β-barrels, duplication is visible with β-hairpins as the repeating unit of the barrel. In contrast to the overall use of duplication in diversification, a computational study hypothesized evolutionary mechanisms other than hairpin duplications leading to increases in the number of strands in outer membrane β-barrels. Specifically, the topology of some 16- and 18-stranded β-barrels appear to have evolved through a loop to β-hairpin transition. Here we test this novel evolutionary mechanism by creating a chimeric protein from an 18-stranded β-barrel and an evolutionarily related 16-stranded β-barrel. The chimeric combination of the two was created by replacing loop L3 of the 16-stranded barrel with the sequentially matched transmembrane β-hairpin region of the 18-stranded barrel. We find the resulting chimeric protein is stable and has characteristics of increased strand number. This study provides the first experimental evidence supporting the evolution through a loop to β-hairpin transition.
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Affiliation(s)
- Rik Dhar
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA. https://twitter.com/Rik_Skywalker
| | - Alexander M Bowman
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Brunojoel Hatungimana
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA
| | - Joanna Sg Slusky
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, USA; Computational Biology Program, The University of Kansas, Lawrence, KS 66047, USA.
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18
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Nazari M, Ahmadi H, Hosseinzadeh S, Sahebkar A, Khademi F. Imipenem resistance associated with amino acid alterations of the OprD porin in Pseudomonas aeruginosa clinical isolates. Acta Microbiol Immunol Hung 2023; 70:206-212. [PMID: 37342895 DOI: 10.1556/030.2023.02060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
Globally, the spread of carbapenem-resistant strains has limited treatment options for multidrug-resistant (MDR) Pseudomonas aeruginosa infections. This study aimed to determine the role of point mutations as well as the expression level of the oprD gene in the emergence of imipenem-resistant P. aeruginosa strains isolated from patients referred to Ardabil hospitals. A total of 48 imipenem-resistant clinical isolates of P. aeruginosa collected between June 2019 and January 2022 were used in this study. Detection of the oprD gene and its amino acid alterations was performed using the polymerase chain reaction (PCR) and DNA sequencing techniques. The expression level of the oprD gene in imipenem-resistant strains was determined using the real-time quantitative reverse transcription PCR (RT-PCR) method. All imipenem-resistant P. aeruginosa strains were positive for the oprD gene based on the PCR results, and also five selected isolates indicated one or more amino acid alterations. Detected amino acid alterations in the OprD porin were Ala210Ile, Gln202Glu, Ala189Val, Ala186Pro, Leu170Phe, Leu127Val, Thr115Lys, and Ser103Thr. Based on the RT-PCR results, the oprD gene was downregulated in 79.1% of imipenem-resistant P. aeruginosa strains. However, 20.9% of strains showed overexpression of the oprD gene. Probably, resistance to imipenem in these strains is associated with the presence of carbapenemases, AmpC cephalosporinase, or efflux pumps. Owing to the high prevalence of imipenem-resistant P. aeruginosa strains due to various resistance mechanisms in Ardabil hospitals, the implementation of surveillance programs to reduce the spread of these resistant microorganisms along with rational selection and prescription of antibiotics is recommended.
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Affiliation(s)
- Maryam Nazari
- 1Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hadi Ahmadi
- 1Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Shahnaz Hosseinzadeh
- 1Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Amirhossein Sahebkar
- 2Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- 3Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- 4Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzad Khademi
- 1Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
- 5Arthropod-Borne Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
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19
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Zhurilov PA, Andriyanov PA, Tutrina AI, Razheva IV, Liskova EA, Gladkova NA, Kashina DD, Yashin IV, Blokhin AA. Characterization and comparative analysis of the Escherichia marmotae M-12 isolate from bank vole (Myodes glareolus). Sci Rep 2023; 13:13949. [PMID: 37626115 PMCID: PMC10457355 DOI: 10.1038/s41598-023-41223-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
The Escherichia marmotae is a bacterium of the Enterobacterales order, which was first isolated from the Himalayan marmot (Marmota himalayana). Recently E. marmotae has been shown to cause severe infections in humans. Wild animals were suggested to be a natural reservoir of this bacterium. The present study describes the first case of E. marmotae isolation from an apparently healthy wild bank vole (Myodes glareolus). Phenotype, as well as genotype-based techniques, were applied to characterize E. marmotae M-12 isolate. E. marmotae M-12 had the capsule-positive phenotype, high adhesion to human erythrocytes and HEp-2 cells as well as a low invasion into HEp-2 cells. E. marmotae M-12 was avirulent in mice. The phylogenomic analyses of E. marmotae showed dispersed phylogenetic structure among isolates of different origins. Virulome analysis of M-12 isolate revealed the presence of the following factors: siderophores, heme uptake systems, capsule synthesis, curli and type I fimbriae, flagella proteins, OmpA porin, etc. Comparative virulome analysis among available E. marmotae genomes revealed the presence of capsule K1 genes mostly in pathogenic isolates and OmpA porin presence among all strains. We assume that the K1 capsule and OmpA porin play a key role in the virulence of E. marmotae. Pathogenesis of the latter might be similar to extraintestinal pathogenic E. coli.
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Affiliation(s)
- Pavel A Zhurilov
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia.
| | - Pavel A Andriyanov
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Anastasia I Tutrina
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Irina V Razheva
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Elena A Liskova
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Nadezda A Gladkova
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Daria D Kashina
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Ivan V Yashin
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
| | - Andrey A Blokhin
- Federal Research Center for Virology and Microbiology, Branch in Nizhny Novgorod, 603950, Nizhny Novgorod, Russia
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20
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Dunstan RA, Bamert RS, Tan KS, Imbulgoda U, Barlow CK, Taiaroa G, Pickard DJ, Schittenhelm RB, Dougan G, Short FL, Lithgow T. Epitopes in the capsular polysaccharide and the porin OmpK36 receptors are required for bacteriophage infection of Klebsiella pneumoniae. Cell Rep 2023; 42:112551. [PMID: 37224021 DOI: 10.1016/j.celrep.2023.112551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
To kill bacteria, bacteriophages (phages) must first bind to a receptor, triggering the release of the phage DNA into the bacterial cell. Many bacteria secrete polysaccharides that had been thought to shield bacterial cells from phage attack. We use a comprehensive genetic screen to distinguish that the capsule is not a shield but is instead a primary receptor enabling phage predation. Screening of a transposon library to select phage-resistant Klebsiella shows that the first receptor-binding event docks to saccharide epitopes in the capsule. We discover a second step of receptor binding, dictated by specific epitopes in an outer membrane protein. This additional and necessary event precedes phage DNA release to establish a productive infection. That such discrete epitopes dictate two essential binding events for phages has profound implications for understanding the evolution of phage resistance and what dictates host range, two issues critically important to translating knowledge of phage biology into phage therapies.
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Affiliation(s)
- Rhys A Dunstan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Rebecca S Bamert
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Kher Shing Tan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Uvini Imbulgoda
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Christopher K Barlow
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Clayton, VIC, Australia
| | - Derek J Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesca L Short
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
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21
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Moon SH, Huang E. Cefiderocol Resistance in Klebsiella pneumoniae Is Linked to SHV Extended-Spectrum β-Lactamase Activities and Functional Loss of the Outer Membrane Porin OmpK35. Microbiol Spectr 2023; 11:e0349622. [PMID: 37097174 PMCID: PMC10269512 DOI: 10.1128/spectrum.03496-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
Klebsiella pneumoniae AR 0047 from the CDC and FDA Antibiotic Resistance Isolate Bank is resistant to cefiderocol, a siderophore-conjugated cephalosporin. Genomics analysis and genetic complementation revealed that a frameshift mutation in ompK35 contributed to cefiderocol resistance. Heterologous expression of blaSHV-5 or blaSHV-12 in Escherichia coli increased the host resistance to cefiderocol. Moreover, avibactam, a β-lactamase inhibitor, enhanced cefiderocol activity against the resistant strain. Therefore, cefiderocol resistance is linked to SHV and the loss of ompK35. IMPORTANCE Understanding cefiderocol resistance mechanisms is essential for providing solutions to treat infections and to prevent resistance development. Cefiderocol resistance in Klebsiella pneumoniae AR 0047 is linked to SHV β-lactamase activities and functional loss of outer membrane porin. The cefiderocol-avibactam combination represents an opportunity to increase potency against cefiderocol-resistant pathogens.
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Affiliation(s)
- Sun Hee Moon
- Department of Environmental Health Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - En Huang
- Department of Environmental Health Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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22
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Sass AM, Coenye T. The Small RNA NcS25 Regulates Biological Amine-Transporting Outer Membrane Porin BCAL3473 in Burkholderia cenocepacia. mSphere 2023; 8:e0008323. [PMID: 36971554 PMCID: PMC10117139 DOI: 10.1128/msphere.00083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Regulation of porin expression in bacteria is complex and often involves small-RNA regulators. Several small-RNA regulators have been described for Burkholderia cenocepacia, and this study aimed to characterize the biological role of the conserved small RNA NcS25 and its cognate target, outer membrane protein BCAL3473. The B. cenocepacia genome carries a large number of genes encoding porins with yet-uncharacterized functions. Expression of the porin BCAL3473 is strongly repressed by NcS25 and activated by other factors, such as a LysR-type regulator and nitrogen-depleted growth conditions. The porin is involved in transport of arginine, tyrosine, tyramine, and putrescine across the outer membrane. Porin BCAL3473, with NcS25 as a major regulator, plays an important role in the nitrogen metabolism of B. cenocepacia. IMPORTANCE Burkholderia cenocepacia is a Gram-negative bacterium which causes infections in immunocompromised individuals and in people with cystic fibrosis. A low outer membrane permeability is one of the factors giving it a high level of innate resistance to antibiotics. Porins provide selective permeability for nutrients, and antibiotics can also traverse the outer membrane by this means. Knowing the properties and specificities of porin channels is therefore important for understanding resistance mechanisms and for developing new antibiotics and could help in overcoming permeability issues in antibiotic treatment.
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Affiliation(s)
- Andrea M. Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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23
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Grant TA, López-Pérez M, Haro-Moreno JM, Almagro-Moreno S. Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance. PLoS Genet 2023; 19:e1010490. [PMID: 36972246 PMCID: PMC10079234 DOI: 10.1371/journal.pgen.1010490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 04/06/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Antimicrobial resistance (AMR) remains a major threat to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here, we developed a framework that exploits genetic diversity from environmental bacterial populations to decode emergent phenotypes such as AMR. OmpU is a porin that can make up to 60% of the outer membrane of Vibrio cholerae, the cholera pathogen. This porin is directly associated with the emergence of toxigenic clades and confers resistance to numerous host antimicrobials. In this study, we examined naturally occurring allelic variants of OmpU in environmental V. cholerae and established associations that connected genotypic variation with phenotypic outcome. We covered the landscape of gene variability and found that the porin forms two major phylogenetic clusters with striking genetic diversity. We generated 14 isogenic mutant strains, each encoding a unique ompU allele, and found that divergent genotypes lead to convergent antimicrobial resistance profiles. We identified and characterized functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Specifically, we identified four conserved domains that are linked with resistance to bile and host-derived antimicrobial peptides. Mutant strains for these domains exhibit differential susceptibility patterns to these and other antimicrobials. Interestingly, a mutant strain in which we exchanged the four domains of the clinical allele for those of a sensitive strain exhibits a resistance profile closer to a porin deletion mutant. Finally, using phenotypic microarrays, we uncovered novel functions of OmpU and their connection with allelic variability. Our findings highlight the suitability of our approach towards dissecting the specific protein domains associated with the emergence of AMR and can be naturally extended to other bacterial pathogens and biological processes.
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Affiliation(s)
- Trudy-Ann Grant
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Mario López-Pérez
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Jose Manuel Haro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
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24
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Onishi R, Shigemura K, Osawa K, Yang YM, Maeda K, Tanimoto H, Kado M, Fang SB, Fujisawa M. Molecular characteristics and genetic analysis of the genes related to carbapenemase, efflux pump, and outer membrane proteins in carbapenem-resistant Klebsiella pneumoniae. Lett Appl Microbiol 2023; 76:6955820. [PMID: 36763780 DOI: 10.1093/lambio/ovac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/29/2022] [Accepted: 12/19/2022] [Indexed: 02/12/2023]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a life-threatening pathogen that has not been fully investigated on a molecular basis. Therefore, the molecular mechanisms of carbapenem resistance in CRKP collected from medical institutions in Hyogo Prefecture has been analyzed. Antimicrobial susceptibilities and the presence of carbapenemase along with epidemiological analyzes using multilocus sequence typing (MLST) have been investigated. The relative expression of efflux pump genes and mutations of ompK35 and ompK36, encoding the outer membrane porin, were also assessed for their relationship with carbapenem resistance. Most of the collected 22 CRKP isolates were non-susceptible to imipenem (68.2%), meropenem (90.9%), and ertapenem (81.8%), but all 22 strains were susceptible to colistin. Twelve strains (54.5%) were detected for carbapenemase genes such as blaIMP-6. Sequence type 37 was detected by MLST in 10 strains (45.5%). Non-carbapenemase-producing strains had high resistance rates for three carbapenems, and the main cause of resistance was ompK35 mutation. In conclusion, the main cause of resistance was imipenemase metallo-β-lactamase (IMP-6) production in carbapenemase-producing strains, and ompK35 mutation in non-carbapenemase-producing strains. Susceptibility to carbapenem did not differ in CRKP regardless of carbapenemase production, except for imipenem susceptibility. This result contributes to a more insightful understanding of the mechanisms of CRKP in Japan.
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Affiliation(s)
- Reo Onishi
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan
| | - Katsumi Shigemura
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Kayo Osawa
- Department of Medical Technology, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe 653-0838, Japan
| | - Young-Min Yang
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Koki Maeda
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Hiroshi Tanimoto
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan
| | - Mitsuki Kado
- Department of Public Health, Division of Infectious Diseases, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe 654-0142, Japan
| | - Shiuh-Bin Fang
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, Taipei Medical University, 291 Jhong Jheng Road, Jhong Ho District, New Taipei City 23561, Taiwan
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, 250 Wu Hsing Street, Hsin Yi District, Taipei 11031, Taiwan
| | - Masato Fujisawa
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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25
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Mun W, Upatissa S, Lim S, Dwidar M, Mitchell RJ. Outer Membrane Porin F in E. coli Is Critical for Effective Predation by Bdellovibrio. Microbiol Spectr 2022; 10:e0309422. [PMID: 36445149 PMCID: PMC9769668 DOI: 10.1128/spectrum.03094-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
Bdellovibrio and like organisms (BALOs) are a unique bacterial group that live by predating on other bacteria, consuming them from within to grow and replicate before the progeny come out to complete the life cycle. The mechanisms by which these predators recognize their prey and differentiate them from nonprey bacteria, however, are still not clear. Through genetic knockout and complementation studies in different Escherichia coli strains, we found that Bdellovibrio bacteriovorus strain 109J recognizes outer membrane porin F (OmpF) on the E. coli surface and that the activity of the E. coli EnvZ-OmpR regulatory system significantly impacts predation kinetics. OmpF is not the only signal by which BALOs recognize their prey, however, as B. bacteriovorus could eventually predate on the E. coli ΔompF mutant after prolonged incubation. Furthermore, recognizing OmpF as a prey surface structure was dependent on the prey strain, as knocking out OmpF protein homologues in other prey species, including Escherichia fergusonii, Klebsiella pneumoniae, and Salmonella enterica, did not always reduce the predation rate. Consequently, although OmpF was found to be an important surface component used by Bdellovibrio to efficiently recognize and attack E. coli, future work is needed to determine what other prey surface structures are recognized by these predators. IMPORTANCE Bdellovibrio bacteriovorus and like organisms (BALOs) are Gram-negative predatory bacteria that attack other Gram-negative bacteria by penetrating their periplasm and consuming them from within to obtain the nutrients necessary for the predator's growth and replication. How these predators recognize their prey, however, has remained a mystery. Here, we show that the outer membrane porin F (OmpF) in E. coli is recognized by B. bacteriovorus strain 109J and that the loss of this protein leads to severely delayed predation. However, predation of several other prey species was not dependent on the recognition of this protein or its homologues, indicating that there are other structures recognized by the predators on the prey surface that are yet to be discovered.
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Affiliation(s)
- Wonsik Mun
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sumudu Upatissa
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sungbin Lim
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Mohammed Dwidar
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Robert J. Mitchell
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
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26
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Cameron DR, Pitton M, Oberhaensli S, Schlegel K, Prod’hom G, Blanc DS, Jakob SM, Que YA. Parallel Evolution of Pseudomonas aeruginosa during a Prolonged ICU-Infection Outbreak. Microbiol Spectr 2022; 10:e0274322. [PMID: 36342287 PMCID: PMC9769503 DOI: 10.1128/spectrum.02743-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Most knowledge about Pseudomonas aeruginosa pathoadaptation is derived from studies on airway colonization in cystic fibrosis; little is known about adaptation in acute settings. P. aeruginosa frequently affects burned patients and the burn wound niche has distinct properties that likely influence pathoadaptation. This study aimed to genetically and phenotypically characterize P. aeruginosa isolates collected during an outbreak of infection in a burn intensive care unit (ICU). Sequencing reads from 58 isolates of ST1076 P. aeruginosa taken from 23 patients were independently mapped to a complete reference genome for the lineage (H25338); genetic differences were identified and were used to define the population structure. Comparative genomic analysis at single-nucleotide resolution identified pathoadaptive genes that evolved multiple, independent mutations. Three key phenotypic assays (growth performance, motility, carbapenem resistance) were performed to complement the genetic analysis for 47 unique isolates. Population structure for the ST1076 lineage revealed 11 evolutionary sublineages. Fifteen pathoadaptive genes evolved mutations in at least two sublineages. The most prominent functional classes affected were transcription/two-component regulatory systems, and chemotaxis/motility and attachment. The most frequently mutated gene was oprD, which codes for outer membrane porin involved in uptake of carbapenems. Reduced growth performance and motility were found to be adaptive phenotypic traits, as was high level of carbapenem resistance, which correlated with higher carbapenem consumption during the outbreak. Multiple prominent linages evolved each of the three traits in parallel providing evidence that they afford a fitness advantage for P. aeruginosa in the context of human burn infection. IMPORTANCE Pseudomonas aeruginosa is a Gram-negative pathogen causing infections in acutely burned patients. The precise mechanisms required for the establishment of infection in the burn setting, and adaptive traits underpinning prolonged outbreaks are not known. We have assessed genotypic data from 58 independent P. aeruginosa isolates taken from a single lineage that was responsible for an outbreak of infection in a burn ICU that lasted for almost 2.5 years and affected 23 patients. We identified a core set of 15 genes that we predict to control pathoadaptive traits in the burn infection based on the frequency with which independent mutations evolved. We combined the genotypic data with phenotypic data (growth performance, motility, antibiotic resistance) and clinical data (antibiotic consumption) to identify adaptive phenotypes that emerged in parallel. High-level carbapenem resistance evolved rapidly, and frequently, in response to high clinical demand for this antibiotic class during the outbreak.
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Affiliation(s)
- David R. Cameron
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Melissa Pitton
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern, Switzerland
| | - Simone Oberhaensli
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Katja Schlegel
- Institute of Psychology, University of Bern, Bern, Switzerland
| | - Guy Prod’hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S. Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stephan M. Jakob
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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27
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Saïdi F, Mahanta U, Panda A, Kezzo AA, Jolivet NY, Bitazar R, John G, Martinez M, Mellouk A, Calmettes C, Chang YW, Sharma G, Islam ST. Bacterial Outer Membrane Polysaccharide Export (OPX) Proteins Occupy Three Structural Classes with Selective β-Barrel Porin Requirements for Polymer Secretion. Microbiol Spectr 2022; 10:e0129022. [PMID: 36200915 PMCID: PMC9603273 DOI: 10.1128/spectrum.01290-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/08/2022] [Indexed: 12/30/2022] Open
Abstract
Secretion of high-molecular-weight polysaccharides across the bacterial envelope is ubiquitous, as it enhances prokaryotic survival in (a)biotic settings. Such polymers are often assembled by Wzx/Wzy- or ABC transporter-dependent schemes implicating outer membrane (OM) polysaccharide export (OPX) proteins in cell-surface polymer translocation. In the social predatory bacterium Myxococcus xanthus, the exopolysaccharide (EPS) pathway WzaX, major spore coat (MASC) pathway WzaS, and biosurfactant polysaccharide (BPS) pathway WzaB were herein found to be truncated OPX homologues of Escherichia coli Wza lacking OM-spanning α-helices. Comparative genomics across all bacteria (>91,000 OPX proteins identified and analyzed), complemented with cryo-electron tomography cell-envelope analyses, revealed such "truncated" WzaX/S/B architecture to be the most common among three defined OPX-protein structural classes independent of periplasm thickness. Fold recognition and deep learning revealed the conserved M. xanthus proteins MXAN_7418/3226/1916 (encoded beside wzaX/S/B, respectively) to be integral OM β-barrels, with structural homology to the poly-N-acetyl-d-glucosamine synthase-dependent pathway porin PgaA. Such bacterial porins were identified near numerous genes for all three OPX protein classes. Interior MXAN_7418/3226/1916 β-barrel electrostatics were found to match properties of their associated polymers. With MXAN_3226 essential for MASC export, and MXAN_7418 herein shown to mediate EPS translocation, we have designated this new secretion machinery component "Wzp" (i.e., Wz porin), with the final step of M. xanthus EPS/MASC/BPS secretion across the OM now proposed to be mediated by WzpX/S/B (i.e., MXAN_7418/3226/1916). Importantly, these data support a novel and widespread secretion paradigm for polysaccharide biosynthesis pathways in which those containing OPX components that cannot span the OM instead utilize β-barrel porins to mediate polysaccharide transport across the OM. IMPORTANCE Diverse bacteria assemble and secrete polysaccharides that alter their physiologies through modulation of motility, biofilm formation, and host immune system evasion. Most such pathways require outer membrane (OM) polysaccharide export (OPX) proteins for sugar-polymer transport to the cell surface. In the prototypic Escherichia coli Group-1-capsule biosynthesis system, eight copies of this canonical OPX protein cross the OM with an α-helix, forming a polysaccharide-export pore. Herein, we instead reveal that most OPX proteins across all bacteria lack this α-helix, raising questions as to the manner by which most secreted polysaccharides actually exit cells. In the model developmental bacterium Myxococcus xanthus, we show this process to depend on OPX-coupled OM-spanning β-barrel porins, with similar porins encoded near numerous OPX genes in diverse bacteria. Knowledge of the terminal polysaccharide secretion step will enable development of antimicrobial compounds targeted to blocking polymer export from outside the cell, thus bypassing any requirements for antimicrobial compound uptake by the cell.
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Affiliation(s)
- Fares Saïdi
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Utkarsha Mahanta
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Adyasha Panda
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Ahmad A. Kezzo
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Nicolas Y. Jolivet
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Razieh Bitazar
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Gavin John
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abdelkader Mellouk
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Charles Calmettes
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Salim T. Islam
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
- PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
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Curtis MW, Fierros CH, Hahn BL, Surdel MC, Kessler J, Anderson PN, Vandewalle-Capo M, Bonde M, Zhu J, Bergström S, Coburn J. Identification of amino acid domains of Borrelia burgdorferi P66 that are surface exposed and important for localization, oligomerization, and porin function of the protein. Front Cell Infect Microbiol 2022; 12:991689. [PMID: 36211976 PMCID: PMC9539438 DOI: 10.3389/fcimb.2022.991689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/31/2022] [Indexed: 12/01/2022] Open
Abstract
P66, a bifunctional integral outer membrane protein, is necessary for Borrelia burgdorferi to establish initial infection and to disseminate in mice. The integrin binding function of P66 facilitates extravasation and dissemination, but the role of its porin function during murine infection has not been investigated. A limitation to studying P66 porin function during mammalian infection has been the lack of structural information for P66. In this study, we experimentally characterized specific domains of P66 with regard to structure and function. First, we aligned the amino acid sequences of P66 from Lyme disease-causing Borrelia and relapsing fever-causing Borrelia to identify conserved and unique domains between these disease-causing clades. Then, we examined whether specific domains of P66 are exposed on the surface of the bacteria by introducing c-Myc epitope tags into each domain of interest. The c-Myc epitope tag inserted C-terminally to E33 (highly conserved domain), to T187 (integrin binding region domain and a non-conserved domain), and to E334 (non-conserved domain) were all detected on the surface of Borrelia burgdorferi. The c-Myc epitope tag inserted C-terminally to E33 and D303 in conserved domains disrupted P66 oligomerization and porin function. In a murine model of infection, the E33 and D303 mutants exhibited decreased infectivity and dissemination. Taken together, these results suggest the importance of these conserved domains, and potentially P66 porin function, in vivo.
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Affiliation(s)
- Michael W. Curtis
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Christa H. Fierros
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Beth L. Hahn
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Matthew C. Surdel
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Julie Kessler
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Phillip N. Anderson
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Marine Vandewalle-Capo
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Mari Bonde
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jieqing Zhu
- Blood Research Institute, Versiti, Milwaukee, WI, United States
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Sven Bergström
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Jenifer Coburn
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
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29
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García P, Brito B, Alcalde-Rico M, Munita JM, Martínez JRW, Olivares-Pacheco J, Quiroz V, Wozniak A. Acquisition of resistance to ceftazidime-avibactam during infection treatment in Pseudomonas aeruginosa through D179Y mutation in one of two blaKPC-2 gene copies without losing carbapenem resistance. Front Cell Infect Microbiol 2022; 12:981792. [PMID: 36118031 PMCID: PMC9478442 DOI: 10.3389/fcimb.2022.981792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Ceftazidime/Avibactam (CAZ/AVI) is frequently used to treat KPC-producing Pseudomonas aeruginosa (KPC-PA) and Enterobacterales. CAZ/AVI resistance is driven by several mechanisms. In P. aeruginosa this mainly occurs through alteration of AmpC, porins, and/or efflux pump overexpression, whereas in Enterobacterales it frequently occurs through D179Y substitution in the active site of KPC enzyme. This aminoacid change abolishes AVI binding to the KPC active site, hence inhibition is impaired. However, this substitution also decreases KPC-mediated resistance to carbapenems (“see-saw” effect). The goal of this work was to characterize the in vivo acquisition of CAZ/AVI resistance through D179Y substitution in a KPC-PA isolated from a hospitalized patient after CAZ/AVI treatment. Two KPC-PA isolates were obtained. The first isolate, PA-1, was obtained before CAZ/AVI treatment and was susceptible to CAZ/AVI. The second isolate, PA-2, was obtained after CAZ/AVI treatment and exhibited high-level CAZ/AVI resistance. Characterization of isolates PA-1 and PA-2 was performed through short and long-read whole genome sequencing analysis. The hybrid assembly showed that PA-1 and PA-2A had a single plasmid of 54,030 bp, named pPA-1 and pPA-2 respectively. Each plasmid harbored two copies of the blaKPC-containing Tn4401b transposon. However, while pPA-1 carried two copies of blaKPC-2, pPA-2 had one copy of blaKPC-2 and one copy of blaKPC-33, the allele with the D179Y substitution. Interestingly, isolate PA-2 did not exhibit the “see-saw” effect. The blaKPC-33 allele was detected only through hybrid assembly using a long-read-first approach. The present work describes a KPC-PA isolate harboring a plasmid-borne CAZ/AVI resistance mechanism based on two copies of blaKPC-2-Tn4401b and D179Y mutation in one of them, that is not associated with loss of resistance to carbapenems. These findings highlight the usefulness of a fine-tuned combined analysis of short and long-read data to detect similar emerging resistance mechanisms.
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Affiliation(s)
- Patricia García
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Bárbara Brito
- Australian Institute for Microbiology & Infection, Faculty of Science, University of Technology, Sydney, Australia
| | - Manuel Alcalde-Rico
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - José M. Munita
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Jose R. W. Martínez
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Valeria Quiroz
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Aniela Wozniak
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
- *Correspondence: Aniela Wozniak, ;
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30
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Wang Y, Zhang S, Jia W, Fan P, Wang L, Li X, Chen J, Cao Z, Du X, Liu Y, Wang K, Hu C, Zhang J, Hu J, Zhang P, Chen HY, Huang S. Identification of nucleoside monophosphates and their epigenetic modifications using an engineered nanopore. Nat Nanotechnol 2022; 17:976-983. [PMID: 35851382 DOI: 10.1038/s41565-022-01169-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/01/2022] [Indexed: 05/25/2023]
Abstract
RNA modifications play critical roles in the regulation of various biological processes and are associated with many human diseases. Direct identification of RNA modifications by sequencing remains challenging, however. Nanopore sequencing is promising, but the current strategy is complicated by sequence decoding. Sequential nanopore identification of enzymatically cleaved nucleoside monophosphates may simultaneously provide accurate sequence and modification information. Here we show a phenylboronic acid-modified hetero-octameric Mycobacterium smegmatis porin A nanopore, with which direct distinguishing between monophosphates of canonical nucleosides, 5-methylcytidine, N6-methyladenosine, N7-methylguanosine, N1-methyladenosine, inosine, pseudouridine and dihydrouridine was achieved. A custom machine learning algorithm, which reports an accuracy of 0.996, was also applied to the quantitative analysis of modifications in microRNA and natural transfer RNA. It is generally suitable for sensing of a variety of other nucleoside or nucleotide derivatives and may bring new insights to epigenetic RNA sequencing.
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jialu Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Chengzhen Hu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jun Hu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
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31
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Solov'eva TF, Bakholdina SI, Khomenko VA, Sidorin EV, Kim NY, Novikova OD, Shnyrov VL, Stenkova AM, Eremeev VI, Bystritskaya EP, Isaeva MP. Expression of membrane beta-barrel protein in E. coli at low temperatures: Structure of Yersinia pseudotuberculosis OmpF porin inclusion bodies. Biochim Biophys Acta Biomembr 2022; 1864:183971. [PMID: 35643329 DOI: 10.1016/j.bbamem.2022.183971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The recombinant OmpF porin of Yersinia pseudotuberculosis as a model of transmembrane protein of the β-barrel structural family was used to study low growth temperature effect on the structure of the produced inclusion bodies (IBs). This porin showed a very low expression level in E. coli at a growth temperature below optimal 37 °C. The introduction of a N-terminal hexahistidine tag into the mature porin molecule significantly increased the biosynthesis of the protein at low cultivation temperatures. The recombinant His-tagged porin (rOmpF-His) was expressed in E. coli at 30 and 18 °C as inclusion bodies (IB-30 and IB-18). The properties and structural organization of IBs, as well as the structure of rOmpF-His solubilized from the IBs with urea and SDS, were studied using turbidimetry, electron microscopy, dynamic light scattering, optical spectroscopy, and amyloid-specific dyes. IB-18, in comparison with IB-30, has a higher solubility in denaturants, suggesting a difference between IBs in the conformation of the associated polypeptide chains. The spectroscopic analysis revealed that rOmpF-His IBs have a high content of secondary structure with a tertiary-structure elements, including a native-like conformation, the proportion of which in IB-18 is higher than in IB-30. Solubilization of the porin from IBs is accompanied by a modification of its secondary structure. The studied IBs also contain amyloid-like structures. The results obtained in this study expand our knowledge of the structural organization of IBs formed by proteins of different structural classes and also have a contribution into the new approaches development of producing functionally active recombinant membrane proteins.
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Affiliation(s)
- Tamara F Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Svetlana I Bakholdina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia.
| | - Valentina A Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Evgeniy V Sidorin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Natalya Yu Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Olga D Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Valery L Shnyrov
- Departamento de Bioquimica y Biologia Molecular, Universidad de Salamanca, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Anna M Stenkova
- Far Eastern Federal University School of Biomedicine, Russky Island Ajax Bay 10, 690922 Vladivostok, Russia
| | - Vyacheslav I Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Evgenia P Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Marina P Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
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Roy Chowdhury A, Sah S, Varshney U, Chakravortty D. Salmonella Typhimurium outer membrane protein A (OmpA) renders protection from nitrosative stress of macrophages by maintaining the stability of bacterial outer membrane. PLoS Pathog 2022; 18:e1010708. [PMID: 35969640 PMCID: PMC9410544 DOI: 10.1371/journal.ppat.1010708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 08/25/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Bacterial porins are highly conserved outer membrane proteins used in the selective transport of charged molecules across the membrane. In addition to their significant contributions to the pathogenesis of Gram-negative bacteria, their role(s) in salmonellosis remains elusive. In this study, we investigated the role of outer membrane protein A (OmpA), one of the major outer membrane porins of Salmonella, in the pathogenesis of Salmonella Typhimurium (STM). Our study revealed that OmpA plays an important role in the intracellular virulence of Salmonella. An ompA deficient strain of Salmonella (STM ΔompA) showed compromised proliferation in macrophages. We found that the SPI-2 encoded virulence factors such as sifA and ssaV are downregulated in STM ΔompA. The poor colocalization of STM ΔompA with LAMP-1 showed that disruption of SCV facilitated its release into the cytosol of macrophages, where it was assaulted by reactive nitrogen intermediates (RNI). The enhanced recruitment of nitrotyrosine on the cytosolic population of STM ΔompAΔsifA and ΔompAΔssaV compared to STM ΔsifA and ΔssaV showed an additional role of OmpA in protecting the bacteria from host nitrosative stress. Further, we showed that the generation of greater redox burst could be responsible for enhanced sensitivity of STM ΔompA to the nitrosative stress. The expression of several other outer membrane porins such as ompC, ompD, and ompF was upregulated in STM ΔompA. We found that in the absence of ompA, the enhanced expression of ompF increased the outer membrane porosity of Salmonella and made it susceptible to in vitro and in vivo nitrosative stress. Our study illustrates a novel mechanism for the strategic utilization of OmpA by Salmonella to protect itself from the nitrosative stress of macrophages. Salmonella Typhimurium majorly uses SPI-1 and SPI-2 encoded T3SS and virulence factors for thriving in the host macrophages. But the role of non-SPI genes in Salmonella pathogenesis remains unknown. This article illustrates a novel mechanism of how a non-SPI virulent protein, OmpA, helps Salmonella Typhimurium to survive in murine macrophages. Our data revealed that Salmonella lacking OmpA (STM ΔompA) is deficient in producing SPI-2 effector proteins and has a severe defect in maintaining the stability of its outer membrane. It is released into the cytosol of macrophages during infection after disrupting the SCV membrane. STM ΔompA was severely challenged with reactive nitrogen intermediates in the cytosol, which reduced their proliferation in macrophages. We further showed that the deletion of OmpA increased the expression of other larger porins (ompC, ompD, and ompF) on the surface of Salmonella. It was observed that the enhanced expression of OmpF in STM ΔompA increased the outer membrane permeability and made the bacteria more susceptible to in vitro and in vivo nitrosative stress. Altogether our study proposes new insights into the role of Salmonella OmpA as an essential virulence factor.
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Affiliation(s)
- Atish Roy Chowdhury
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail:
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David S, Wong JLC, Sanchez-Garrido J, Kwong HS, Low WW, Morecchiato F, Giani T, Rossolini GM, Brett SJ, Clements A, Beis K, Aanensen DM, Frankel G. Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae. PLoS Pathog 2022; 18:e1010334. [PMID: 35816554 PMCID: PMC9302836 DOI: 10.1371/journal.ppat.1010334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/21/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies. Rapidly rising rates of antibiotic resistance among Klebsiella pneumoniae (KP) necessitate a comprehensive understanding of the diversity, spread and clinical impact of resistance mutations. In KP, mutations in outer membrane porins play an important role in mediating resistance to carbapenems, a key class of antibiotics. Here we show that resistance mutations in the extracellular loop 3 (L3) region of the OmpK36 porin are found at high prevalence among clinical genomes and we characterise their diversity and impact on resistance and virulence. They include amino acid insertions of Aspartate (D), Glycine-Aspartate (GD) and Threonine-Aspartate (TD), which act by decreasing the pore size and restricting entry of carbapenems into the bacterial cell. We show that these L3 insertions are associated with large clonal expansions of resistant lineages and impose a fitness cost evident during in vivo competition. Critically, strains harbouring L3 insertions remain susceptible to novel drugs, including beta lactam-beta lactamase inhibitor combinations. This study highlights the importance of monitoring the emergence and spread of strains with OmpK36 L3 insertions for the control of resistant KP infections and provides crucial data for drug development and treatment strategies.
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Affiliation(s)
- Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Joshua L. C. Wong
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Hok-Sau Kwong
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, United Kingdom
- Department of Life Sciences, Imperial College London; London, United Kingdom
| | - Wen Wen Low
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Stephen J. Brett
- Department of Surgery and Cancer, Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, United Kingdom
| | - Abigail Clements
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Konstantinos Beis
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, United Kingdom
- Department of Life Sciences, Imperial College London; London, United Kingdom
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
- * E-mail:
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Tinney KR, Dover JA, Doore SM, Parent KN. Shigella viruses Sf22 and KRT47 require outer membrane protein C for infection. Biochim Biophys Acta Biomembr 2022; 1864:183920. [PMID: 35358430 PMCID: PMC10037218 DOI: 10.1016/j.bbamem.2022.183920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/18/2022] [Accepted: 03/23/2022] [Indexed: 12/26/2022]
Abstract
Viruses rely on hosts for their replication: thus, a critical step in the infection process is identifying a suitable host cell. Bacterial viruses, known as bacteriophages or phages, often use receptor binding proteins to discriminate between susceptible and non-susceptible hosts. By being able to evade predation, bacteria with modified or deleted receptor-encoding genes often undergo positive selection during growth in the presence of phage. Depending on the specific receptor(s) a phage uses, this may subsequently affect the bacteria's ability to form biofilms, its resistance to antibiotics, pathogenicity, or its phenotype in various environments. In this study, we characterize the interactions between two T4-like phages, Sf22 and KRT47, and their host receptor S. flexneri outer membrane protein C (OmpC). Results indicate that these phages use a variety of surface features on the protein, and that complete resistance most frequently occurs when hosts delete the ompC gene in full, encode premature stop codons to prevent OmpC synthesis, or eliminate specific regions encoding exterior loops.
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Affiliation(s)
- Kendal R Tinney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Sarah M Doore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611.
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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Burbick CR, Alexander TL, Wolking R, Gull T, Ceric O, Reimschuessel R. Non-carbapenemase producing carbapenem-resistant Klebsiella pneumoniae isolated from the urinary tract of a dog. Can Vet J 2022; 63:740-744. [PMID: 35784769 PMCID: PMC9207975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Objective Carbapenems are broad-spectrum β-lactams with excellent activity against multidrug-resistant (MDR) Enterobacterales. Unfortunately, resistance to carbapenems within this bacterial family, known as carbapenem-resistant Enterobacterales (CRE), occurs and challenges the ability to treat difficult MDR infections. Although the impact of carbapenem-resistance has been greatest in human medicine, reports in the veterinary literature are increasing especially as national veterinary antimicrobial resistance surveillance programs are now in place. In this brief communication, we report the isolation of a non-carbapenemase-producing, carbapenem-resistant Klebsiella pneumoniae from the urine of a dog, discuss the likely mechanism of resistance, and wider implications. Animal Canine. Procedure Whole genome sequencing and phenotypic antimicrobial susceptibility testing was performed on a K. pneumoniae isolated from the urine of a dog. Results Antimicrobial susceptibility testing identified phenotypic resistance to imipenem and meropenem. Phenotypic detection of carbapenemase production was negative. Whole genome sequencing identified efflux pump genes associated with carbapenem resistance and point mutations in membrane porin genes. No carbapenemase gene was identified. Conclusion Phenotypic antimicrobial susceptibility testing identified the K. pneumoniae as a non-carbapenemase producing carbapenem-resistant organism with the proposed genotypic mechanism including alteration of efflux pumps and membrane porin activity and/or expression. Clinical significance Currently, there is limited use of carbapenem antimicrobial drugs in veterinary medicine, and practitioners may be unfamiliar or unaware of this type of resistance, its significance on routine antimicrobial susceptibility test reports, and implications for antimicrobial therapy and public health. Carbapenem-resistant Enterobacterales are infrequently isolated from companion animals; however, due to increasing adoption of advanced medical and surgical interventions, they may become more prevalent.
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Affiliation(s)
- Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Rebecca Wolking
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Tamara Gull
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Olgica Ceric
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Renate Reimschuessel
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
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Trampari E, Zhang C, Gotts K, Savva GM, Bavro VN, Webber M. Cefotaxime Exposure Selects Mutations within the CA-Domain of envZ Which Promote Antibiotic Resistance but Repress Biofilm Formation in Salmonella. Microbiol Spectr 2022; 10:e0214521. [PMID: 35475640 PMCID: PMC9241649 DOI: 10.1128/spectrum.02145-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Cephalosporins are important beta lactam antibiotics, but resistance can be mediated by various mechanisms including production of beta lactamase enzymes, changes in membrane permeability or active efflux. We used an evolution model to study how Salmonella adapts to subinhibitory concentrations of cefotaxime in planktonic and biofilm conditions and characterized the mechanisms underpinning this adaptation. We found that Salmonella rapidly adapts to subinhibitory concentrations of cefotaxime via selection of multiple mutations within the CA-domain region of EnvZ. We showed that changes in this domain affect the ATPase activity of the enzyme and in turn impact OmpC, OmpF porin expression and hence membrane permeability leading to increased tolerance to cefotaxime and low-level resistance to different classes of antibiotics. Adaptation to cefotaxime through EnvZ also resulted in a significant cost to biofilm formation due to downregulation of curli. We assessed the role of the mutations identified on the activity of EnvZ by genetic characterization, biochemistry and in silico analysis and confirmed that they are responsible for the observed phenotypes. We observed that sublethal cefotaxime exposure selected for heterogeneity in populations with only a subpopulation carrying mutations within EnvZ and being resistant to cefotaxime. Population structure and composition dynamically changed depending on the presence of the selection pressure, once selected, resistant subpopulations were maintained even in extended passage without drug. IMPORTANCE Understanding mechanisms of antibiotic resistance is crucial to guide how best to use antibiotics to minimize emergence of resistance. We used a laboratory evolution system to study how Salmonella responds to cefotaxime in both planktonic and biofilm conditions. In both contexts, we observed rapid selection of mutants within a single hot spot within envZ. The mutations selected altered EnvZ which in turn triggers changes in porin production at the outer membrane. Emergence of mutations within this region was repeatedly observed in parallel lineages in different conditions. We used a combination of genetics, biochemistry, phenotyping and structural analysis to understand the mechanisms. This data show that the changes we observe provide resistance to cefotaxime but come at a cost to biofilm formation and the fitness of mutants changes greatly depending on the presence or absence of a selective drug. Studying how resistance emerges can inform selective outcomes in the real world.
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Affiliation(s)
| | - Chuanzhen Zhang
- Quadram Institute Bioscience, Norwich, United Kingdom
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Drug Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Kathryn Gotts
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Vassiliy N. Bavro
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Mark Webber
- Quadram Institute Bioscience, Norwich, United Kingdom
- Medical School, University of East Anglia, Norfolk, United Kingdom
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Diorio-Toth L, Irum S, Potter RF, Wallace MA, Arslan M, Munir T, Andleeb S, Burnham CAD, Dantas G. Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance. Microbiol Spectr 2022; 10:e0076622. [PMID: 35638817 PMCID: PMC9241860 DOI: 10.1128/spectrum.00766-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 01/15/2023] Open
Abstract
Carbapenem resistance in Pseudomonas aeruginosa is increasing globally, and surveillance to define the mechanisms of such resistance in low- and middle-income countries is limited. This study establishes the genotypic mechanisms of β-lactam resistance by whole-genome sequencing (WGS) in 142 P. aeruginosa clinical isolates recovered from three hospitals in Islamabad and Rawalpindi, Pakistan between 2016 and 2017. Isolates were subjected to antimicrobial susceptibility testing (AST) by Kirby-Bauer disk diffusion, and their genomes were assembled from Illumina sequencing data. β-lactam resistance was high, with 46% of isolates resistant to piperacillin-tazobactam, 42% to cefepime, 48% to ceftolozane-tazobactam, and 65% to at least one carbapenem. Twenty-two percent of isolates were resistant to all β-lactams tested. WGS revealed that carbapenem resistance was associated with the acquisition of metallo-β-lactamases (MBLs) or extended-spectrum β-lactamases (ESBLs) in the blaGES, blaVIM, and blaNDM families, and mutations in the porin gene oprD. These resistance determinants were found in globally distributed lineages, including ST235 and ST664, as well as multiple novel STs which have been described in a separate investigation. Analysis of AST results revealed that acquisition of MBLs/ESBLs on top of porin mutations had an additive effect on imipenem resistance, suggesting that there is a selective benefit for clinical isolates to encode multiple resistance determinants to the same drugs. The strong association of these resistance determinants with phylogenetic background displays the utility of WGS for monitoring carbapenem resistance in P. aeruginosa, while the presence of these determinants throughout the phylogenetic tree shows that knowledge of the local epidemiology is crucial for guiding potential treatment of multidrug-resistant P. aeruginosa infections. IMPORTANCE Pseudomonas aeruginosa is associated with serious infections, and treatment can be challenging. Because of this, carbapenems and β-lactam/β-lactamase inhibitor combinations have become critical tools in treating multidrug-resistant (MDR) P. aeruginosa infections, but increasing resistance threatens their efficacy. Here, we used WGS to study the genotypic and phylogenomic patterns of 142 P. aeruginosa isolates from the Potohar region of Pakistan. We sequenced both MDR and antimicrobial susceptible isolates and found that while genotypic and phenotypic patterns of antibiotic resistance correlated with phylogenomic background, populations of MDR P. aeruginosa were found in all major phylogroups. We also found that isolates possessing multiple resistance mechanisms had significantly higher levels of imipenem resistance compared to the isolates with a single resistance mechanism. This study demonstrates the utility of WGS for monitoring patterns of antibiotic resistance in P. aeruginosa and potentially guiding treatment choices based on the local spread of β-lactamase genes.
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Affiliation(s)
- Luke Diorio-Toth
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sidra Irum
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Robert F. Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Muhammad Arslan
- Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Tehmina Munir
- Department of Microbiology, Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Saadia Andleeb
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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Gaibani P, Bianco G, Amadesi S, Boattini M, Ambretti S, Costa C. Increased blaKPC Copy Number and OmpK35 and OmpK36 Porins Disruption Mediated Resistance to Imipenem/Relebactam and Meropenem/Vaborbactam in a KPC-Producing Klebsiella pneumoniae Clinical Isolate. Antimicrob Agents Chemother 2022; 66:e0019122. [PMID: 35416711 PMCID: PMC9112950 DOI: 10.1128/aac.00191-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/23/2022] [Indexed: 12/31/2022] Open
Abstract
Herein, we report the in vivo evolution of imipenem/relebactam-resistance in KPC-producing K. pneumoniae (KPC-Kp) isolated from a critically-ill patient treated with multiple combination therapies based on ceftazidime-avibactam or meropenem-vaborbactam. Imipenem/relebactam-resistance was associated to meropenem-vaborbactam cross-resistance and was due to truncated OmpK35 and OmpK36 porins and increased copy of blaKPC copy number. Genome analysis demonstrated that imipenem/relebactam-resistant KPC-Kp harbored a second copy of blaKPC-carrying Tn4401 in a ColRNAI plasmid as a consequence of a transposition event.
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Affiliation(s)
- Paolo Gaibani
- Division of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Gabriele Bianco
- Division of Microbiology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Stefano Amadesi
- Division of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Matteo Boattini
- Division of Microbiology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
| | - Simone Ambretti
- Division of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Cristina Costa
- Division of Microbiology, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Torino, Italy
- University of Torino, Torino, Italy
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Yılmaz İ, Korkmaz F. Investigations of pH-dependent dynamic properties of OmpG-16SL, an outer membrane protein G mutant by ATR-FTIR spectroscopy. Biochim Biophys Acta Proteins Proteom 2022; 1870:140780. [PMID: 35405324 DOI: 10.1016/j.bbapap.2022.140780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
In this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 β-strands in its structure, the mutant is designed to have 16 β-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the 1H/2H exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.
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Affiliation(s)
- İrem Yılmaz
- Physics Unit, Biophysics Laboratory, Atilim University, 06836 Ankara, Turkey
| | - Filiz Korkmaz
- Physics Unit, Biophysics Laboratory, Atilim University, 06836 Ankara, Turkey.
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Liu Y, Yang F, Wang S, Chi W, Ding L, Liu T, Zhu F, Ji D, Zhou J, Fang Y, Zhang J, Xiang P, Zhang Y, Zhao H. HopE and HopD Porin-Mediated Drug Influx Contributes to Intrinsic Antimicrobial Susceptibility and Inhibits Streptomycin Resistance Acquisition by Natural Transformation in Helicobacter pylori. Microbiol Spectr 2022; 10:e0198721. [PMID: 35234510 PMCID: PMC9045298 DOI: 10.1128/spectrum.01987-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/21/2022] [Indexed: 12/14/2022] Open
Abstract
Helicobacter pylori is a human pathogen competent for natural transformation. Intrinsic and acquired antibiotic resistance contribute to the survival and multiplication of H. pylori under antibiotics. While drug-resistance dissemination by natural transformation (NT)-mediated horizontal gene transfer remains poorly understood in H. pylori. The purpose of the study was to investigate the role of H. pylori porins (HopA, HopB, HopC, HopD, and HopE) in the intrinsic antibiotic resistance and to preliminarily reveal the potential effect of HopE and HopD porins in streptomycin resistance acquisition after NT in the presence of antibiotics. Using traditional antibiotic susceptibility tests and growth curve analysis, we found the MIC values of metronidazole, clarithromycin, levofloxacin, tetracycline, rifampin, and streptomycin in mutants lacking HopE and/or HopD were significantly elevated compare to those in wild-type strain. The quantitative analysis of the tetramethyl rhodamine isothiocyanate (TRITC)-labeled streptomycin accumulation at the single-cell level showed reduced streptomycin intracellular fluorescence in ΔhopE and ΔhopD mutant cells. Furthermore, in the presence of translation-inhibiting antibiotic streptomycin, the resistance acquisition frequency was decreased in the wild-type strain, which could be reversed by mutants lacking HopE and HopD that restored relatively high resistance acquisition frequencies. By transforming a pUC19-rpsLmut-sfgfp linear plasmid carrying a streptomycin conferring mutation, we observed that the impaired ability of rpsLmut synthesis in the wild-type strain was restored in the ΔhopE and ΔhopD mutant transformants. Our study revealed that in the presence of streptomycin, resistance acquisition at least partially relied on the deletion of the hopE and hopD genes, because their loss reduced streptomycin concentration in the cell and thus restored the expression of the resistance-conferring gene, which was inhibited by streptomycin in wild-type strain. The loss of HopE and HopD influx activity may also preserve resistance acquisition by transformation in the presence of antibiotics with other modes of action. IMPORTANCE Helicobacter pylori is constitutively competent for natural transformation (NT) and possesses an efficient system for homologous recombination, which could be utilized to study the NT-mediated horizontal gene transfer induced antibiotic resistance acquisition. Bacterial porins have drawn renewed attention because of their crucial role in antibiotic susceptibility. From the perspective of porin-mediated influx in H. pylori, our study preliminarily revealed the important role of HopE and HopD porins not only in preserving the intrinsic susceptibility to specific antibiotic but also in evading acquired antibiotic resistance by NT in the presence of translation-inhibiting antimicrobial. Therefore, the loss of HopE or HopD porin in H. pylori genomes, combined with the large number of secreted or cell-free genetic elements carrying mutations conferring antibiotic resistance, may raise the possibility that this mechanism plays a potential role in the propagation of antibiotic resistance within H. pylori communities.
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Affiliation(s)
- Yixin Liu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Feng Yang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Su Wang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Wenjing Chi
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Li Ding
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Tao Liu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Feng Zhu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Danian Ji
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Jun Zhou
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Yi Fang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Jinghao Zhang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Ping Xiang
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Yanmei Zhang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
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Muhsin EA, Sajid Al-Jubori S, Abdulhemid Said L. Prevalence of Efflux Pump and Porin-Related Antimicrobial Resistance in Clinical Klebsiella pneumoniae in Baghdad, Iraq. Arch Razi Inst 2022; 77:785-798. [PMID: 36284955 PMCID: PMC9548288 DOI: 10.22092/ari.2022.356976.1952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/16/2022] [Indexed: 05/24/2023]
Abstract
Klebsiella pneumoniae is an opportunistic bacterium that causes many infections, including septicemia, pneumonia, urinary tract infection, and liver abscesses. There are many mechanisms for antibiotic resistance and K. pneumonia is considered a multidrug-resistant pathogen. This study aimed to find the correlation between the susceptibility of K. pneumonia to certain antibiotics with the porin-related resistance and pumps mechanisms. In total, two genes that are responsible for porin formation were considered in the current study OmpK-35gene and OmpK-36 gene, in addition to other four genes (CfiaS, CfiaL, MFS, and MdtK genes) related to an efflux pump mechanism of antibiotic resistance. The bacterial resistance was investigated towards five cephalosporins (Cefazolin, Cefoxitin, Ceftazidime, Ceftriaxone, and Cefepime) and two carbapenems (imipenem and ertapenem). Clinical samples, including blood, swabs, and urine, consisting of 20 specimens for each group, were collected from patients who attended three hospitals in Baghdad. The VITEK-2 system and genetic tests (polymerase chain reaction and sequencing) of bacterial isolates were applied to confirm the diagnosis of K. pneumoniae and detect the antibiotic sensitivity profile. The results showed that 51 (85%) and 15 (25%) of the total 60 isolates had positive results for OmpK-35 and Omp-K36 genes, respectively. The MFS and MdtK genes were observed (70-88.3%) in cephalosporin-resistant isolates of K. pneumoniae. There were no significant variations of bacterial resistance genes of antibiotics within the specimen groups. It was concluded that the bacterial resistance of the selected antibiotics was elevated markedly with the loss of the OmpK-36 gene with a high expression of MFS and MdtK genes and a slight minimal occurrence in the new generation of carbapenems. The best antimicrobial agent was ertapenem with a percentage of 0% of resistance in all bacterial isolates.
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Affiliation(s)
| | - S Sajid Al-Jubori
- Biology Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - L Abdulhemid Said
- Biology Department, College of Science, Mustansiriyah University, Baghdad, Iraq
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Guan X, Wang Y, Zhang J, Shao W, Huang S, Zhang D. [Unsupervised deep learning for identifying the O 6-carboxymethyl guanine by nanopore sequencing]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2022; 39:139-148. [PMID: 35231975 DOI: 10.7507/1001-5515.202104068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
O 6-carboxymethyl guanine(O 6-CMG) is a highly mutagenic alkylation product of DNA that causes gastrointestinal cancer in organisms. Existing studies used mutant Mycobacterium smegmatis porin A (MspA) nanopore assisted by Phi29 DNA polymerase to localize it. Recently, machine learning technology has been widely used in the analysis of nanopore sequencing data. But the machine learning always need a large number of data labels that have brought extra work burden to researchers, which greatly affects its practicability. Accordingly, this paper proposes a nano-Unsupervised-Deep-Learning method (nano-UDL) based on an unsupervised clustering algorithm to identify methylation events in nanopore data automatically. Specially, nano-UDL first uses the deep AutoEncoder to extract features from the nanopore dataset and then applies the MeanShift clustering algorithm to classify data. Besides, nano-UDL can extract the optimal features for clustering by joint optimizing the clustering loss and reconstruction loss. Experimental results demonstrate that nano-UDL has relatively accurate recognition accuracy on the O 6-CMG dataset and can accurately identify all sequence segments containing O 6-CMG. In order to further verify the robustness of nano-UDL, hyperparameter sensitivity verification and ablation experiments were carried out in this paper. Using machine learning to analyze nanopore data can effectively reduce the additional cost of manual data analysis, which is significant for many biological studies, including genome sequencing.
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Affiliation(s)
- Xiaoyu Guan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, P. R. China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Shao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, P. R. China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, P. R. China
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Lian T, Zhang B, Giacani L, Kou C, Yang X, Zhang R, Wang Q. Full-length TprK of Treponema pallidum subsp. pallidum in lipid nanodiscs is a monomeric porin. Enzyme Microb Technol 2022; 153:109897. [PMID: 34670182 PMCID: PMC10929906 DOI: 10.1016/j.enzmictec.2021.109897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/27/2021] [Accepted: 08/23/2021] [Indexed: 11/22/2022]
Abstract
TprK is a key virulence factor of Treponema pallidum subsp. pallidum (T. pallidum) due to its ability to undergo intra-strain antigenic variation through gene conversion. This mechanism can generate millions of tprK gene and protein variants to allow immune evasion and pathogen persistence during infection. In silico structural modeling supports that TprK is an outer membrane β-barrel with porin function and with several surface-exposed loops, seven of which corresponding to the variable regions. No definitive structural of functional data, however, exist for this protein aside from its role in immune evasion. Studies to elucidate TprK biological function as a porin, are hindered by the evidence that TprK is not abundant on T. pallidum outer membrane, and by the fragility of T. pallidum envelope. To gain insight onto TprK structure and possible function as a porin, we used an Escherichia coli - based expression system that yielded highly pure full-length TprK without any intermediate denaturation step, and proceeded to reconstitute it in detergents and lipid nanodiscs. Visualization of TprK in nanodiscs using negative staining electron microscopy supported that TprK is a monomeric porin in an artificial lipid environment mimicking T. pallidum membrane. Our work provided evidence that TprK is a possible porin transporter of T. pallidum, a biological function compatible with its structural models. These results bring us closer to a comprehensive understanding of the function of this important virulence factor in syphilis pathogenesis and T. pallidum biology.
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Affiliation(s)
- Tingting Lian
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China.
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 200120, China.
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Caixia Kou
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China.
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 200120, China.
| | - Ruili Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210042, China.
| | - Qianqiu Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China.
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Savinova T, Samchenko A, Bocharova Y, Mayansky N, Chebotar I. Computer Program for Detection and Analyzing the Porin-Mediated Antibiotic Resistance of Bacteria. Sovrem Tekhnologii Med 2021; 13:15-22. [PMID: 35265355 PMCID: PMC8858402 DOI: 10.17691/stm2021.13.6.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this work was to develop a new software tool for identifying gene mutations that determine the porin-mediated resistance to antibiotics in gram-negative bacteria and to demonstrate the functionality of this program by detecting porin-mediated resistance to carbapenems in clinical isolates of Pseudomonas aeruginosa.
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Affiliation(s)
- T.A. Savinova
- Leading Researcher, Laboratory of Molecular Microbiology; Pirogov National Research Medical University, 1 Ostrovityanova St., Moscow, 117997, Russia
| | - A.A. Samchenko
- Researcher, Laboratory of Structure and Dynamics of Biomolecular Systems; Institute of Cell Biophysics of the Russian Academy of Sciences — Subdivision of the Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 3 Institutskaya St., Moscow Region, Pushchino, 142290, Russia
| | - Y.A. Bocharova
- Senior Researcher, Laboratory of Molecular Microbiology; Pirogov National Research Medical University, 1 Ostrovityanova St., Moscow, 117997, Russia
| | - N.A. Mayansky
- Professor of the Russian Academy of Sciences, Head of the Center for Laboratory Diagnostics, Russian Children’s Clinical Hospital; Pirogov National Research Medical University, 1 Ostrovityanova St., Moscow, 117997, Russia
| | - I.V. Chebotar
- Head of the Laboratory of Molecular Microbiology; Pirogov National Research Medical University, 1 Ostrovityanova St., Moscow, 117997, Russia
- Corresponding author: Igor V. Chebotar, e-mail:
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Stokowa-Sołtys K, Wojtkowiak K, Dzyhovskyi V, Wieczorek R. Effect of Copper(II) Ion Binding by Porin P1 Precursor Fragments from Fusobacterium nucleatum on DNA Degradation. Int J Mol Sci 2021; 22:ijms222212541. [PMID: 34830424 PMCID: PMC8623562 DOI: 10.3390/ijms222212541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
Fusobacterium nucleatum is one of the most notorious species involved in colorectal cancer. It was reported that numerous outer membrane proteins (OMP) are actively involved in carcinogenesis. In this paper, the structure and stability of certain complexes, as well as DNA cleavage and ROS generation by fragments of OMP, were investigated using experimental and theoretical methods. Mass spectrometry, potentiometry, UV-Vis, CD, EPR, gel electrophoresis and calculations at the density functional theory (DFT) level were applied. Two consecutive model peptides, Ac-AKGHEHQLE-NH2 and Ac-FGEHEHGRD-NH2, were studied. Both of these were rendered to form a variety of thermodynamically stable complexes with copper(II) ions. All of the complexes were stabilized, mainly due to interactions of metal with nitrogen and oxygen donor atoms, as well as rich hydrogen bond networks. It was also concluded that these complexes in the presence of hydrogen peroxide or ascorbic acid can effectively produce hydroxyl radicals and have an ability to cleave the DNA strands. Surprisingly, the second studied ligand at the micromolar concentration range causes overall DNA degradation.
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Lin MJ, Haynes AM, Addetia A, Lieberman NAP, Phung Q, Xie H, Nguyen TV, Molini BJ, Lukehart SA, Giacani L, Greninger AL. Longitudinal TprK profiling of in vivo and in vitro-propagated Treponema pallidum subsp. pallidum reveals accumulation of antigenic variants in absence of immune pressure. PLoS Negl Trop Dis 2021; 15:e0009753. [PMID: 34492041 PMCID: PMC8480903 DOI: 10.1371/journal.pntd.0009753] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/29/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022] Open
Abstract
Immune evasion by Treponema pallidum subspecies pallidum (T. pallidum) has been attributed to antigenic variation of its putative outer-membrane protein TprK. In TprK, amino acid diversity is confined to seven variable (V) regions, and generation of sequence diversity within the V regions occurs via a non-reciprocal segmental gene conversion mechanism where donor cassettes recombine into the tprK expression site. Although previous studies have shown the significant role of immune selection in driving accumulation of TprK variants, the contribution of baseline gene conversion activity to variant diversity is less clear. Here, combining longitudinal tprK deep sequencing of near clonal Chicago C from immunocompetent and immunosuppressed rabbits along with the newly developed in vitro cultivation system for T. pallidum, we directly characterized TprK alleles in the presence and absence of immune selection. Our data confirm significantly greater sequence diversity over time within the V6 region during syphilis infection in immunocompetent rabbits compared to immunosuppressed rabbits, consistent with previous studies on the role of TprK in evasion of the host immune response. Compared to strains grown in immunocompetent rabbits, strains passaged in vitro displayed low level changes in allele frequencies of TprK variable region sequences similar to that of strains passaged in immunosuppressed rabbits. Notably, we found significantly increased rates of V6 allele generation relative to other variable regions in in vitro cultivated T, pallidum strains, illustrating that the diversity within these hypervariable regions occurs in the complete absence of immune selection. Together, our results demonstrate antigenic variation in T. pallidum can be studied in vitro and occurs even in the complete absence of immune pressure, allowing the T. pallidum population to continuously evade the immune system of the infected host.
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Affiliation(s)
- Michelle J. Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Haynes
- Pathobiology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Tien V. Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Barbara J. Molini
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Yan S, Zhang J, Wang Y, Guo W, Zhang S, Liu Y, Cao J, Wang Y, Wang L, Ma F, Zhang P, Chen HY, Huang S. Single Molecule Ratcheting Motion of Peptides in a Mycobacterium smegmatis Porin A (MspA) Nanopore. Nano Lett 2021; 21:6703-6710. [PMID: 34319744 DOI: 10.1021/acs.nanolett.1c02371] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diverse functions of proteins, including synthesis, catalysis, and signaling, result from their highly variable amino acid sequences. The technology allowing for direct analysis of protein sequences, however, is still unsatisfactory. Recent developments of nanopore sequencing of DNA or RNA have motivated attempts to realize nanopore sequencing of peptides in a similar manner. The core challenge has been to achieve a controlled ratcheting motion of the target peptide, which is currently restricted to a limited choice of compatible enzymes. By constructing peptide-oligonucleotide conjugates (POCs) and measurements with nanopore-induced phase-shift sequencing (NIPSS), direct observation of the ratcheting motion of peptides has been successfully achieved. The generated events show a clear sequence dependence on the peptide that is being tested. The method is compatible with peptides with either a conjugated N- or C-terminus. The demonstrated results suggest a proof of concept of nanopore sequencing of peptide and can be useful for peptide fingerprinting.
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Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Weiming Guo
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jiao Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Fubo Ma
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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Li Q, Hu Y, Fei X, Du Y, Guo W, Chu D, Wang X, Wang S, Shi H. OmpC, a novel factor H-binding surface protein, is dispensable for the adherence and virulence of Salmonella enterica serovar Typhimurium. Vet Microbiol 2021; 259:109157. [PMID: 34197978 DOI: 10.1016/j.vetmic.2021.109157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/15/2021] [Indexed: 11/24/2022]
Abstract
Salmonella enterica serovar Typhimurium utilizes a series of strategies to evade host innate immune defenses, including the serum complement system. Many microbial pathogens have evolved the ability to bind the complement regulatory protein factor H (FH) through their surface factor H-binding proteins (FHBPs) to circumvent the complement-mediated bactericidal effect. However, the roles of FHBPs in Salmonella pathogenesis are not well understood. In this study, we demonstrated that the survival of S. Typhimurium in human serum was decreased in a time and concentration dependent manner. Pre-incubation with FH attenuated the sensitivity of S. Typhimurium strain χ3761 to complement-mediated serum killing, suggesting FH binding enhance survival in serum. We aimed to identify novel S. Typhimurium FHBPs and characterize their biological functions. Here, six potential FHBPs were identified by two-dimensional (2D)-Far-western blot, and three of them were further confirmed to bind FH by Far-western blot and dot blot. We found that deletion of ompC (ΔompC) significantly inhibited the survival of S. Typhimurium strain χ3761 in human serum. Our results indicated that the ompC mutation does not affect χ3761 adhesion to HeLa cells. Furthermore, a mice infection model showed that deletion of ompC had no significant effect on the histopathological lesions or viability compared with the wild-type strain χ3761. In summary, these results suggested that OmpC is an important FHBP, but not a critical virulence factor of S. Typhimurium.
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Affiliation(s)
- Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Yuhan Hu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Xia Fei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Yuanzhao Du
- Yebio Bioengineering Co., Ltd of Qingdao, Qingdao, 266114, China.
| | - Weiwei Guo
- Yebio Bioengineering Co., Ltd of Qingdao, Qingdao, 266114, China.
| | - Dianfeng Chu
- Yebio Bioengineering Co., Ltd of Qingdao, Qingdao, 266114, China.
| | - Xiaobo Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
| | - Shifeng Wang
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611-0880, USA.
| | - Huoying Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China; Key Laboratory of Animal Infectious Diseases, Ministry of Agriculture, Yangzhou University, China; Jiangsu Key Laboratory of Preventive Veterinary Medicine, Yangzhou University, China.
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Li K, Xu Q, Gao S, Zhang S, Ma Y, Zhao G, Guo Y. Highly stable selenium nanoparticles: Assembly and stabilization via flagellin FliC and porin OmpF in Rahnella aquatilis HX2. J Hazard Mater 2021; 414:125545. [PMID: 33667801 DOI: 10.1016/j.jhazmat.2021.125545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Microorganisms play a critical role in the reduction of the more toxic selenite and selenate to the less toxic elemental selenium. However, the assembly process and stability of selenium nanoparticles (SeNPs) remain understudied. The plant growth-promoting rhizobacterium Rahnella aquatilis HX2 can reduce selenite to biogenic SeNPs (BioSeNPs). Two main proteins, namely flagellin FliC and porin OmpF were identified in the BioSeNPs. The fliC and ompF gene mutation experiments demonstrated that the FliC and OmpF could control the assembly of BioSeNPs in vivo. At the same time, the expressed and purified FliC and OmpF could control the assembly of SeNPs in vitro. BioSeNPs produced by R. aquatilis HX2 exhibited high stability under various ionic strengths, while the chemically synthesized SeNPs (CheSeNPs) showed a high level of aggregation. The in vitro experiments verified that FliC and OmpF could prevent the aggregation of the CheSeNPs under various ionic strengths. This work reports the preparation of highly stable BioSeNPs produced by strain R. aquatilis HX2 and verifies that FliC and OmpF both could control the assembly and stability of BioSeNPs. BioSeNPs with high stability could be suitable as nutritional supplement to remedy selenium deficiency and in nanomedicine applications.
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Affiliation(s)
- Kui Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Qiaolin Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Shanshan Gao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Sasa Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yuhui Ma
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS-HKU Joint Laboratory of Metallomics on Health & Environment, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Guishen Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China.
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Wang Y, Guan X, Zhang S, Liu Y, Wang S, Fan P, Du X, Yan S, Zhang P, Chen HY, Li W, Zhang D, Huang S. Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A. Nat Commun 2021; 12:3368. [PMID: 34099723 PMCID: PMC8185011 DOI: 10.1038/s41467-021-23764-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Folding of RNA can produce elaborate tertiary structures, corresponding to their diverse roles in the regulation of biological activities. Direct observation of RNA structures at high resolution in their native form however remains a challenge. The large vestibule and the narrow constriction of a Mycobacterium smegmatis porin A (MspA) suggests a sensing mode called nanopore trapping/translocation, which clearly distinguishes between microRNA, small interfering RNA (siRNA), transfer RNA (tRNA) and 5 S ribosomal RNA (rRNA). To further profit from the acquired event characteristics, a custom machine learning algorithm is developed. Events from measurements with a mixture of RNA analytes can be automatically classified, reporting a general accuracy of ~93.4%. tRNAs, which possess a unique tertiary structure, report a highly distinguishable sensing feature, different from all other RNA types tested in this study. With this strategy, tRNAs from different sources are measured and a high structural conservation across different species is observed in single molecule.
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MESH Headings
- Machine Learning
- MicroRNAs/chemistry
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Dynamics Simulation
- Molecular Weight
- Mycobacterium smegmatis/genetics
- Mycobacterium smegmatis/metabolism
- Nanopores
- Nucleic Acid Conformation
- Porins/chemistry
- Porins/genetics
- Porins/metabolism
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Folding
- RNA Transport
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiaoyu Guan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Sha Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
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