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Shariati A, Kashi M, Chegini Z, Hosseini SM. Antibiotics-free compounds for managing carbapenem-resistant bacteria; a narrative review. Front Pharmacol 2024; 15:1467086. [PMID: 39355778 PMCID: PMC11442292 DOI: 10.3389/fphar.2024.1467086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 09/04/2024] [Indexed: 10/03/2024] Open
Abstract
Carbapenem-resistant (CR) Gram-negative bacteria have become a significant public health problem in the last decade. In recent years, the prevalence of CR bacteria has increased. The resistance to carbapenems could result from different mechanisms such as loss of porin, penicillin-binding protein alteration, carbapenemase, efflux pump, and biofilm community. Additionally, genetic variations like insertion, deletion, mutation, and post-transcriptional modification of corresponding coding genes could decrease the susceptibility of bacteria to carbapenems. In this regard, scientists are looking for new approaches to inhibit CR bacteria. Using bacteriophages, natural products, nanoparticles, disulfiram, N-acetylcysteine, and antimicrobial peptides showed promising inhibitory effects against CR bacteria. Additionally, the mentioned compounds could destroy the biofilm community of CR bacteria. Using them in combination with conventional antibiotics increases the efficacy of antibiotics, decreases their dosage and toxicity, and resensitizes CR bacteria to antibiotics. Therefore, in the present review article, we have discussed different aspects of non-antibiotic approaches for managing and inhibiting the CR bacteria and various methods and procedures used as an alternative for carbapenems against these bacteria.
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Affiliation(s)
- Aref Shariati
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
| | - Milad Kashi
- Student research committee, Arak University of Medical Sciences, Arak, Iran
| | - Zahra Chegini
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Mostafa Hosseini
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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2
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Dicks LMT, Vermeulen W. Bacteriophage-Host Interactions and the Therapeutic Potential of Bacteriophages. Viruses 2024; 16:478. [PMID: 38543843 PMCID: PMC10975011 DOI: 10.3390/v16030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/23/2024] Open
Abstract
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Affiliation(s)
- Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
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3
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Maciejewska B, Squeglia F, Latka A, Privitera M, Olejniczak S, Switala P, Ruggiero A, Marasco D, Kramarska E, Drulis-Kawa Z, Berisio R. Klebsiella phage KP34gp57 capsular depolymerase structure and function: from a serendipitous finding to the design of active mini-enzymes against K. pneumoniae. mBio 2023; 14:e0132923. [PMID: 37707438 PMCID: PMC10653864 DOI: 10.1128/mbio.01329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/19/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE In this work, we determined the structure of Klebsiella phage KP34p57 capsular depolymerase and dissected the role of individual domains in trimerization and functional activity. The crystal structure serendipitously revealed that the enzyme can exist in a monomeric state once deprived of its C-terminal domain. Based on the crystal structure and site-directed mutagenesis, we localized the key catalytic residues in an intra-subunit deep groove. Consistently, we show that C-terminally trimmed KP34p57 variants are monomeric, stable, and fully active. The elaboration of monomeric, fully active phage depolymerases is innovative in the field, as no previous example exists. Indeed, mini phage depolymerases can be combined in chimeric enzymes to extend their activity ranges, allowing their use against multiple serotypes.
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Affiliation(s)
- Barbara Maciejewska
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Agnieszka Latka
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Mario Privitera
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Sebastian Olejniczak
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Paulina Switala
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | | | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Eliza Kramarska
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
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4
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Cai R, Ren Z, Zhao R, Lu Y, Wang X, Guo Z, Song J, Xiang W, Du R, Zhang X, Han W, Ru H, Gu J. Structural biology and functional features of phage-derived depolymerase Depo32 on Klebsiella pneumoniae with K2 serotype capsular polysaccharides. Microbiol Spectr 2023; 11:e0530422. [PMID: 37750730 PMCID: PMC10581125 DOI: 10.1128/spectrum.05304-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 08/03/2023] [Indexed: 09/27/2023] Open
Abstract
Hypervirulent Klebsiella pneumoniae with capsular polysaccharides (CPSs) causes severe nosocomial- and community-acquired infections. Phage-derived depolymerases can degrade CPSs from K. pneumoniae to attenuate bacterial virulence, but their antimicrobial mechanisms and clinical potential are not well understood. In the present study, Klebsiella phage GH-K3-derived depolymerase Depo32 (encoded by gene gp32) was identified to exhibit high efficiency in specifically degrading the CPSs of K2 serotype K. pneumoniae. The cryo-electron microscopy structure of trimeric Depo32 at a resolution up to 2.32 Å revealed potential catalytic centers in the cleft of each of the two adjacent subunits. K. pneumoniae subjected to Depo32 became more sensitive to phagocytosis by RAW264.7 cells and activated the cells by the mitogen-activated protein kinase signaling pathway. In addition, intranasal inoculation with Depo32 (a single dose of 200 µg, 20 µg daily for 3 days, or in combination with gentamicin) rescued all C57BL/6J mice infected with a lethal dose of K. pneumoniae K7 without interference from its neutralizing antibody. In summary, this work elaborates on the mechanism by which Depo32 targets the degradation of K2 serotype CPSs and its potential as an antivirulence agent. IMPORTANCE Depolymerases specific to more than 20 serotypes of Klebsiella spp. have been identified, but most studies only evaluated the single-dose treatment of depolymerases with relatively simple clinical evaluation indices and did not reveal the anti-infection mechanism of these depolymerases in depth. On the basis of determining the biological characteristics, the structure of Depo32 was analyzed by cryo-electron microscopy, and the potential active center was further identified. In addition, the effects of Depo32 on macrophage phagocytosis, signaling pathway activation, and serum killing were revealed, and the efficacy of the depolymerase (single treatment, multiple treatments, or in combination with gentamicin) against acute pneumonia caused by Klebsiella pneumoniae was evaluated. Moreover, the roles of the active sites of Depo32 were also elucidated in the in vitro and in vivo studies. Therefore, through structural biology, cell biology, and in vivo experiments, this study demonstrated the mechanism by which Depo32 targets K2 serotype K. pneumoniae infection.
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Affiliation(s)
- Ruopeng Cai
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhuolu Ren
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Rihong Zhao
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Yan Lu
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xinwu Wang
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Changchun, Jilin, China
| | - Zhimin Guo
- Infectious Diseases and Pathogen Biology Center, Clinical Laboratory Department, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jinming Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Wentao Xiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiaokang Zhang
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Inter disciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, China
| | - Wenyu Han
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Heng Ru
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingmin Gu
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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5
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Kao CY, Zhang YZ, Bregente CJB, Kuo PY, Chen PK, Chao JY, Duong TTT, Wang MC, Thuy TTD, Hidrosollo JH, Tsai PF, Li YC, Lin WH. A 24-year longitudinal study of Klebsiella pneumoniae isolated from patients with bacteraemia and urinary tract infections reveals the association between capsular serotypes, antibiotic resistance, and virulence gene distribution. Epidemiol Infect 2023; 151:e155. [PMID: 37675569 PMCID: PMC10548544 DOI: 10.1017/s0950268823001486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023] Open
Abstract
Longitudinal studies on the variations of phenotypic and genotypic characteristics of K. pneumoniae across two decades are rare. We aimed to determine the antimicrobial susceptibility and virulence factors for K. pneumoniae isolated from patients with bacteraemia or urinary tract infection (UTI) from 1999 to 2022. A total of 699 and 1,267 K. pneumoniae isolates were isolated from bacteraemia and UTI patients, respectively, and their susceptibility to twenty antibiotics was determined; PCR was used to identify capsular serotypes and virulence-associated genes. K64 and K1 serotypes were most frequently observed in UTI and bacteraemia, respectively, with an increasing frequency of K20, K47, and K64 observed in recent years. entB and wabG predominated across all isolates and serotypes; the least frequent virulence gene was htrA. Most isolates were susceptible to carbapenems, amikacin, tigecycline, and colistin, with the exception of K20, K47, and K64 where resistance was widespread. The highest average number of virulence genes was observed in K1, followed by K2, K20, and K5 isolates, which suggest their contribution to the high virulence of K1. In conclusion, we found that the distribution of antimicrobial susceptibility, virulence gene profiles, and capsular types of K. pneumoniae over two decades were associated with their clinical source.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Zhen Zhang
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Carl Jay Ballena Bregente
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pek Kee Chen
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jo-Yen Chao
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tran Thi Thuy Duong
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jazon Harl Hidrosollo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pei-Fang Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chi Li
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
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6
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Cui X, Du B, Feng J, Feng Y, Fan Z, Chen J, Cui J, Gan L, Fu T, Tian Z, Zhang R, Yan C, Zhao H, Xu W, Xu Z, Yu Z, Ding Z, Li Z, Chen Y, Xue G, Yuan J. A novel phage carrying capsule depolymerase effectively relieves pneumonia caused by multidrug-resistant Klebsiella aerogenes. J Biomed Sci 2023; 30:75. [PMID: 37653407 PMCID: PMC10470133 DOI: 10.1186/s12929-023-00946-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Klebsiella aerogenes can cause ventilator-associated pneumonia by forming biofilms, and it is frequently associated with multidrug resistance. Phages are good antibiotic alternatives with unique advantages. There has been a lack of phage therapeutic explorations, kinetic studies, and interaction mechanism research targeting K. aerogenes. METHODS Plaque assay, transmission electron microscopy and whole-genome sequencing were used to determine the biology, morphology, and genomic characteristics of the phage. A mouse pneumonia model was constructed by intratracheal/endobronchial delivery of K. aerogenes to assess the therapeutic effect of phage in vivo. Bioinformatics analysis and a prokaryotic protein expression system were used to predict and identify a novel capsule depolymerase. Confocal laser scanning microscopy, Galleria mellonella larvae infection models and other experiments were performed to clarify the function of the capsule depolymerase. RESULTS A novel lytic phage (pK4-26) was isolated from hospital sewage. It was typical of the Podoviridae family and exhibited serotype specificity, high lytic activity, and high environmental adaptability. The whole genome is 40,234 bp in length and contains 49 coding domain sequences. Genomic data show that the phage does not carry antibiotic resistance, virulence, or lysogenic genes. The phage effectively lysed K. aerogenes in vivo, reducing mortality and alleviating pneumonia without promoting obvious side effects. A novel phage-derived depolymerase was predicted and proven to be able to digest the capsule, remove biofilms, reduce bacterial virulence, and sensitize the bacteria to serum killing. CONCLUSIONS The phage pK4-26 is a good antibiotic alternative and can effectively relieve pneumonia caused by multidrug-resistant K. aerogenes. It carries a depolymerase that removes biofilms, reduces virulence, and improves intrinsic immune sensitivity.
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Affiliation(s)
- Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jinfeng Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Wenjian Xu
- Department of Clinical Laboratory, Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zanbo Ding
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhoufei Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yujie Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, 100020, China.
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7
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Wu JW, Wang JT, Lin TL, Liu YZ, Wu LT, Pan YJ. Identification of three capsule depolymerases in a bacteriophage infecting Klebsiella pneumoniae capsular types K7, K20, and K27 and therapeutic application. J Biomed Sci 2023; 30:31. [PMID: 37210493 DOI: 10.1186/s12929-023-00928-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae capsular types K1, K2, K5, K20, K54, and K57 are prevalent hypervirulent types associated with community infections, and worrisomely, hypervirulent strains that acquired drug resistance have been found. In the search for alternative therapeutics, studies have been conducted on phages that infect K. pneumoniae K1, K2, K5, and K57-type strains and their phage-encoded depolymerases. However, phages targeting K. pneumoniae K20-type strains and capsule depolymerases capable of digesting K20-type capsules have rarely been reported. In this study, we characterized a phage that can infect K. pneumoniae K20-type strains, phage vB_KpnM-20. METHODS A phage was isolated from sewage water in Taipei, Taiwan, its genome was analyzed, and its predicted capsule depolymerases were expressed and purified. The host specificity and capsule-digesting activity of the capsule depolymerases were determined. The therapeutic effect of the depolymerase targeting K. pneumoniae K20-type strains was analyzed in a mouse infection model. RESULTS The isolated Klebsiella phage, vB_KpnM-20, infects K. pneumoniae K7, K20, and K27-type strains. Three capsule depolymerases, K7dep, K20dep, and K27dep, encoded by the phage were specific to K7, K20, and K27-type capsules, respectively. K20dep also recognized Escherichia coli K30-type capsule, which is highly similar to K. pneumoniae K20-type. The survival of K. pneumoniae K20-type-infected mice was increased following administration of K20dep. CONCLUSIONS The potential of capsule depolymerase K20dep for the treatment of K. pneumoniae infections was revealed using an in vivo infection model. In addition, K7dep, K20dep, and K27dep capsule depolymerases could be used for K. pneumoniae capsular typing.
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Affiliation(s)
- Jia-Wen Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, Taiwan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Lung Lin
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Zhu Liu
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung, Taiwan
| | - Lii-Tzu Wu
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung, Taiwan.
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8
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Alrafaie AM, Stafford GP. Enterococcal bacteriophage: A survey of the tail associated lysin landscape. Virus Res 2023; 327:199073. [PMID: 36787848 DOI: 10.1016/j.virusres.2023.199073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located mainly within the phage tail structure. In this paper we surveyed and analysed the genomes of 506 isolated bacteriophage and prophage infecting or harboured within the genomes of the medically important Enterococcus faecalis and faecium. We highlight and characterise the major features of the genomes of phage in the morphological groups podovirus, siphovirus and myovirus, and explore their categorisation according to the new ICTV classifications, with a focus on putative extracellular lysins chiefly within tail modules. Our analysis reveals a range of potential cell-wall targeting enzyme domains that are part of tail, tape measure or other predicted base structures of these phages or prophages. These largely fall into protein domains targeting pentapeptide or glycosidic linkages within peptidoglycan but also potentially the enterococcal polysaccharide antigen (EPA) and wall teichoic acids of these species (i.e., Pectinesterases and Phosphodiesterases). Notably, there is a great variety of domain architectures that reveal the diversity of evolutionary solutions to attack the Enterococcus cell wall. Despite this variety, most phage and prophage possess a putative endopeptidase (70%), reflecting the ubiquity of this cell surface barrier. We also identified a predicted lytic transglycosylase domain belonging to the glycosyl hydrolase (GH) family 23 and present exclusively within tape measure proteins. Our data also reveal distinct features of the genomes of podo-, sipho- and myo-type viruses that most likely relate to their size and complexity. Overall, we lay a foundation for expression of recombinant TAL proteins and engineering of enterococcal and other phage that will be invaluable for researchers in this field.
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Affiliation(s)
- Alhassan M Alrafaie
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, United Kingdom; Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Graham P Stafford
- Integrated BioSciences, School of Clinical Dentistry, University of Sheffield, Sheffield, United Kingdom.
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9
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Pertics BZ, Kovács T, Schneider G. Characterization of a Lytic Bacteriophage and Demonstration of Its Combined Lytic Effect with a K2 Depolymerase on the Hypervirulent Klebsiella pneumoniae Strain 52145. Microorganisms 2023; 11:microorganisms11030669. [PMID: 36985241 PMCID: PMC10051899 DOI: 10.3390/microorganisms11030669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen. Among its virulence factors is the capsule with a prominent role in defense and biofilm formation. Bacteriophages (phages) can evoke the lysis of bacterial cells. Due to the mode of action of their polysaccharide depolymerase enzymes, phages are typically specific for one bacterial strain and its capsule type. In this study, we characterized a bacteriophage against the capsule-defective mutant of the nosocomial K. pneumoniae 52145 strain, which lacks K2 capsule. The phage showed a relatively narrow host range but evoked lysis on a few strains with capsular serotypes K33, K21, and K24. Phylogenetic analysis showed that the newly isolated Klebsiella phage 731 belongs to the Webervirus genus in the Drexlerviridae family; it has a 31.084 MDa double-stranded, linear DNA with a length of 50,306 base pairs and a G + C content of 50.9%. Out of the 79 open reading frames (ORFs), we performed the identification of orf22, coding for a trimeric tail fiber protein with putative capsule depolymerase activity, along with the mapping of other putative depolymerases of phage 731 and homologous phages. Efficacy of a previously described recombinant K2 depolymerase (B1dep) was tested by co-spotting phage 731 on K. pneumoniae strains, and it was demonstrated that the B1dep-phage 731 combination allows the lysis of the wild type 52145 strain, originally resistant to the phage 731. With phage 731, we showed that B1dep is a promising candidate for use as a possible antimicrobial agent, as it renders the virulent strain defenseless against other phages. Phage 731 alone is also important due to its efficacy on K. pneumoniae strains possessing epidemiologically important serotypes.
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Affiliation(s)
- Botond Zsombor Pertics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Kertváros St. 2., H-7632 Pécs, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-536-200 (ext. 1908)
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Wang S, Ding Q, Zhang Y, Zhang A, Wang Q, Wang R, Wang X, Jin L, Ma S, Wang H. Evolution of Virulence, Fitness, and Carbapenem Resistance Transmission in ST23 Hypervirulent Klebsiella pneumoniae with the Capsular Polysaccharide Synthesis Gene wcaJ Inserted via Insertion Sequence Elements. Microbiol Spectr 2022; 10:e0240022. [PMID: 36222687 PMCID: PMC9769677 DOI: 10.1128/spectrum.02400-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/23/2022] [Indexed: 01/06/2023] Open
Abstract
Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is recognized as a threat worldwide, but the mechanisms underlying its emergence remain unclear. As most CR-hvKP isolates are not hypermucoviscous, we speculated that the evolution of the capsule might result in the convergence of carbapenem resistance and hypervirulence. Here, 2,096 K. pneumoniae isolates were retrospectively collected to screen the ST23-K1 clone, and hypervirulence was roughly defined as being highly resistant to serum killing. The effect of wcaJ on the capsule, virulence, fitness, and resistance acquisition was further analyzed. The capsule gene wcaJ, inserted by ISKpn26/ISKpn74, was identified via whole-genome sequencing in four hvKP, but not hypermucoviscous, isolates. Uronic acid quantitation results revealed that these isolates produced significantly less capsular polysaccharides than NTUH-K2044. A significant increase in capsular production was observed in wcaJ-complemented isolates and confirmed by transmission electron microscopy. Further, all wcaJ-complemented isolates acquired greater resistance to macrophage phagocytosis, and one representative isolate resulted in a significantly higher mortality rate than the parental isolate in mice, indicating that wcaJ inactivation might compromise virulence. However, isolates with wcaJ interruption demonstrated a lower fitness cost and a high conjugation frequency of the blaKPC-2 plasmid, raising concerns about the emergence of carbapenem resistance in hvKP. IMPORTANCE Klebsiella pneumoniae is one of the most common nosocomial pathogens worldwide, and we speculated that the evolution of the capsule might result in the convergence of carbapenem resistance and hypervirulence of K. pneumoniae. The wcaJ gene was first reported to be interrupted by insertion sequence elements in ST23-K1 hypervirulent Klebsiella pneumoniae, resulting in little capsule synthesis, which plays an important role in virulence. We examined the effect of wcaJ on the capsule, virulence, and fitness. Isolates with wcaJ interruption might compromise virulence and demonstrated a lower fitness cost and a high conjugation frequency of the blaKPC-2 plasmid, highlighting its role as a potential factor facilitating hypervirulence and carbapenem resistance.
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Affiliation(s)
- Shuyi Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Qi Ding
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Anru Zhang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Shuai Ma
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
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The Molecular Epidemiology of Prevalent Klebsiella pneumoniae Strains and Humoral Antibody Responses against Carbapenem-Resistant K. pneumoniae Infections among Pediatric Patients in Shanghai. mSphere 2022; 7:e0027122. [PMID: 36069436 PMCID: PMC9599505 DOI: 10.1128/msphere.00271-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has caused wide dissemination among pediatric patients globally and thus has aroused public concern. Here, we investigated the clinical epidemiological characteristics of 140 nonreplicate clinical K. pneumoniae strains isolated from pediatric patients between January and December 2021. Of all isolates, 16.43% (23 of 140) were CRKP strains, which predominantly contained KPC carbapenemase. wzi sequencing demonstrated that KL47 (65.22%, 15 of 23) was the most frequent capsular type, followed by KL64 (17.39%, 4 of 23). A total of 23 CRKP strains were classified into three different O-genotypes, including OL101 (65.22%, 15 of 23), O1 (26.09%, 6 of 23), and O3 (8.7%, 2 of 23). Interestingly, KL47 strains were strongly associated with OL101, while KL64 strains were all linked with O1. Some capsule-deficient strains were identified by serological typing, phage-typing, depolymerase-typing, and uronic acid assay. In this study, compared with healthy children, higher titers of anti-capsular polysaccharides (CPS) IgG were first detected in the sera of K47 and K64 K. pneumoniae-infected children, which had the effective bactericidal activity against corresponding serotype K. pneumoniae strains. These findings will facilitate the development of novel therapeutic and vaccine strategies against K. pneumoniae infection in children. IMPORTANCE The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains resistant to numerous antibiotics and the limited therapeutic options available have become an urgent health threat to the immunocompromised pediatric population. Vaccines and antibodies, especially those targeting capsular polysaccharides, may be novel and effective prevention and treatment options. Thus, it is important to understand the spread of CRKP in pediatric populations. This research presents OL101:KL47 and O1:KL64 as the predominant combinations among CRKP strains in children in Shanghai, China. The primary carbapenemase gene is KPC in CRKP strains. Additionally, this study found elevated levels of anti-CPS IgG against K47 and K64 K. pneumoniae strains in pediatric patients for the first time. The significant bactericidal activity of these anti-CPS IgGs was confirmed.
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Hua Y, Wu Y, Guo M, Ma R, Li Q, Hu Z, Chen H, Zhang X, Li H, Li Q, He P. Characterization and Functional Studies of a Novel Depolymerase Against K19-Type Klebsiella pneumoniae. Front Microbiol 2022; 13:878800. [PMID: 35814656 PMCID: PMC9257171 DOI: 10.3389/fmicb.2022.878800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/31/2022] [Indexed: 12/14/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), a pathogen that causes severe nosocomial infections and yields a high mortality rate, poses a serious threat to global public health due to its high antimicrobial resistance. Bacteriophages encode polysaccharide-degrading enzymes referred to as depolymerases that cleave the capsular polysaccharide (CPS), one of the main virulence factors of K. pneumoniae. In this study, we identified and characterized a new capsule depolymerase K19-Dpo41 from K. pneumoniae bacteriophage SH-KP156570. Our characterization of K19-Dpo41 demonstrated that this depolymerase showed specific activities against K19-type K. pneumoniae. K19-Dpo41-mediated treatments promoted the sensitivity of a multidrug-resistant K19-type K. pneumoniae strain to the bactericidal effect of human serum and significantly increased the survival rate of Galleria mellonella infected with K19-type K. pneumoniae. Our results provided strong primary evidence that K19-Dpo41 was not only effective in capsular typing of K19-type K. pneumoniae but promising in terms of developing new alternative therapeutic strategies against K19-type CRKP infections in the future.
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Affiliation(s)
- Yunfen Hua
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongqin Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjie Guo
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA, United States
| | - Ruijing Ma
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Qingchuan Li
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheyuan Hu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongrui Chen
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingyu Zhang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qingtian Li,
| | - Ping He
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
- Ping He,
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In Vitro and In Vivo Assessments of Two Newly Isolated Bacteriophages against an ST13 Urinary Tract Infection Klebsiella pneumoniae. Viruses 2022; 14:v14051079. [PMID: 35632820 PMCID: PMC9144312 DOI: 10.3390/v14051079] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance represents a major public health concern requiring new alternatives including phage therapy. Klebsiella pneumoniae belongs to the ESKAPE bacteria and can cause urinary tract infections (UTIs). The aims of this study were to isolate and characterize new bacteriophages against a K. pneumoniae strain isolated from UTIs and to assess their efficacy in vitro and in vivo in a Galleria (G.) mellonella larvae model. For this purpose, two bacteriophages were newly isolated against an ST13 K. pneumoniae strain isolated from a UTI and identified as K3 capsular types by wzi gene PCR. Genomic analysis showed that these bacteriophages, named vB_KpnP_K3-ULINTkp1 and vB_KpnP_K3-ULINTkp2, belong to the Drulisvirus genus. Bacteriophage vB_KpnP_K3-ULINTkp1 had the narrowest host spectrum (targeting only K3), while vB_KpnP_K3-ULINTkp2 also infected other Klebsiella types. Short adsorption times and latent periods were observed for both bacteriophages. In vivo experiments showed their ability to replicate in G. mellonella larvae and to decrease host bacterial titers. Moreover, both bacteriophages improved the survival of the infected larvae. In conclusion, these two bacteriophages had different in vitro properties and showed in vivo efficacy in a G. mellonella model with a better efficiency for vB_KpnP_K3-ULINTkp2.
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