1
|
Lv Z, Zhang X, Zhao K, Du L, Wang X, Chu Y, Huang T. Co-immunization with DNA vaccines encoding yidR and IL-17 augments host immune response against Klebsiella pneumoniae infection in mouse model. Virulence 2024; 15:2345019. [PMID: 38656137 PMCID: PMC11057650 DOI: 10.1080/21505594.2024.2345019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Klebsiella pneumoniae is an important gram-negative bacterium that causes severe respiratory and healthcare-associated infections. Although antibiotic therapy is applied to treat severe infections caused by K. pneumoniae, drug-resistant isolates pose a huge challenge to clinical practices owing to adverse reactions and the mismanagement of antibiotics. Several studies have attempted to develop vaccines against K. pneumoniae, but there are no licensed vaccines available for the control of K. pneumoniae infection. In the current study, we constructed a novel DNA vaccine, pVAX1-YidR, which encodes a highly conserved virulence factor YidR and a recombinant expression plasmid pVAX1-IL-17 encoding Interleukin-17 (IL-17) as a molecular adjuvant. Adaptive immune responses were assessed in immunized mice to compare the immunogenicity of the different vaccine schemes. The results showed that the targeted antigen gene was expressed in HEK293T cells using an immunofluorescence assay. Mice immunized with pVAX1-YidR elicited a high level of antibodies, induced strong cellular immune responses, and protected mice from K. pneumoniae challenge. Notably, co-immunization with pVAX1-YidR and pVAX1-IL-17 significantly augmented host adaptive immune responses and provided better protection against K. pneumoniae infections in vaccinated mice. Our study demonstrates that combined DNA vaccines and molecular adjuvants is a promising strategy to develop efficacious antibacterial vaccines against K. pneumoniae infections.
Collapse
Affiliation(s)
- Zheng Lv
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Xuan Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Lianming Du
- Institute for Advanced Study, Chengdu University, Chengdu, China
| | - Xinrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Ting Huang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
- Antiinfective Agent Creation Engineering Research Centre of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| |
Collapse
|
2
|
Verburg I, Hernández Leal L, Waar K, Rossen JWA, Schmitt H, García-Cobos S. Klebsiella pneumoniae species complex: From wastewater to the environment. One Health 2024; 19:100880. [PMID: 39263320 PMCID: PMC11387367 DOI: 10.1016/j.onehlt.2024.100880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024] Open
Abstract
Klebsiella pneumoniae plays a significant role in nosocomial infections and spreading antibiotic resistance, and therefore forms a major threat to public health. In this study, we investigated the role of the wastewater pathway in the spread of pathogenic bacteria and more specifically, in the spread of antibiotic resistant Klebsiella pneumoniae subspecies. Whole-genome sequencing was performed of 185 K. pneumoniae isolates collected from hospital, nursing home, and community wastewater, the receiving wastewater treatment plant (WWTP), and clinical isolates from the investigated hospital. K. pneumoniae isolates from different sources were not genetically related, except for WWTP influent (46.5%) and effluent (62.5%), revealing survival of bacteria from wastewater treatment. The content of antibiotic resistance (ARGs), virulence, and plasmid replicon genes differed between K. pneumoniae subspecies and their origin. While chromosomal bla genes were specific for each K. pneumoniae subspecies, bla genes predicted in plasmid contigs were found in several K. pneumoniae subspecies, implying possible gene transfer between subspecies. Transferable ARGs were most abundant in patients and hospital isolates (70%), but the average number of plasmid replicon genes per isolate was similar across all sources, showing plasmid content being more relevant than plasmid quantity. Most patient (90%) and hospital wastewater (34%) isolates were K. pneumoniae subsp. pneumoniae, and the yersiniabactin cluster genes ybt, fyuA, and irp12 were only found in this subspecies, as were the IncFII(pECLA), IncHI2A, and IncHI2 plasmid replicon genes, suggesting the clinical origin of these type of plasmids.
Collapse
Affiliation(s)
- Ilse Verburg
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
| | - Lucia Hernández Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
| | - Karola Waar
- Certe Medische Microbiologie Friesland, 8900, JA, Leeuwarden, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, 8900, CC, Leeuwarden, the Netherlands
- Institute for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721, MA, Bilthoven, the Netherlands
| | - Silvia García-Cobos
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713, GZ, Groningen, the Netherlands
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
3
|
Lei TY, Liao BB, Yang LR, Wang Y, Chen XB. Hypervirulent and carbapenem-resistant Klebsiella pneumoniae: A global public health threat. Microbiol Res 2024; 288:127839. [PMID: 39141971 DOI: 10.1016/j.micres.2024.127839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 08/16/2024]
Abstract
The evolution of hypervirulent and carbapenem-resistant Klebsiella pneumoniae can be categorized into three main patterns: the evolution of KL1/KL2-hvKp strains into CR-hvKp, the evolution of carbapenem-resistant K. pneumoniae (CRKp) strains into hv-CRKp, and the acquisition of hybrid plasmids carrying carbapenem resistance and virulence genes by classical K. pneumoniae (cKp). These strains are characterized by multi-drug resistance, high virulence, and high infectivity. Currently, there are no effective methods for treating and surveillance this pathogen. In addition, the continuous horizontal transfer and clonal spread of these bacteria under the pressure of hospital antibiotics have led to the emergence of more drug-resistant strains. This review discusses the evolution and distribution characteristics of hypervirulent and carbapenem-resistant K. pneumoniae, the mechanisms of carbapenem resistance and hypervirulence, risk factors for susceptibility, infection syndromes, treatment regimens, real-time surveillance and preventive control measures. It also outlines the resistance mechanisms of antimicrobial drugs used to treat this pathogen, providing insights for developing new drugs, combination therapies, and a "One Health" approach. Narrowing the scope of surveillance but intensifying implementation efforts is a viable solution. Monitoring of strains can be focused primarily on hospitals and urban wastewater treatment plants.
Collapse
Affiliation(s)
- Ting-Yu Lei
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Bin-Bin Liao
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Liang-Rui Yang
- First Affiliated Hospital of Dali University, Yunnan 671000, China.
| | - Ying Wang
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Xu-Bing Chen
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| |
Collapse
|
4
|
Liu M, Wu J, Zhao J, Xi Y, Jin Y, Yang H, Chen S, Long J, Duan G. Global epidemiology and genetic diversity of mcr-positive Klebsiella pneumoniae: A systematic review and genomic analysis. ENVIRONMENTAL RESEARCH 2024; 259:119516. [PMID: 38950813 DOI: 10.1016/j.envres.2024.119516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
The rapid increase of mcr-positive Klebsiella pneumoniae (K. pneumoniae) has received considerable attention and poses a major public health concern. Here, we systematically analyzed the global distribution of mcr-positive K. pneumoniae isolates based on published articles as well as publicly available genomes. Combining strain information from 78 articles and 673 K. pneumoniae genomes, a total of 1000 mcr-positive K. pneumoniae isolates were identified. We found that mcr-positive K. pneumoniae has disseminated widely worldwide, especially in Asia, with a higher diversity of sequence types (STs). These isolates were disseminated in 57 countries and were associated with 12 different hosts. Most of the isolates were found in China and were isolated from human sources. Moreover, MLST analysis showed that ST15 and ST11 accounted for the majority of mcr-positive K. pneumoniae, which deserve sustained attention in further surveillance programs. mcr-1 and mcr-9 were the dominant mcr variants in mcr-positive K. pneumoniae. Furthermore, a Genome-wide association study (GWAS) demonstrated that mcr-1- and mcr-9-producing genomes exhibited different antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), thereby indicating a distinct evolutionary path. Notably, the phylogenetic analysis suggested that certain mcr-positive K. pneumoniae genomes from various geographical areas and hosts harbored a high degree of genetic similarities (<20 SNPs), suggesting frequent cross-region and cross-host clonal transmission. Overall, our results emphasize the significance of monitoring and exploring the transmission and evolution of mcr-positive K. pneumoniae in the context of "One health".
Collapse
Affiliation(s)
- Mengyue Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Wu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaxue Zhao
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanyan Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jinzhao Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
5
|
Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024; 22:598-616. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
Collapse
Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
6
|
Patnaik N, Orekonday N, Dey RJ. Isothermal recombinase polymerase amplification and silver nanoparticle assay: a sustainable approach for ultrasensitive detection of Klebsiella pneumoniae. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39323405 DOI: 10.1039/d4ay00993b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Our study addresses the urgent need for effective detection of Klebsiella pneumoniae, a recognized threat by the World Health Organization (WHO). Current challenges in managing K. pneumoniae infections include the lack of rapid and affordable detection tools, particularly in resource-limited point-of-care (POC) settings. To tackle this, we developed an innovative molecular detection pipeline combining three POC-compatible methods. Firstly, we employed Insta DNA™ card-based sample collection and DNA extraction for simplicity and ease of use. Next, we utilized recombinase polymerase amplification (RPA) targeting the Klebsiella hemolysin gene, khe, specific to the K. pneumoniae species complex (KpSC). Finally, we integrated a silver nanoparticle (AgNP) aggregation assay for visual detection, offering a rapid, sensitive, and specific method capable of detecting as few as ∼3 bacteria of K. pneumoniae within ∼45 minutes. This approach eliminates the need for complex equipment, making it highly suitable for field and resource-limited POC applications. Moreover, our method introduces an environmentally significant detection strategy. The method developed minimizes chemical reagent usage and reduces the carbon footprint associated with sample transportation. Furthermore, our method reduces waste compared to the traditional detection techniques, offering a safer alternative to ethidium bromide or other DNA dyes which are often genotoxic and mutagenic in nature. Silver nanoparticles, being environmentally safer, can also be recycled from the waste, contributing to sustainability in nanoparticle production and disposal. Overall, our technique presents a promising solution for detecting K. pneumoniae in various settings, including environmental, water, and food samples, as well as industrial or hospital effluents. By aligning with global efforts to improve public health and environmental sustainability, our approach holds significant potential for enhancing disease management and reducing environmental impact.
Collapse
Affiliation(s)
- Naresh Patnaik
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Telangana State 500078, India.
| | - Nidhi Orekonday
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Telangana State 500078, India.
| | - Ruchi Jain Dey
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Telangana State 500078, India.
| |
Collapse
|
7
|
Zhao M, Li H, Gan D, Wang M, Deng H, Yang QE. Antibacterial effect of phage cocktails and phage-antibiotic synergy against pathogenic Klebsiella pneumoniae. mSystems 2024; 9:e0060724. [PMID: 39166877 PMCID: PMC11406915 DOI: 10.1128/msystems.00607-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/15/2024] [Indexed: 08/23/2024] Open
Abstract
The global rise of antibiotic resistance has renewed interest in phage therapy, as an alternative to antibiotics to eliminate multidrug-resistant (MDR) bacterial pathogens. However, optimizing the broad-spectrum efficacy of phage therapy remains a challenge. In this study, we addressed this issue by employing strategies to improve antimicrobial efficacy of phage therapy against MDR Klebsiella pneumoniae strains, which are notorious for their resistance to conventional antibiotics. This includes the selection of broad host range phages, optimization of phage formulation, and combinations with last-resort antibiotics. Our findings unveil that having a broad host range was a dominant trait of isolated phages, and increasing phage numbers in combination with antibiotics significantly enhanced the suppression of bacterial growth. The decreased incidence of bacterial infection was explained by a reduction in pathogen density and emergence of bacterial resistance. Furthermore, phage-antibiotic synergy (PAS) demonstrated considerable broad-spectrum antibacterial potential against different clades of clinical MDR K. pneumoniae pathogens. The improved treatment outcomes of optimized PAS were also evident in a murine model, where mice receiving optimized PAS therapy demonstrated a reduced bacterial burden in mouse tissues. Taken together, these findings offer an important development in optimizing PAS therapy and its efficacy in the elimination of MDR K. pneumoniae pathogens. IMPORTANCE The worldwide spread of antimicrobial resistance (AMR) has posed a great challenge to global public health. Phage therapy has become a promising alternative against difficult-to-treat pathogens. One important goal of this study was to optimize the therapeutic efficiency of phage-antibiotic combinations, known as phage-antibiotic synergy (PAS). Through comprehensive analysis of the phenotypic and genotypic characteristics of a large number of CRKp-specific phages, we developed a systematic model for phage cocktail combinations. Crucially, our finding demonstrated that PAS treatments not only enhance the bactericidal effects of colistin and tigecycline against multidrug-resistant (MDR) K. pneumoniae strains in in vitro and in vivo context but also provide a robust response when antibiotics fail. Overall, the optimized PAS therapy demonstrates considerable potential in combating diverse K. pneumoniae pathogens, highlighting its relevance as a strategy to mitigate antibiotic resistance threats effectively.
Collapse
Affiliation(s)
- Mengshi Zhao
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongru Li
- Department of Infectious Disease, Shengli Medical College, Fujian Medical University, Fujian Provincial Hospital, Fuzhou University affiliated Provincial Hospital,, Fuzhou, China
| | - Dehao Gan
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengzhu Wang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Deng
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiu E Yang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
8
|
Stein M, Brinks E, Loop J, Habermann D, Cho GS, Franz CMAP. Antibiotic resistance plasmids in Enterobacteriaceae isolated from fresh produce in northern Germany. Microbiol Spectr 2024:e0036124. [PMID: 39287384 DOI: 10.1128/spectrum.00361-24] [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: 02/14/2024] [Accepted: 07/25/2024] [Indexed: 09/19/2024] Open
Abstract
In this study, the genomes of 22 Enterobacteriaceae isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two Citrobacter isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that Enterobacteriaceae from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for Enterobacteriaceae from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system. IMPORTANCE This study showed that Enterobacteriaceae from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria.
Collapse
Affiliation(s)
- Maria Stein
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Jannike Loop
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Diana Habermann
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Kiel, Germany
| |
Collapse
|
9
|
Dong W, Fan X, Guo Y, Wang S, Jia S, Lv N, Yuan T, Pan Y, Xue Y, Chen X, Xiong Q, Yang R, Zhao W, Zhu B. An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. Nat Commun 2024; 15:8084. [PMID: 39278950 PMCID: PMC11402979 DOI: 10.1038/s41467-024-51864-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/16/2024] [Indexed: 09/18/2024] Open
Abstract
Virulence factor genes (VFGs) play pivotal roles in bacterial infections and have been identified within the human gut microbiota. However, their involvement in chronic diseases remains poorly understood. Here, we establish an expanded VFG database (VFDB 2.0) consisting of 62,332 nonredundant orthologues and alleles of VFGs using species-specific average nucleotide identity ( https://github.com/Wanting-Dong/MetaVF_toolkit/tree/main/databases ). We further develop the MetaVF toolkit, facilitating the precise identification of pathobiont-carried VFGs at the species level. A thorough characterization of VFGs for 5452 commensal isolates from healthy individuals reveals that only 11 of 301 species harbour these factors. Further analyses of VFGs within the gut microbiomes of nine chronic diseases reveal both common and disease-specific VFG features. Notably, in type 2 diabetes patients, long HiFi sequencing confirms that shared VF features are carried by pathobiont strains of Escherichia coli and Klebsiella pneumoniae. These findings underscore the critical importance of identifying and understanding VFGs in microbiome-associated diseases.
Collapse
Affiliation(s)
- Wanting Dong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinyue Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaqiong Guo
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, 100089, China
| | - Siyi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulei Jia
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Yuan
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Xue
- National Engineering and Technology Research Center for Fruits and Vegetables, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xi Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Xiong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Weigang Zhao
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China.
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250117, China.
- Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing, 100101, China.
| |
Collapse
|
10
|
Zhu L, Zhang H, Xiao X, Sun S, Tong Y, Zhuang S, Sheng Z, Fan Y, Ma W, Liu Y, Qing S, Zhang W. Shuanghuanglian volatile oil exerts antipyretic, anti-inflammatory, and antibacterial synergistic effects through multiple pathways. JOURNAL OF ETHNOPHARMACOLOGY 2024; 337:118795. [PMID: 39278293 DOI: 10.1016/j.jep.2024.118795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 09/18/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese Medicine (TCM) has a rich history spanning 2000 years. Shuanghuanglian, a traditional Chinese herbal formula composed of three botanicals, is primarily used to treat colds, respiratory infections (including bacterial pneumonia), and pharyngitis. Previous research has found that the volatile oil of Shuanghuanglian is crucial for its efficacy. However, there is a lack of studies investigating its mechanisms. AIM OF THE STUDY This study aims to explore the antibacterial and anti-inflammatory mechanisms of Shuanghuanglian volatile oil and its potential to enhance the antibacterial effects when used in conjunction with antibiotics. METHODS Determination of the GC-MS fingerprint of SVO using Gas Chromatography-Mass Spectrometry (GC-MS), The antibacterial effects of SVO on multidrug-resistant Klebsiella pneumoniae (MDR-KP) were assessed by detecting MIC, checkerboard method assay, time-kill curves, resistance growth curves, transcriptome sequencing analysis, scanning electron microscopy(SEM), purification, and quantitative analysis of extracellular polysaccharides(EPS). In vivo part, an MDR-KP induced mouse pneumonia model was established to evaluate the mitigating effects of SVO on mouse pneumonia, using comprehensive network pharmacology and bioinformatics to identify genes related to bacterial pneumonia and potential targets of SVO. Validation was performed through molecular docking, qPCR, and ELISA tests. RESULTS SVO modulates the expression of MDR-KP mRNA for wecB, wecC, murA, murD, murE, murF, inhibiting the synthesis of O-antigen polysaccharides and peptidoglycans, thereby compromising bacterial cell wall integrity and affecting the synthesis of biofilms. These actions not only exhibit antibacterial effects but also enhance antibacterial activity, restoring the sensitivity of CEF to MDR-KP. SVO suppresses the biological activity of PTGS2, reducing the production of Prostaglandin E2 (PGE2), thereby exerting antipyretic and anti-inflammatory effects, providing new insights for the development of natural non-steroidal anti-inflammatory drugs (NSAIDs). CONCLUSIONS Our research indicates that SVO exerts antipyretic, anti-inflammatory, and antibacterial synergistic effects through multiple pathways.
Collapse
Affiliation(s)
- Leixin Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Hanwen Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China
| | - Xinglan Xiao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Shaoqiang Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China
| | - Yinchao Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Shen Zhuang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Zhenwei Sheng
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Yunpeng Fan
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Wuren Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Yingqiu Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China
| | - Suzhu Qing
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China.
| | - Weimin Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China; Institute of Traditional Chinese Veterinary Medicine, Northwest A&F University, Yangling, 712100, PR China.
| |
Collapse
|
11
|
Subramanian S, Geng H, Wu L, Du C, Peiper AM, Bu HF, Chou PM, Wang X, Tan SC, Iyer NR, Khan NH, Zechner EL, Fox JG, Breinbauer R, Qi C, Yamini B, Ting JP, De Plaen IG, Karst SM, Tan XD. Microbiota regulates neonatal disease tolerance to virus-evoked necrotizing enterocolitis by shaping the STAT1-NLRC5 axis in the intestinal epithelium. Cell Host Microbe 2024:S1931-3128(24)00320-2. [PMID: 39293437 DOI: 10.1016/j.chom.2024.08.013] [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: 02/05/2024] [Revised: 05/10/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024]
Abstract
Microbiota and feeding modes influence the susceptibility of premature newborns to necrotizing enterocolitis (NEC) through mechanisms that remain unknown. Here, we show that microbiota colonization facilitated by breastmilk feeding promotes NOD-like receptor family CARD domain containing 5 (Nlrc5) gene expression in mouse intestinal epithelial cells (IECs). Notably, inducible knockout of the Nlrc5 gene in IECs predisposes neonatal mice to NEC-like injury in the small intestine upon viral inflammation in an NK1.1+ cell-dependent manner. By contrast, formula feeding enhances neonatal gut colonization with environment-derived tilivalline-producing Klebsiella spp. Remarkably, tilivalline disrupts microbiota-activated STAT1 signaling that controls Nlrc5 gene expression in IECs through a PPAR-γ-mediated mechanism. Consequently, this dysregulation hinders the resistance of neonatal intestinal epithelium to self-NK1.1+ cell cytotoxicity upon virus infection/colonization, promoting NEC development. Together, we discover the underappreciated role of intestinal microbiota colonization in shaping a disease tolerance program to viral inflammation and elucidate the mechanisms impacting NEC development in neonates.
Collapse
Affiliation(s)
- Saravanan Subramanian
- Pediatric Mucosal Inflammation and Regeneration Research Program, Center for Pediatric Translational Research and Education, Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hua Geng
- Pediatric Mucosal Inflammation and Regeneration Research Program, Center for Pediatric Translational Research and Education, Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Longtao Wu
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, IL 60637, USA
| | - Chao Du
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Amy M Peiper
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Heng-Fu Bu
- Pediatric Mucosal Inflammation and Regeneration Research Program, Center for Pediatric Translational Research and Education, Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Pauline M Chou
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Xiao Wang
- Pediatric Mucosal Inflammation and Regeneration Research Program, Center for Pediatric Translational Research and Education, Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stephanie C Tan
- Department of Medical Education, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA
| | - Neha R Iyer
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Nazeer Hussain Khan
- Pediatric Mucosal Inflammation and Regeneration Research Program, Center for Pediatric Translational Research and Education, Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rolf Breinbauer
- Institute of Organic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Chao Qi
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bakhtiar Yamini
- Department of Surgery, Section of Neurosurgery, The University of Chicago, Chicago, IL 60637, USA
| | - Jenny P Ting
- Department of Genetics, Department of Microbiology-Immunology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Isabelle G De Plaen
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stephanie M Karst
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Xiao-Di Tan
- Pediatric Mucosal Inflammation and Regeneration Research Program, Center for Pediatric Translational Research and Education, Department of Pediatrics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA; Department of Research & Development, Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA.
| |
Collapse
|
12
|
Fuhrmeister ER, Kim S, Mairal SA, McCormack C, Chieng B, Swarthout JM, Paulos AH, Njenga SM, Pickering AJ. Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612745. [PMID: 39314343 PMCID: PMC11419053 DOI: 10.1101/2024.09.12.612745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs bla CTX-M and bla TEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containing bla TEM and one cluster containing bla CTX-M that were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia , and Haemophilus influenzae across sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.
Collapse
|
13
|
Stanton TD, Wyres KL. What defines hypervirulent Klebsiella pneumoniae? EBioMedicine 2024; 108:105331. [PMID: 39260040 DOI: 10.1016/j.ebiom.2024.105331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Affiliation(s)
- Thomas D Stanton
- Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria 3004, Australia; Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria 3004, Australia; Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia.
| |
Collapse
|
14
|
Xu DY, Leung KM, Lai GKK, Leung FCC, Griffin SDJ. Complete genome sequence of Klebsiella pneumoniae RX.G5M15, a methanol-metabolizing strain recovered from the sole of a shoe. Microbiol Resour Announc 2024; 13:e0045124. [PMID: 39162448 PMCID: PMC11384749 DOI: 10.1128/mra.00451-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
The methanol-metabolizing strain Klebsiella pneumoniae RX.G5M15 was isolated from the sole of a shoe in Hong Kong. Its complete genome, a single chromosome and two plasmids totaling 5,381,940 bp (G+C 57.43%), was established through the hybrid assembly.
Collapse
Affiliation(s)
- D Y Xu
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - K M Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - G K K Lai
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - F C C Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| | - S D J Griffin
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong SAR, China
| |
Collapse
|
15
|
Li F, Xu T, Fang D, Wang Z, Liu Y. Inosine reverses multidrug resistance in Gram-negative bacteria carrying mobilized RND-type efflux pump gene cluster tmexCD-toprJ. mSystems 2024:e0079724. [PMID: 39254032 DOI: 10.1128/msystems.00797-24] [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: 06/11/2024] [Accepted: 08/19/2024] [Indexed: 09/11/2024] Open
Abstract
Antimicrobial resistance is rapidly increasing worldwide, highlighting the urgent need for pharmaceutical and nonpharmaceutical interventions to tackle different-to-treat bacterial infections. Tigecycline, a semi-synthesis glycylcycline for parenteral administration, is widely recognized as one of the few effective therapies available against pan-drug resistant Gram-negative pathogens. Regrettably, the efficacy of multiple drugs, including tigecycline, is currently being undermined due to the emergence of a recently discovered mobilized resistance-nodulation-division-type efflux pump gene cluster tmexCD1-toprJ1. Herein, by employing untargeted metabolomic approaches, we reveal that the expression of tmexCD1-toprJ1 disrupts bacterial purine metabolism, with inosine being identified as a crucial biomarker. Notably, the supplementation of inosine effectively reverses tigecycline resistance in tmexCD1-toprJ1-positive bacteria. Mechanistically, exogenous inosine enhanced bacterial proton motive force, which promotes the uptake of tigecycline. Furthermore, inosine enhances succinate biosynthesis by stimulating the tricarboxylic acid cycle. Succinate interacts with the two-component system EnvZ/OmpR and upregulates OmpK 36, thereby promoting the influx of tigecycline. These actions collectively lead to the increased intracellular accumulation of tigecycline. Overall, our study offers a distinct combinational strategy to manage infections caused by tmexCD-toprJ-positive bacteria. IMPORTANCE TMexCD1-TOprJ1, a mobilized resistance-nodulation-division-type efflux pump, confers phenotypic resistance to multiple classes of antibiotics. Nowadays, tmexCD-toprJ has disseminated among diverse species of clinical pathogens, exacerbating the need for novel anti-infective strategies. In this study, we report that tmexCD1-toprJ1-negative and -positive bacteria exhibit significantly different metabolic flux and characteristics, especially in purine metabolism. Intriguingly, the addition of inosine, a purine metabolite, effectively restores the antibacterial activity of tigecycline by promoting antibiotic uptake. Our findings highlight the correlation between bacterial mechanism and antibiotic resistance, and offer a distinct approach to overcome tmexCD-toprJ-mediated multidrug resistance.
Collapse
Affiliation(s)
- Fulei Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Tianqi Xu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Dan Fang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| |
Collapse
|
16
|
Park G, Kadyan S, Hochuli N, Salazar G, Laitano O, Chakrabarty P, Efron PA, Zafar MA, Wilber A, Nagpal R. An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice. J Infect Dis 2024; 230:S95-S108. [PMID: 39255397 PMCID: PMC11385593 DOI: 10.1093/infdis/jiae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/26/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied. METHODS A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis. RESULTS K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations. CONCLUSIONS The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.
Collapse
Affiliation(s)
- Gwoncheol Park
- The Gut Biome Lab, Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
| | - Saurabh Kadyan
- The Gut Biome Lab, Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
| | - Nathaniel Hochuli
- The Gut Biome Lab, Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
| | - Gloria Salazar
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
| | - Orlando Laitano
- Department of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, Florida, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Philip A Efron
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, USA
| | - M Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Aaron Wilber
- Department of Psychology and Program in Neuroscience, Florida State University, Tallahassee, Florida, USA
| | - Ravinder Nagpal
- The Gut Biome Lab, Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, Florida, USA
| |
Collapse
|
17
|
van Linge CCA, Kullberg RFJ, Chouchane O, Roelofs JJTH, Goessens WHF, van 't Veer C, Sirard JC, de Vos AF, van der Poll T. Topical adjunctive treatment with flagellin augments pulmonary neutrophil responses and reduces bacterial dissemination in multidrug-resistant K. pneumoniae infection. Front Immunol 2024; 15:1450486. [PMID: 39295863 PMCID: PMC11408203 DOI: 10.3389/fimmu.2024.1450486] [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: 06/17/2024] [Accepted: 08/19/2024] [Indexed: 09/21/2024] Open
Abstract
Objective Antimicrobial resistance is an emerging problem and multi-drug resistant (MDR) Klebsiella pneumoniae (K. pneumoniae) represents an enormous risk of failing therapy in hospital-acquired pneumonia. The current study aimed to determine the immunomodulatory effect of topical flagellin in addition to antibiotic treatment during respiratory infection evoked by hypervirulent antibiotic-susceptible and antibiotic-resistant K. pneumoniae in mice. Methods C57BL6 mice were inoculated intranasally with hypervirulent K. pneumoniae (K2:O1) which was either antibiotic-susceptible or multi-drug resistant. Six hours after infection, mice were treated with antibiotics intraperitoneally and flagellin or vehicle intranasally. Mice were sacrificed 24 hours after infection. Samples were analyzed for bacterial loads and for inflammatory and coagulation markers. Results Flagellin therapy induced neutrophil influx in the lung during antibiotic-treated pneumonia evoked by either antibiotic-susceptible or -resistant K. pneumoniae. The pulmonary neutrophil response was matched by elevated levels of neutrophil-attracting chemokines, neutrophil degranulation products, and local coagulation activation. The combined therapy of effective antibiotics and flagellin did not impact K. pneumoniae outgrowth in the lung, but decreased bacterial counts in distant organs. Neutrophil depletion abrogated the flagellin-mediated effect on bacterial dissemination and local coagulation responses. Conclusion Topical flagellin administration as an adjunctive to antibiotic treatment augments neutrophil responses during pneumonia evoked by MDR-K. pneumoniae, thereby reducing bacterial dissemination to distant organs.
Collapse
Affiliation(s)
- Christine C A van Linge
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
| | - Robert F J Kullberg
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
| | - Osoul Chouchane
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
| | - Joris J T H Roelofs
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
- Department of Pathology, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Wil H F Goessens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Cornelis van 't Veer
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
| | - Jean-Claude Sirard
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, U1019 - UMR9017, centre hospitalier universitaire (CHU) Lille, Centre national de la recherche scientifique (CNRS), L'institut national de la santé et de la recherche médicale (INSERM), University of Lille, Lille, France
| | - Alex F de Vos
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection & Immunity Institute, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
18
|
Isogai M, Kawamura K, Yagi T, Kayama S, Sugai M, Doi Y, Suzuki M. Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis. Microb Genom 2024; 10. [PMID: 39298254 DOI: 10.1099/mgen.0.001295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that causes both community- and healthcare-associated infections. Although various virulence factors and highly pathogenic phenotypes have been reported, the pathogenicity of K. pneumoniae is still not fully understood. In this study, we utilized whole-genome sequencing data of 168 clinical K. pneumoniae strains to assess pathogenicity. This work was based on the concept that the genetic composition of individual genomes (referred to as holistic gene content) of the strains may contribute to their pathogenicity. Holistic gene content analysis revealed two distinct groups of K. pneumoniae strains ('major group' and 'minor group'). The minor group included strains with known highly pathogenic clones (ST23, ST375, ST65 and ST86). The minor group had higher rates of capsular genotype K1 and presence of nine specific virulence genes (rmpA, iucA, iutA, irp2, fyuA, ybtS, iroN, allS and clbA) compared to the major group. Pathogenicity was assessed using Galleria mellonella larvae. Infection experiments revealed lower survival rates of larvae infected with strains from the minor group, indicating higher virulence. In addition, the minor group had a higher string test positivity rate than the major group. Holistic gene content analysis predicted possession of virulence genes, string test positivity and pathogenicity as observed in the G. mellonella infection model. Moreover, the findings suggested the presence of as yet unrecognized genomic elements that are either involved in the acquisition of virulence genes or associated with pathogenicity.
Collapse
Affiliation(s)
- Miyu Isogai
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kumiko Kawamura
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shizuo Kayama
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
- Center for Innovative Antimicrobial Therapy, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
| |
Collapse
|
19
|
Cardoso Almeida AP, de Moraes MA, da Silva AKF, Oliveira-Silva M, Nakamura-Silva R, de Almeida FM, Pappas Junior GJ, Pitondo-Silva A, de Campos TA. Long-term occurrence of multiple antimicrobial drug resistant Klebsiella pneumoniae isolates harboring virulent potential in a tertiary hospital from Brazil. Braz J Microbiol 2024; 55:2313-2320. [PMID: 38743244 PMCID: PMC11405615 DOI: 10.1007/s42770-024-01358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Klebsiella pneumoniae strains are globally associated with a plethora of opportunistic and severe human infections and are known to spread genes conferring antimicrobial resistance. Some strains harbor virulence determinants that enable them to cause serious disease in any patient, both in the hospital and in the community. The aim of this study was to determine the frequency of antimicrobial resistance and virulence traits (by gene detection and string test) among 83 K. pneumoniae isolates obtained from patient cultures of a scholar tertiary hospital in the Midwestern Brazil (Brasília, DF). Antimicrobial susceptibility analysis showed that 94% (78/83) of the isolates presented one of the following resistance profiles: resistant (R, 39), multidrug-resistant (MDR, 29), or extensively drug-resistant (XDR, 10). Several MDR and XDR strains harbored multiple virulence genes and displayed hypermucoviscous phenotype. These characteristics were observed among isolates obtained throughout all the sample collection period (2013 - 2017). The K2 serotype gene, a molecular marker of hypervirulence, was detected in three isolates, one of which classified as XDR. Sequence typing revealed the occurrence of isolates belonged to high-risk (ST13) and multiple resistance-spreading clones (ST105). Thus, our findings showed the occurrence of virulent potential isolates that also presented MDR/XDR phenotypes from 2013 to 2015. This study also indicates the probable convergence of virulence and resistance since at least 2013 in Brazil.
Collapse
Affiliation(s)
- Ana Paula Cardoso Almeida
- Programa de Pós-Graduação Em Biologia Microbiana, Universidade de Brasília, Brasília, Distrito Federal, Brasil
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasilia, DF, CEP70910-900, Brazil
| | - Miguel Augusto de Moraes
- Faculdade de Ciências Farmacêuticas, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
- Programa de Pós-Graduação Em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
| | - Amanda Kamyla Ferreira da Silva
- Faculdade de Ciências Farmacêuticas, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
- Programa de Pós-Graduação Em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
| | - Mariana Oliveira-Silva
- Programa de Pós-Graduação Em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
| | - Rafael Nakamura-Silva
- Programa de Pós-Graduação Em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
| | | | - Georgios Joannis Pappas Junior
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasilia, DF, CEP70910-900, Brazil
- Programa de Pós-Graduação Em Biologia Molecular, Universidade de Brasília, Brasília, DF, Brasil
| | - André Pitondo-Silva
- Faculdade de Ciências Farmacêuticas, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
- Programa de Pós-Graduação Em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
- Programa de Pós-Graduação Em Odontologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brasil
| | - Tatiana Amabile de Campos
- Programa de Pós-Graduação Em Biologia Microbiana, Universidade de Brasília, Brasília, Distrito Federal, Brasil.
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasilia, DF, CEP70910-900, Brazil.
| |
Collapse
|
20
|
Li T, Ren X, Luo X, Wang Z, Li Z, Luo X, Shen J, Li Y, Yuan D, Nussinov R, Zeng X, Shi J, Cheng F. A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection. Nat Commun 2024; 15:7538. [PMID: 39214978 PMCID: PMC11364768 DOI: 10.1038/s41467-024-51933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Development of potent and broad-spectrum antimicrobial peptides (AMPs) could help overcome the antimicrobial resistance crisis. We develop a peptide language-based deep generative framework (deepAMP) for identifying potent, broad-spectrum AMPs. Using deepAMP to reduce antimicrobial resistance and enhance the membrane-disrupting abilities of AMPs, we identify, synthesize, and experimentally test 18 T1-AMP (Tier 1) and 11 T2-AMP (Tier 2) candidates in a two-round design and by employing cross-optimization-validation. More than 90% of the designed AMPs show a better inhibition than penetratin in both Gram-positive (i.e., S. aureus) and Gram-negative bacteria (i.e., K. pneumoniae and P. aeruginosa). T2-9 shows the strongest antibacterial activity, comparable to FDA-approved antibiotics. We show that three AMPs (T1-2, T1-5 and T2-10) significantly reduce resistance to S. aureus compared to ciprofloxacin and are effective against skin wound infection in a female wound mouse model infected with P. aeruginosa. In summary, deepAMP expedites discovery of effective, broad-spectrum AMPs against drug-resistant bacteria.
Collapse
Affiliation(s)
- Tingting Li
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, Guangdong Province, China
| | - Xuanbai Ren
- College of Information Science and Engineering, Hunan University, Changsha, China
| | - Xiaoli Luo
- College of Information Science and Engineering, Hunan University, Changsha, China
| | - Zhuole Wang
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, Guangdong Province, China
| | - Zhenlu Li
- School of Life Science, Tianjin University, Tianjin, 300072, China
| | - Xiaoyan Luo
- College of Information Science and Engineering, Hunan University, Changsha, China
| | - Jun Shen
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, Guangdong Province, China
| | - Yun Li
- Department of Ophthalmology, The 2nd Xiangya Hospital of Central South University, Changsha, China
| | - Dan Yuan
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, Guangdong Province, China
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Xiangxiang Zeng
- College of Information Science and Engineering, Hunan University, Changsha, China.
| | - Junfeng Shi
- Affiliated Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha, China.
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, 511300, Guangdong Province, China.
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Genome Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
21
|
Ferriol-González C, Concha-Eloko R, Bernabéu-Gimeno M, Fernández-Cuenca F, Cañada-García JE, García-Cobos S, Sanjuán R, Domingo-Calap P. Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy. Microbiol Spectr 2024:e0025424. [PMID: 39194291 DOI: 10.1128/spectrum.00254-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/06/2024] [Indexed: 08/29/2024] Open
Abstract
Klebsiella pneumoniae is one of the most threatening multi-drug-resistant pathogens today, with phage therapy being a promising alternative for personalized treatments. However, the intrinsic capsule diversity in Klebsiella spp. poses a substantial barrier to the phage host range, complicating the development of broad-spectrum phage-based treatments. Here, we have isolated and genomically characterized phages capable of infecting each of the acquired 77 reference serotypes of Klebsiella spp., including capsular types widespread among high-risk K. pneumoniae clones causing nosocomial infections. We demonstrated the possibility of isolating phages for all capsular types in the collection, revealing high capsular specificity among taxonomically related phages, in contrast to a few phages that exhibited broad-spectrum infection capabilities. To decipher the determinants of the specificity of these phages, we focused on their receptor-binding proteins, with particular attention to depolymerases. We also explored the possibility of designing a broad-spectrum phage cocktail based on phages isolated in reference capsular-type strains and determining the ability to lyse relevant clinical isolates. A combination of 12 phages capable of infecting 55% of the reference Klebsiella spp. serotypes was tested on a panel of carbapenem-resistant K. pneumoniae clinical isolates. Thirty-one percent of isolates were susceptible to the phage cocktail. However, our results suggest that in a highly variable encapsulated bacterial host, phage hunting must be directed to the specific Klebsiella isolates. This work is a step forward in the understanding of the complexity of phage-host interactions and highlights the importance of implementing precise and phage-specific strategies to treat K. pneumoniae infections worldwide.IMPORTANCEThe emergence of resistant bacteria is a serious global health problem. In the absence of effective treatments, phages are a personalized and effective therapeutic alternative. However, little is still known about phage-host interactions, which are key to implementing effective strategies. Here, we focus on the study of Klebsiella pneumoniae, a highly pathogenic encapsulated bacterium. The complexity and variability of the capsule, where in most cases phage receptors are found, make it difficult for phage-based treatments. Here, we isolated a large collection of Klebsiella phages against all the reference strains and in a cohort of clinical isolates. Our results suggest that clinical isolates represent a challenge, especially high-risk clones. Thus, we propose targeted phage hunting as an effective strategy to implement phage-derived therapies. Our results are a step forward for new phage-based strategies to control K. pneumoniae infections, highlighting the importance of understanding phage-host interactions to design personalized treatments against Klebsiella spp.
Collapse
Affiliation(s)
- Celia Ferriol-González
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Robby Concha-Eloko
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Mireia Bernabéu-Gimeno
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena-CSIC-Universidad de Sevilla, Sevilla, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier E Cañada-García
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia García-Cobos
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Sanjuán
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| |
Collapse
|
22
|
Gray J, Torres VVL, Goodall E, McKeand SA, Scales D, Collins C, Wetherall L, Lian ZJ, Bryant JA, Milner MT, Dunne KA, Icke C, Rooke JL, Schneiders T, Lund PA, Cunningham AF, Cole JA, Henderson IR. Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum. eLife 2024; 12:RP88971. [PMID: 39189918 PMCID: PMC11349299 DOI: 10.7554/elife.88971] [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] [Indexed: 08/28/2024] Open
Abstract
Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
Collapse
Affiliation(s)
- Jessica Gray
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Von Vergel L Torres
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Emily Goodall
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Samantha A McKeand
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Danielle Scales
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christy Collins
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Laura Wetherall
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Zheng Jie Lian
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Matthew T Milner
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Karl A Dunne
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christopher Icke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jessica L Rooke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Thamarai Schneiders
- Division of Infection Medicine, University of EdinburghEdinburghUnited Kingdom
| | - Peter A Lund
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of BirminghamBirminghamUnited Kingdom
| | - Jeff A Cole
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| |
Collapse
|
23
|
Vornhagen J, Rao K, Bachman MA. Gut community structure as a risk factor for infection in Klebsiella pneumoniae-colonized patients. mSystems 2024; 9:e0078624. [PMID: 38975759 PMCID: PMC11334466 DOI: 10.1128/msystems.00786-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
The primary risk factor for infection with members of the Klebsiella pneumoniae species complex is prior gut colonization, and infection is often caused by the colonizing strain. Despite the importance of the gut as a reservoir for infectious K. pneumoniae, little is known about the association between the gut microbiome and infection. To explore this relationship, we undertook a case-control study comparing the gut community structure of K. pneumoniae-colonized intensive care and hematology/oncology patients. Cases were K. pneumoniae-colonized patients infected by their colonizing strain (N = 83). Controls were K. pneumoniae-colonized patients who remained asymptomatic (N = 149). First, we characterized the gut community structure of K. pneumoniae-colonized patients agnostic to case status. Next, we determined that gut community data is useful for classifying cases and controls using machine learning models and that the gut community structure differed between cases and controls. K. pneumoniae relative abundance, a known risk factor for infection, had the greatest feature importance, but other gut microbes were also informative. Finally, we show that integration of gut community structure with bacterial genotype data enhanced the ability of machine learning models to discriminate cases and controls. Interestingly, inclusion of patient clinical variables failed to improve the ability of machine learning models to discriminate cases and controls. This study demonstrates that including gut community data with K. pneumoniae-derived biomarkers improves our ability to classify infection in K. pneumoniae-colonized patients.IMPORTANCEColonization is generally the first step in pathogenesis for bacteria with pathogenic potential. This step provides a unique window for intervention since a given potential pathogen has yet to cause damage to its host. Moreover, intervention during the colonization stage may help alleviate the burden of therapy failure as antimicrobial resistance rises. Yet, to understand the therapeutic potential of interventions that target colonization, we must first understand the biology of colonization and if biomarkers at the colonization stage can be used to stratify infection risk. The bacterial genus Klebsiella includes many species with varying degrees of pathogenic potential. Members of the K. pneumoniae species complex have the highest pathogenic potential. Patients colonized in their gut by these bacteria are at higher risk of subsequent infection with their colonizing strain. However, we do not understand if other members of the gut microbiota can be used as a biomarker to predict infection risk. In this study, we show that the gut microbiota differs between colonized patients who develop an infection versus those who do not. Additionally, we show that integrating gut microbiota data with bacterial factors improves the ability to classify infections. Surprisingly, patient clinical factors were not useful for classifying infections alone or when added to microbiota-based models. This indicates that the bacterial genotype and the microbial community in which it exists may determine the progression to infection. As we continue to explore colonization as an intervention point to prevent infections in individuals colonized by potential pathogens, we must develop effective means for predicting and stratifying infection risk.
Collapse
Affiliation(s)
- Jay Vornhagen
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Krishna Rao
- Department of Internal Medicine/Infectious Diseases Division, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
24
|
Gholizadeh O, Ghaleh HEG, Tat M, Ranjbar R, Dorostkar R. The potential use of bacteriophages as antibacterial agents against Klebsiella pneumoniae. Virol J 2024; 21:191. [PMID: 39160541 PMCID: PMC11334591 DOI: 10.1186/s12985-024-02450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/29/2024] [Indexed: 08/21/2024] Open
Abstract
One of the most common bacteria that cause nosocomial infections is Klebsiella pneumonia (K. pneumoniae), especially in patients who are very sick and admitted to the intensive care unit (ICU). The frequency of multi-drug-resistant Klebsiella pneumoniae (MDRKP) has dramatically increased worldwide in recent decades, posing an urgent threat to public health. The Western world's bacteriophage (phage) studies have been revitalized due to the increasing reports of antimicrobial resistance and the restricted development and discovery of new antibiotics. These factors have also spurred innovation in other scientific domains. The primary agent in phage treatment is an obligately lytic organism (called bacteriophage) that kills the corresponding bacterial host while sparing human cells and lessening the broader effects of antibiotic usage on commensal bacteria. Phage treatment is developing quickly, leading to many clinical studies and instances of life-saving medicinal use. In addition, phage treatment has a few immunological adverse effects and consequences in addition to its usefulness. Since K. pneumoniae antibiotic resistance has made treating multidrug-resistant (MDR) infections challenging, phage therapy (PT) has emerged as a novel therapeutic strategy. The effectiveness of phages has also been investigated in K. pneumoniae biofilms and animal infection models. Compared with antibiotics, PT exhibits numerous advantages, including a particular lysis spectrum, co-evolution with bacteria to avoid the emergence of phage resistance, and a higher abundance and diversity of phage resources than found in antibiotics. Moreover, phages are eliminated in the absence of a host bacterium, which makes them the only therapeutic agent that self-regulates at the sites of infection. Therefore, it is essential to pay attention to the role of PT in treating these infections. This study summarizes the state of knowledge on Klebsiella spp. phages and provides an outlook on the development of phage-based treatments that target K. pneumoniae in clinical trials.
Collapse
Affiliation(s)
- Omid Gholizadeh
- Student Research Committee, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hadi Esmaeili Gouvarchin Ghaleh
- Applied Virology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdi Tat
- Applied Virology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ruhollah Dorostkar
- Applied Virology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
25
|
Khan MM, Mushtaq MA, Abbas N, Fatima F, Gibbon MJ, Schierack P, Mohsin M. Occurrence, antimicrobial resistance and genomic features of Klebsiella pneumoniae from broiler chicken in Faisalabad, Pakistan. Front Vet Sci 2024; 11:1433124. [PMID: 39224453 PMCID: PMC11366712 DOI: 10.3389/fvets.2024.1433124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction The dissemination of antimicrobial resistance (AMR) in critical priority pathogens is a significant threat. Non-clinical reservoirs of AMR, such as agriculture and food production facilities, may contribute to the transmission of clinically relevant pathogens such as multidrug-resistant (MDR) Klebsiella pneumoniae. There is currently very limited knowledge regarding the population structure and genomic diversity of K. pneumoniae in poultry production in Pakistan. Methods We explored healthy broilers in a commercial farm from Faisalabad, Pakistan, and identified six K. pneumoniae strains from 100 broiler birds. We characterized the strains, determining clonality, virulence and antimicrobial resistance genes using next generation sequencing. Results The evaluation of antimicrobial susceptibility revealed that all the strains were MDR. Genomic analysis showed that 3/6 strains belonged to ST152, harbouring acquired resistance aminoglycosides [aadA2, aph(4')-Ia], β-lactams (blaSHV-187 , blaLAP2 ), fosfomycin (fosA6), tetracycline (tetA), trimethoprim (dfrA12), quinolone (qnrS1), sulphonamides (sul2) and phenicol (floR). All the strains harboured the efflux pump genes oqxA, oqxB, emrR, kpnG, kpnH, kpnF, baeR, mtdB and mtdC. All six strains encoded identical virulence profiles possessing six genes, i.e., ureA, iutA, entB, allS, fimH and mrkD. Phylogenomic analysis of the dominant sequence type (ST152) present in our dataset with publicly available genomes showed that the isolates clustered to strains mainly from human sources and could pose a potential threat to food safety and public health. Discussion The combination of these findings with antimicrobial use data would allow a better understanding of the selective pressures that may be driving the spread of AMR. This is the first report of MDR K. pneumoniae isolated from broiler hens in Pakistan, and the finding suggests that routine surveillance of WHO critical priority pathogens in such settings would be beneficial to the development of effective control strategies to reduce AMR.
Collapse
Affiliation(s)
- Muhammad Moman Khan
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Muhammad Ahmed Mushtaq
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Nayyar Abbas
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Fariha Fatima
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Marjorie J. Gibbon
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Peter Schierack
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| |
Collapse
|
26
|
Ikhimiukor OO, Zac Soligno NI, Akintayo IJ, Marcovici MM, Souza SSR, Workman A, Martin IW, Andam CP. Clonal background and routes of plasmid transmission underlie antimicrobial resistance features of bloodstream Klebsiella pneumoniae. Nat Commun 2024; 15:6969. [PMID: 39138200 PMCID: PMC11322185 DOI: 10.1038/s41467-024-51374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Bloodstream infections caused by the opportunistic pathogen Klebsiella pneumoniae are associated with adverse health complications and high mortality rates. Antimicrobial resistance (AMR) limits available treatment options, thus exacerbating its public health and clinical burden. Here, we aim to elucidate the population structure of K. pneumoniae in bloodstream infections from a single medical center and the drivers that facilitate the dissemination of AMR. Analysis of 136 short-read genome sequences complemented with 12 long-read sequences shows the population consisting of 94 sequence types (STs) and 99 clonal groups, including globally distributed multidrug resistant and hypervirulent clones. In vitro antimicrobial susceptibility testing and in silico identification of AMR determinants reveal high concordance (90.44-100%) for aminoglycosides, beta-lactams, carbapenems, cephalosporins, quinolones, and sulfonamides. IncF plasmids mediate the clonal (within the same lineage) and horizontal (between lineages) transmission of the extended-spectrum beta-lactamase gene blaCTX-M-15. Nearly identical plasmids are recovered from isolates over a span of two years indicating long-term persistence. The genetic determinants for hypervirulence are carried on plasmids exhibiting genomic rearrangement, loss, and/or truncation. Our findings highlight the importance of considering both the genetic background of host strains and the routes of plasmid transmission in understanding the spread of AMR in bloodstream infections.
Collapse
Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| | - Nicole I Zac Soligno
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Ifeoluwa J Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M Marcovici
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| |
Collapse
|
27
|
Wu K, Lin X, Lu Y, Dong R, Jiang H, Svensson SL, Zheng J, Shen N, Camilli A, Chao Y. RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence. Nat Commun 2024; 15:6946. [PMID: 39138169 PMCID: PMC11322559 DOI: 10.1038/s41467-024-51213-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging bacterial pathogen causing invasive infection in immune-competent humans. The hypervirulence is strongly linked to the overproduction of hypermucoviscous capsule, but the underlying regulatory mechanisms of hypermucoviscosity (HMV) have been elusive, especially at the post-transcriptional level mediated by small noncoding RNAs (sRNAs). Using a recently developed RNA interactome profiling approach iRIL-seq, we interrogate the Hfq-associated sRNA regulatory network and establish an intracellular RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNAs that repress or promote HMV. One of the strongest HMV repressors is ArcZ, which is activated by the catabolite regulator CRP and targets many HMV-related genes including mlaA and fbp. We discover that MlaA and its function in phospholipid transport is crucial for capsule retention and HMV, inactivation of which abolishes Klebsiella virulence in mice. ArcZ overexpression drastically reduces bacterial burden in mice and reduces HMV in multiple hypervirulent and carbapenem-resistant clinical isolates, indicating ArcZ is a potent RNA inhibitor of bacterial pneumonia with therapeutic potential. Our work unravels a novel CRP-ArcZ-MlaA regulatory circuit of HMV and provides mechanistic insights into the posttranscriptional virulence control in a superbug of global concern.
Collapse
Affiliation(s)
- Kejing Wu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xingyu Lin
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Lu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Dong
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Hongnian Jiang
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sarah L Svensson
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Zheng
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of RNA Innovation, Science and Engineering (RISE), Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
28
|
Jiang C, Yu C, Sun S, Lin J, Cai M, Wei Z, Feng L, Li J, Zhang Y, Dong K, Guo X, Qin J, Zhang Y. A new anti-CRISPR gene promotes the spread of drug-resistance plasmids in Klebsiella pneumoniae. Nucleic Acids Res 2024; 52:8370-8384. [PMID: 38888121 DOI: 10.1093/nar/gkae516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
The Klebsiella pneumoniae (K. pneumoniae, Kp) populations carrying both resistance-encoding and virulence-encoding mobile genetic elements (MGEs) significantly threaten global health. In this study, we identified a new anti-CRISPR gene (acrIE10) on a conjugative plasmid with self-target sequence in K. pneumoniae with type I-E* CRISPR-Cas system. AcrIE10 interacts with the Cas7* subunit of K. pneumoniae I-E* CRISPR-Cas system. The crystal structure of the AcrIE10-KpCas7* complex suggests that AcrIE10 suppresses the I-E* CRISPR-Cas by binding directly to Cas7 to prevent its hexamerization, thereby preventing the surveillance complex assembly and crRNA loading. Bioinformatic and functional analyses revealed that AcrIE10 is functionally widespread across diverse species. Our study reports a novel anti-CRISPR and highlights its potential role in spreading resistance and virulence among pathogens.
Collapse
Affiliation(s)
- Chunyu Jiang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chengzhi Yu
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyi Sun
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Lin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mufeng Cai
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhenquan Wei
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingling Feng
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jianhui Li
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ke Dong
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinhong Qin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- NHC Key Laboratory of Parasite and Vector Biology (National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention), Shanghai 200025, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
29
|
Yan W, Xu D, Shen Y, Dong F, Ji L. Molecular epidemiology of string test-positive Klebsiella pneumoniae isolates in Huzhou, China, 2020-2023. Front Cell Infect Microbiol 2024; 14:1411658. [PMID: 39165917 PMCID: PMC11333340 DOI: 10.3389/fcimb.2024.1411658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/15/2024] [Indexed: 08/22/2024] Open
Abstract
Objective This study used whole-genome sequencing (WGS) to explore the genetic diversity, virulence factors, and antimicrobial resistance determinants of string test-positive Klebsiella pneumoniae (KP) over a 4-year surveillance period in Huzhou, China. Methods In total, 632 clinical isolates were collected via hospital surveillance from 2020 to 2023; 100 were positive in the string test and these 100 strains were subjected to antimicrobial susceptibility testing using an agar dilution method followed by WGS. Results The resistance rates to cefotaxime (77.0%), trimethoprim-sulfamethoxazole (67.0%), and nalidixic acid (64.0%) were high. Multilocus sequence typing revealed high genetic diversity; there were 33 sequence types (STs) and 15 capsular serotypes. The most common ST was ST23 (16.0%) and the most common capsular serotype was K1 (22.5%). Virulome analysis revealed among-strain differences in virulence factors that affected bacterial adherence, efflux pump action, iron uptake, nutritional factors, metabolic regulation, the secretion system, and toxin production. The Kleborate strain-specific virulence scores of all 100 string test-positive KPs were derived: 28 strains scored 5, 28 scored 4, 21 scored 3, 12 scored 1, and 11 scored 0. All 77 strains with scores of 3 to 5 contained the iucA gene. The phylogeny based on whole-genome single nucleotide polymorphisms (wgSNPs) indicated high clonality; the string test-positive KP strains were grouped into six clades. Closely related isolates in each genetic cluster usually shared STs. Conclusion The present study highlights the significance of the KP iucA gene in terms of hypervirulence and the diverse genotypes of string test-positive KP strains isolated in Huzhou hospitals.
Collapse
Affiliation(s)
| | | | | | | | - Lei Ji
- Microbe Laboratory, Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| |
Collapse
|
30
|
Liu C, Guo J, Fan S, Guo W, Qi H, Baker S, Du P, Cao B. An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic. Drug Resist Updat 2024; 77:101124. [PMID: 39128195 DOI: 10.1016/j.drup.2024.101124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Klebsiella pneumoniae (Kp) is a common community-acquired and nosocomial pathogen. Carbapenem-resistant and hypervirulent (CR-hvKp) variants can emerge rapidly within healthcare facilities and impacted by other infectious agents such as COVID-19 virus. METHODS To understand the impact of COVID-19 virus on the prevalence of CR-hvKp, we accessed Kp genomes with corresponding metadata from GenBank. Sequence types (STs), antimicrobial resistance genes, and virulence genes, and those scores and CR-hvKp were identified. We analyzed population diversity and phylogenetic characteristics of five most common STs, measured the prevalence of CR-hvKp, identified CR-hvKp subtypes, and determined associations between carbapenem resistance gene subtypes with STs and plasmid types. These variables were compared pre- and during the COVID-19 pandemic. FINDINGS The proportion of CR-hvKp isolates increased within multiple STs in different continents during the COVID-19 pandemic and persistent CR-hvKp subtypes were found in common STs. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 and its subtypes were prevalent in ST15 (80.5 %). The possession of carbapenemase genes was different among subclades from different origins in different periods of time within each ST. IncFIB/IncHI1B hybrid plasmids contained virulence genes and carbapenemase genes and were predominant in ST147 (67.37 %) and ST307 (56.25 %). INTERPRETATION The prevalence of CR-hvKp increased during the COVID-19 pandemic, which was evident by an increase in local endemic clones. This process was facilitated by the convergence of plasmids containing carbapenemase genes and virulence genes. These findings have implications for the appropriate use of antimicrobials and infection prevention and control during outbreaks of respiratory viruses and pandemic management.
Collapse
Affiliation(s)
- Chao Liu
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Jun Guo
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Shuaihua Fan
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Wei Guo
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Huaiqing Qi
- Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Department of Respiratory Medicine, Capital Medical University, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijiing, China.
| |
Collapse
|
31
|
Zhang Y, Liu M, Zhang J, Wu J, Hong L, Zhu L, Long J. Large-scale comparative analysis reveals phylogenomic preference of bla NDM-1 and bla KPC-2 transmission among Klebsiella pneumoniae. Int J Antimicrob Agents 2024; 64:107225. [PMID: 38810941 DOI: 10.1016/j.ijantimicag.2024.107225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
blaNDM-1 and blaKPC-2 are responsible for the global increase in carbapenem-resistant Klebsiella pneumoniae, posing a great challenge to public health. However, the impact of phylogenetic factors on the dissemination of blaNDM-1 and blaKPC-2 is not yet fully understood. This study established a global dataset of 4051 blaNDM-1+ and 10,223 blaKPC-2+ K. pneumoniae genomes, and compared their transmission modes on a global scale. The results showed that blaNDM-1+ K. pneumoniae genomes exhibited a broader geographical distribution and higher sequence type (ST) richness than blaKPC-2+ genomes, indicating higher transmissibility of the blaNDM-1 gene. Furthermore, blaNDM-1+ genomes displayed significant differences in ST lineage, antibiotic resistance gene composition, virulence gene composition and genetic environments compared with blaKPC-2+ genomes, suggesting distinct dissemination mechanisms. blaNDM-1+ genomes were predominantly associated with ST147 and ST16, whereas blaKPC-2+ genomes were mainly found in ST11 and ST258. Significantly different accessory genes were identified between blaNDM-1+ and blaKPC-2+ genomes. The preference for blaKPC-2 distribution across certain countries, ST lineages and genetic environments underscores vertical spread as the primary mechanism driving the expansion of blaKPC-2. In contrast, blaNDM-1+ genomes did not display such a strong preference, confirming that the dissemination of blaNDM-1 mainly depends on horizontal gene transfer. Overall, this study demonstrates different phylogenetic drivers for the dissemination of blaNDM-1 and blaKPC-2, providing new insights into their global transmission dynamics.
Collapse
Affiliation(s)
- Yali Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mengyue Liu
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangfeng Zhang
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou, Henan, China
| | - Jie Wu
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Lijuan Hong
- Department Hospital-Acquired Infection Control, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China.
| | - LiQiang Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Jinzhao Long
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|
32
|
Qian J, Jin P, Yang Y, Ma N, Yang Z, Zhang X. Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models. Microb Pathog 2024; 193:106727. [PMID: 38851362 DOI: 10.1016/j.micpath.2024.106727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat to public health. The protein function of this bacterium is not well known, thus a systematic investigation of K. pneumoniae proteome is in urgent need. In this study, the protein functions of this bacteria were re-annotated, and their function groups were analyzed. Moreover, three machine learning models were built to identify novel virulence factors. Results showed that the functions of 16 uncharacterized proteins were first annotated by sequence alignment. In addition, K. pneumoniae proteins share a high proportion of homology with Haemophilus influenzae and a low homology proportion with Chlamydia pneumoniae. By sequence analysis, 10 proteins were identified as potential drug targets for this bacterium. Our model achieved a high accuracy of 0.901 in the benchmark dataset. By applying our models to K. pneumoniae, we identified 39 virulence factors in this pathogen. Our findings could provide novel clues for the treatment of K. pneumoniae infection.
Collapse
Affiliation(s)
- Jinyang Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Pengfei Jin
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Yueyue Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Xiaoli Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| |
Collapse
|
33
|
Sultana S, Ashwini BS, Ansari MA, Alomary MN, Jamous YF, Ravikiran T, Niranjana SR, Begum MY, Siddiqua A, Lakshmeesha TR. Catharanthus roseus-assisted bio-fabricated zinc oxide nanoparticles for promising antibacterial potential against Klebsiella pneumoniae. Bioprocess Biosyst Eng 2024; 47:1259-1269. [PMID: 38526617 DOI: 10.1007/s00449-024-03001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
This study emphasized on the synthesis of zinc oxide nanoparticles (ZnO NPs) in an environmentally friendly manner from the extract of Catharanthus roseus leaves and its antibacterial assessment against the pneumonia-causing pathogen Klebsiella pneumoniae. This simple and convenient phytosynthesis approach is found to be beneficial over conventional methods, wherein plants serve as excellent reducing, capping, and stabilizing agents that enables the formation of ZnO NPs without the use of harmful chemicals. The formation of ZnO NPs was confirmed through several characterization techniques such as UV-visible spectroscopy, XRD, FT-IR, SEM, HR-TEM, and EDX. XRD analysis revealed high polycrystallinity with crystallite size of approximately 13 nm. SEM and HR-TEM revealed the hexagonal structure of ZnO NPs with the particle size range of 20-50 nm. The EDX shows the elemental purity without any impurity. Furthermore, the antibacterial efficacy by the technique of disc diffusion exhibited clear inhibition zones in ZnO NPs-treated discs. In addition, 125 µg/mL of ZnO NP concentration showed minimum inhibition by the microbroth dilution method. The potent inhibitory activity was further validated with trypan blue dye exclusion and fluorescence microscopy. Finally, SEM examination confirmed the efficient antibacterial potential of ZnO NPs through disruption of the intact morphology of Klebsiella pneumoniae.
Collapse
Affiliation(s)
- Sumreen Sultana
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru, 560056, India
| | - Bagepalli Shivaram Ashwini
- Department of Microbiology, Shri Atal Bihari Vajpayee Medical College & Research Institute, Bengaluru, 560001, India
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia.
| | - Mohammad N Alomary
- Advanced Diagnostic and Therapeutic Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Yahya F Jamous
- Vaccine and Bioprocessing Center, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Tekupalli Ravikiran
- Department of Microbiology and Biotechnology, Bangalore University, Jnana Bharathi Campus, Bengaluru, 560056, India
| | | | - M Yasmin Begum
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ayesha Siddiqua
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | | |
Collapse
|
34
|
Mo X, Zhang H, Fan J, Xu L, Fu H, Yue J, Dong K, Luo Q, Wan F. Co-existence of two plasmids harboring transferable resistance-nodulation-division pump gene cluster, tmexCD1-toprJ1, and colistin resistance gene mcr-8 in Klebsiella pneumoniae. Ann Clin Microbiol Antimicrob 2024; 23:67. [PMID: 39061085 PMCID: PMC11282740 DOI: 10.1186/s12941-024-00727-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND The emergence of plasmid-mediated mobile colistin resistance (mcr) gene poses a great challenge to the clinical application of polymyxins. To date, mcr-1 to mcr-10 have been found in animals, humans, and the environment. Among them, mcr-8 was first identified in Klebsiella pneumoniae (K. pneumoniae) of swine origin, and then mcr-8.1 to mcr-8.5 were successively identified. Notably, K. pneumoniae is the major host of the mcr-8 gene in both animals and humans. This study aims to explore the characteristics of K. pneumoniae strains carrying the mcr-8 gene and tmexCD1-toprJ1 gene cluster and investigate the correlation between these two antibiotic resistance genes. METHODS The isolates from the poultry farms and the surrounding villages were identified by mass spectrometer, and the strains positive for mcr-1 to mcr-10 were screened by polymerase chain reaction (PCR). The size of the plasmid and the antimicrobial resistance genes carried were confirmed by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern hybridization, and the transferability of the plasmid was verified by conjugation experiments. Antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS) were used to characterize the strains. RESULTS Two K. pneumoniae isolates (KP26 and KP29) displaying polymyxin resistance were identified as mcr-8 gene carriers. Besides that, tigecycline-resistant gene cluster tmexCD1-toprJ1 was also found on the other plasmid which conferred strain resistance to tigecycline. Through epidemiological analysis, we found that the mcr-8 gene has dispersed globally, circulating in the human, animals, and the environment. Furthermore, our analysis suggests that the coexistence of mcr-8 and tmexCD1-toprJ1 on a single plasmid might evolved through plasmid recombination. CONCLUSIONS Although the mcr-8 and tmexCD1-toprJ1 gene clusters in the two strains of K. pneumoniae in this study were on two different plasmids, they still pose a potential threat to public health, requiring close monitoring and further study.
Collapse
Affiliation(s)
- Xiaofen Mo
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Hui Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Junfeng Fan
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China
| | - Linna Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Fu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School, College of Medicine, Zhejiang University, Hangzhou, China
| | - Junpeng Yue
- The First Affiliated Hospital of Medical School, College of Medicine, Zhejiang University, Hangzhou, China
| | - Kaixuan Dong
- The First Affiliated Hospital of Medical School, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Fen Wan
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China.
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, Hangzhou, China.
| |
Collapse
|
35
|
Liu J, Spencer N, Utter DR, Grossman AS, Lei L, Dos Santos NC, Shi W, Baker JL, Hasturk H, He X, Bor B. Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation. MICROBIOME 2024; 12:132. [PMID: 39030586 PMCID: PMC11264962 DOI: 10.1186/s40168-024-01854-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/03/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear. RESULTS Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions. CONCLUSIONS Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella's enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts. Video Abstract.
Collapse
Affiliation(s)
- Jett Liu
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Nell Spencer
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Daniel R Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alex S Grossman
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Lei Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases &, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Nídia Castro Dos Santos
- Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
- Albert Einstein School of Dental Medicine, Albert Einstein Israelite Hospital, São Paulo, SP, Brazil
| | - Wenyuan Shi
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Hatice Hasturk
- Center for Clinical and Translational Research, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Xuesong He
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Batbileg Bor
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA.
| |
Collapse
|
36
|
Zhou X, Yang M, Chen F, Wang L, Han P, Jiang Z, Shen S, Rao G, Yang F. Prediction of antimicrobial resistance in Klebsiella pneumoniae using genomic and metagenomic next-generation sequencing data. J Antimicrob Chemother 2024:dkae248. [PMID: 39028665 DOI: 10.1093/jac/dkae248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/04/2024] [Indexed: 07/21/2024] Open
Abstract
OBJECTIVES Klebsiella pneumoniae is a significant pathogen with increasing resistance and high mortality rates. Conventional antibiotic susceptibility testing methods are time-consuming. Next-generation sequencing has shown promise for predicting antimicrobial resistance (AMR). This study aims to develop prediction models using whole-genome sequencing data and assess their feasibility with metagenomic next-generation sequencing data from clinical samples. METHODS On the basis of 4170 K. pneumoniae genomes, the main genetic characteristics associated with AMR were identified using a LASSO regression model. Consequently, the prediction model was established, validated and optimized using clinical isolate read simulation sequences. To evaluate the efficacy of the model, clinical specimens were collected. RESULTS Four predictive models for amikacin, ciprofloxacin, levofloxacin and piperacillin/tazobactam, initially had positive predictive values (PPVs) of 90%, 85%, 84% and 94%, respectively, when they were originally constructed. When applied to clinical specimens, their PPVs increased to 96%, 96%, 95% and 100%, respectively. Meanwhile, there were negative predictive values (NPVs) of 100% for ciprofloxacin and levofloxacin, and 'not applicable' (NA) for amikacin and piperacillin/tazobactam. Our method achieved antibacterial phenotype classification accuracy rates of 96.08% for amikacin, 96.15% for ciprofloxacin, 95.31% for levofloxacin and 100% for piperacillin/tazobactam. The sequence-based prediction antibiotic susceptibility testing (AST) reported results in an average time of 19.5 h, compared with the 67.9 h needed for culture-based AST, resulting in a significant reduction of 48.4 h. CONCLUSIONS These preliminary results demonstrated that the performance of prediction model for a clinically significant antimicrobial-species pair was comparable to that of phenotypic methods, thereby encouraging the expansion of sequence-based susceptibility prediction and its clinical validation and application.
Collapse
Affiliation(s)
- Xun Zhou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Ming Yang
- The Second Affiliated Hospital of Air Force Military Medical University, Xi'an, China
| | | | - Leilei Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Peng Han
- Genskey Medical Technology Co. Ltd., Beijing, China
| | - Zhi Jiang
- Genskey Medical Technology Co. Ltd., Beijing, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Guanhua Rao
- Genskey Medical Technology Co. Ltd., Beijing, China
| | - Fan Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| |
Collapse
|
37
|
O’Brien B, Yushchenko A, Suh J, Jung D, Cai Z, Nguyen NS, Semret M, Dufour S, Ronholm J. Draft genome sequences of 148 Klebsiella pneumoniae species complex members from bovine and human hosts. Microbiol Resour Announc 2024; 13:e0013224. [PMID: 38864639 PMCID: PMC11256802 DOI: 10.1128/mra.00132-24] [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: 02/13/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Klebsiella pneumoniae species complex members, particularly K. pnemoniae sensu stricto, are common bovine clinical mastitis pathogens and often the cause of hospital- and community-acquired infections in humans. Here, we present 148 draft genome assemblies and annotations of K. pneumoniae species complex members from bovine and human hosts in Canada.
Collapse
Affiliation(s)
- Bridget O’Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Alla Yushchenko
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Jinha Suh
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
- Mastitis Network, Saint-Hyacinthe, Québec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Zhangbin Cai
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Ngoc Sang Nguyen
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Makeda Semret
- McGill University Health Centre (Infectious Diseases and Medical Microbiology), Montréal, Québec, Canada
| | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Québec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
- Mastitis Network, Saint-Hyacinthe, Québec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| |
Collapse
|
38
|
Noreen M, Bilal M, Usman Qamar M, Rasool N, Mahmood A, Umar Din S, Ali Shah T, Bin Jardan YA, Bourhia M, Ouahmane L. Facile Synthesis of 5-Bromo- N-Alkylthiophene-2-Sulfonamides and Its Activities Against Clinically Isolated New Delhi Metallo- β-Lactamase Producing Klebsiella pneumoniae ST147. Infect Drug Resist 2024; 17:2943-2955. [PMID: 39011342 PMCID: PMC11249070 DOI: 10.2147/idr.s455979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024] Open
Abstract
Introduction New Delhi Metallo-β-lactamase producing Klebsiella pneumoniae (NDM-1-KP) sequence type (ST) 147 poses a significant threat in clinical settings due to its evolution into two distinct directions: hypervirulence and carbapenem resistance. Hypervirulence results from a range of virulence factors, while carbapenem resistance stems from complex biological mechanisms. The NDM-1-KP ST147 clone has emerged as a recent addition to the family of successful clones within the species. Methods In this study, we successfully synthesized 5-bromo-N-alkylthiophene-2-sulfonamides (3a-c) by reacting 5-bromothiophene-2-sulfonamide (1) with various alkyl bromides (2) using LiH. We also synthesized a series of compounds (4a-g) from compound (3b) using the Suzuki-Miyaura cross-coupling reaction with fair to good yields (56-72%). Further, we screened the synthesized molecules against clinically isolated New Delhi Metallo-β-lactamase producing Klebsiella pneumoniae ST147. Subsequently, we conducted in-silico tests on compound 3b against a protein extracted from NDM-KP ST147 with PDB ID: 5N5I. Results The compound (3b) with favourable drug candidate status, MIC of 0.39 μg/mL, and MBC of 0.78 μg/mL. This low molecular weight compound exhibited the highest potency against the resistant bacterial strains. The in-silico tests revealed that the compound 3b against a protein extracted from NDM-KP ST147 with PDB ID: 5N5I demonstrated H-bond and hydrophobic interactions. Conclusion The 5-bromo-N-alkylthiophene-2-sulfonamides displayed antibacterial efficacy against New Delhi Metallo-β-lactamase producing Klebsiella pneumoniae ST147. After the in-vivo trial, this substance might offer an alternative therapeutic option.
Collapse
Affiliation(s)
- Mnaza Noreen
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Bilal
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College, University Faisalabad, Faisalabad, 38000, Pakistan
- Division of Infectious Disease and Department of Medicine, University of Geneva, Geneva, Switzerland
| | - Nasir Rasool
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Abid Mahmood
- Department of Pharmaceutical Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Sobia Umar Din
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Tawaf Ali Shah
- College of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 25500, People’s Republic of China
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, 70000, Morocco
| | - Lahcen Ouahmane
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (Biomage), Labeled Research Unit-CNRSTN°4, Cadi Ayyad University, Marrakesh, 40000, Morocco
| |
Collapse
|
39
|
Elgayar FA, Gouda MK, Badran AA, El Halfawy NM. Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt. BMC Microbiol 2024; 24:256. [PMID: 38987681 PMCID: PMC11234735 DOI: 10.1186/s12866-024-03389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic. METHODS In the current study, one hundred extended spectrum β-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate. RESULTS The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7 Mb with an estimated 5,718 protein-coding genes and a G + C content of 56.98 mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several β-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer. CONCLUSIONS This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.
Collapse
Affiliation(s)
- Fatma A Elgayar
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Mona K Gouda
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Alaa Aboelnour Badran
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nancy M El Halfawy
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt.
| |
Collapse
|
40
|
Almutairy B. Extensively and multidrug-resistant bacterial strains: case studies of antibiotics resistance. Front Microbiol 2024; 15:1381511. [PMID: 39027098 PMCID: PMC11256239 DOI: 10.3389/fmicb.2024.1381511] [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: 02/03/2024] [Accepted: 06/11/2024] [Indexed: 07/20/2024] Open
Abstract
The development of antibiotic resistance compromises the effectiveness of our most effective defenses against bacterial infections, presenting a threat to global health. To date, a large number of research articles exist in the literature describing the case reports associated with extensively drug-resistant (XDR) and multidrug-resistant (MDR) bacterial strains. However, these findings are scattered, making it time-consuming for researchers to locate promising results and there remains a need for a comparative study to compile these case reports from various geographical regions including the Kingdom of Saudi Arabia. Additionally, no study has yet been published that compares the genetic variations and case reports of MDR and XDR strains identified from Saudi Arabia, the Middle East, Central Europe, and Asian countries. This study attempts to provide a comparative analysis of several MDR and XDR case reports from Saudi Arabia alongside other countries. Furthermore, the purpose of this work is to demonstrate the genetic variations in the genes underlying the resistance mechanisms seen in MDR and XDR bacterial strains that have been reported in Saudi Arabia and other countries. To cover the gap, this comprehensive review explores the complex trends in antibiotic resistance and the growing risk posed by superbugs. We provide context on the concerning spread of drug-resistant bacteria by analyzing the fundamental mechanisms of antibiotic resistance and looking into individual case reports. In this article, we compiled various cases and stories associated with XDR and MDR strains from Saudi Arabia and various other countries including China, Egypt, India, Poland, Pakistan, and Taiwan. This review will serve as basis for highlighting the growing threat of MDR, XDR bacterial strains in Saudi Arabia, and poses the urgent need for national action plans, stewardship programs, preventive measures, and novel antibiotics research in the Kingdom.
Collapse
Affiliation(s)
- Bandar Almutairy
- Department of Pharmacology, College of Pharmacy, Shaqra University, Shaqra, Saudi Arabia
| |
Collapse
|
41
|
Yan Z, Fu B, Zhu Y, Zhang Y, Wu Y, Xiong P, Zhou H, Wang Y, Wang S, Chen G, Zhang R, Sun C. High intestinal carriage of Clostridium perfringens in healthy individuals and ICU patients in Hangzhou, China. Microbiol Spectr 2024; 12:e0338523. [PMID: 38771047 PMCID: PMC11218483 DOI: 10.1128/spectrum.03385-23] [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: 09/22/2023] [Accepted: 04/09/2024] [Indexed: 05/22/2024] Open
Abstract
Clostridium perfringens has emerged as a growing public health concern due to its ability to cause various infections and its increasing resistance to antibiotics. To assess its current epidemiology in clinical settings, we conducted a survey involving 426 healthy individuals and 273 ICU inpatients at a provincial hospital in China. Our findings revealed a high prevalence of C. perfringens in healthy individuals (45.77%, 95% CI: 41.0%-50.6%) and ICU patients (12.82%, 95% CI: 9.1%-17.4%). The identified 220 C. perfringens isolates displayed substantial resistance to erythromycin (57.9%), clindamycin (50.7%), and tetracycline (32.0%), primarily attributed to the presence of erm(Q) (54.4%), lnu(P) (13.8%), tetB(P) (83.6%), and tetA(P) (66.7%). Notably, C. perfringens isolates from this particular hospital demonstrated a high degree of sequence type diversity and phylogenic variation, suggesting that the potential risk of infection primarily arises from the bacteria's gut colonization rather than clonal transmissions within the clinical environment. This study provides an updated analysis of the current epidemiology of C. perfringens in healthy individuals and ICU patients in China and emphasizes the need to optimize intervention strategies against its public health threat. IMPORTANCE Clostridium perfringens is a bacterium of growing public health concern due to its ability to cause infections and its increasing resistance to antibiotics. Understanding its epidemiology in clinical settings is essential for intervention strategies. This study surveyed healthy individuals and ICU inpatients in a provincial hospital in China. It found a high prevalence of C. perfringens, indicating infection risk. The isolates also showed significant antibiotic resistance. Importantly, the study revealed diverse sequence types and phylogenetic variation, suggesting infection risk from intestinal colonization rather than clonal transmission in hospitals. This analysis emphasizes the need to optimize intervention strategies against this public health threat.
Collapse
Affiliation(s)
- Zelin Yan
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Bo Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yanyan Zhu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Yanyan Zhang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Yuchen Wu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Panfeng Xiong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics and Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Hongwei Zhou
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Gongxiang Chen
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Rong Zhang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Chengtao Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| |
Collapse
|
42
|
Zhu L, Li C, Wang D. Photodynamic inactivation of antibiotic-resistant bacteria in whole blood using riboflavin photodynamic method. Front Microbiol 2024; 15:1404468. [PMID: 39015739 PMCID: PMC11250595 DOI: 10.3389/fmicb.2024.1404468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/13/2024] [Indexed: 07/18/2024] Open
Abstract
Treating bacteremia caused by antibiotic-resistant bacteria is a global concern. Antibacterial photodynamic inactivation is a promising strategy to combat it. However, it's challenging to achieve the inactivation of antibiotic-resistant bacteria in whole blood because of its opacity and complexity. We investigated a riboflavin photodynamic method to effectively inactivate antibiotic-resistant bacteria in whole blood. Four strains of antibiotic-resistant bacteria were isolated, identified, and cultured in this research: methicillin-resistant Staphylococcus aureus (MRSA), pan-drug-resistant Acinetobacter baumannii (PDRAB), ESBLs-producing Escherichia coli (EPEC) and pan-drug-resistant Klebsiella pneumoniae (PDRKP). To simulate bacteremia, antibiotic-resistant bacteria was added into whole blood. Whole blood was treated using riboflavin photodynamic method with ultraviolet irradiation (308 nm and 365 nm). The ultraviolet irradiation dose was divided into 18 J/cm2, 36 J/cm2, and 54 J/cm2. Microbial count of antibiotic-resistant bacteria in whole blood was used for evaluating inactivation effectiveness. The roles of red blood cells, lymphocytes, coagulation factors, and platelets in whole blood were assessed. In results, inactivation effectiveness increased as the ultraviolet dose increased from 18 J/cm2 to 54 J/cm2. At the dose of 18 J/cm2, inactivation effectiveness of four antibiotic-resistant bacteria were more than 80%, while only 67% of MRSA. The antibacterial effect was enhanced by the combination of riboflavin photodynamic treatment and antibiotic. The red blood cell function was susceptible to ultraviolet dose. At the dose of 18 J/cm2, hemolysis rate was less than 0.8% and there was no change in levels of ATP and 2,3-DPG. At the same dose, the proliferation, cell killing, and cytokine secretion activities of lymphocytes decreased 20-70%; Factor V and Factor VIII activities decreased 50%; Fibrinogen and platelet function loss significantly but reparable. Consequently, we speculated that riboflavin photodynamic method with a ultraviolet dose of 18 J/cm2 was effective in inactivating four antibiotic-resistant bacteria in whole blood while whole blood function was preserved. We also provided a novel extracorporeal circulation phototherapy mode for treating bacteremia caused by antibiotic-resistant bacteria.
Collapse
Affiliation(s)
- Liguo Zhu
- Department of Blood Transfusion, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Changqing Li
- Institute of Blood Transfusion, Peking Union Medical College and Chinese Academy of Medical Sciences, Chengdu, China
| | - Deqing Wang
- Department of Blood Transfusion Medicine, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
43
|
Rahmat Ullah S, Jamal M, Rahman A, Andleeb S. Comprehensive insights into Klebsiella pneumoniae: unravelling clinical impact, epidemiological trends and antibiotic-resistance challenges. J Antimicrob Chemother 2024; 79:1484-1492. [PMID: 38832539 DOI: 10.1093/jac/dkae184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Klebsiella pneumoniae, a challenging opportunistic bacterium, became a notable global health concern owing to its clinical impact, widespread epidemiology and escalating antibiotic resistance. This comprehensive review delves into the multifaceted dimensions of K. pneumoniae, with a focus on its clinical implications, epidemiological patterns and the critical issue of antibiotic resistance. The review also emphasizes the implications of K. pneumoniae in the context of antimicrobial stewardship and infection control. Epidemiological aspects are scrutinized, shedding light on the global distribution and prevalence of K. pneumoniae. Factors influencing its transmission and persistence in healthcare facilities and communities are examined, with patient demographics, healthcare practices and geographical variations. The review centres on antibiotic resistance, a critical issue in the era of bacteria displaying resistance to multiple drugs. The mechanisms of resistance used by K. pneumoniae against various classes of antibiotics are elucidated, along with the alarming rise of carbapenem-resistant strains. It also highlights ongoing research efforts and innovative strategies aimed at addressing this critical public health issue. This comprehensive review offers a holistic understanding of K. pneumoniae, emphasizing its clinical significance, global epidemiology and the immediate necessity for effective strategies to combat antibiotic resistance. It serves as a valuable resource for healthcare practitioners, researchers and policymakers seeking to manage better and mitigate the impact of this pathogen on public health.
Collapse
Affiliation(s)
- Sidra Rahmat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Mardan, 23200 Mardan, Pakistan
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| |
Collapse
|
44
|
Mills RO, Dadzie I, Le-Viet T, Baker DJ, Addy HPK, Akwetey SA, Donkoh IE, Quansah E, Semanshia PS, Morgan J, Mensah A, Adade NE, Ampah EO, Owusu E, Mwintige P, Amoako EO, Spadar A, Holt KE, Foster-Nyarko E. Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. J Antimicrob Chemother 2024; 79:1529-1539. [PMID: 38751093 PMCID: PMC11215549 DOI: 10.1093/jac/dkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVES Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana are scarce. This study investigated the genomic diversity, antimicrobial resistance patterns, and clonal relationships of 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana-predominantly from paediatric patients aged under 5 years (67/103; 65%), with the majority collected from urine (32/103; 31%) and blood (25/103; 24%) cultures. METHODS We generated hybrid Nanopore-Illumina assemblies and employed Pathogenwatch for genotyping via Kaptive [capsular (K) locus and lipopolysaccharide (O) antigens] and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome MLST (cgMLST). RESULTS Of 44 distinct STs detected, ST133 was the most common, comprising 23% of isolates (n = 23/103). KL116 (28/103; 27%) and O1 (66/103; 64%) were the most prevalent K-locus and O-antigen types. Single-linkage clustering highlighted the global spread of MDR clones such as ST15, ST307, ST17, ST11, ST101 and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, 17 isolates constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103; 85%) carried resistance genes for ≥3 antibiotic classes, with the blaCTX-M-15 gene present in 78% (n = 80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n = 10/103) of the isolates. CONCLUSIONS Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.
Collapse
Affiliation(s)
- Richael O Mills
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Isaac Dadzie
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Thanh Le-Viet
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - David J Baker
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Humphrey P K Addy
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel A Akwetey
- Department of Clinical Microbiology, University of Development Studies, Tamale, Ghana
| | - Irene E Donkoh
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Elvis Quansah
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
- Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Prince S Semanshia
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Jennifer Morgan
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Abraham Mensah
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Nana E Adade
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Emmanuel O Ampah
- Microbiology Department, Greater Accra Regional Hospital, Ridge, Accra, Ghana
| | - Emmanuel Owusu
- Microbiology Department, Greater Accra Regional Hospital, Ridge, Accra, Ghana
| | - Philimon Mwintige
- Microbiology Laboratory, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Eric O Amoako
- Public Health Laboratory, Effia Nkwanta Regional Hospital, Sekondi-Takoradi, Ghana
| | - Anton Spadar
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Ebenezer Foster-Nyarko
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| |
Collapse
|
45
|
Kelly SD, Williams DM, Zhu S, Kim T, Jana M, Nothof J, Thota VN, Lowary TL, Whitfield C. Klebsiella pneumoniae O-polysaccharide biosynthesis highlights the diverse organization of catalytic modules in ABC transporter-dependent glycan assembly. J Biol Chem 2024; 300:107420. [PMID: 38815868 PMCID: PMC11231755 DOI: 10.1016/j.jbc.2024.107420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/19/2024] [Indexed: 06/01/2024] Open
Abstract
Klebsiella pneumoniae provides influential prototypes for lipopolysaccharide O antigen (OPS) biosynthesis in Gram-negative bacteria. Sequences of OPS-biosynthesis gene clusters in serotypes O4 and O7 suggest fundamental differences in the organization of required enzyme modules compared to other serotypes. Furthermore, some required activities were not assigned by homology shared with characterized enzymes. The goal of this study was therefore to resolve the serotype O4 and O7 pathways to expand our broader understanding of glycan polymerization and chain termination processes. The O4 and O7 antigens were produced from cloned genetic loci in recombinant Escherichia coli. Systematic in vivo and in vitro approaches were then applied to assign each enzyme in each of the pathways, defining the necessary components for polymerization and chain termination. OPS assembly is accomplished by multiprotein complexes formed by interactions between polymerase components variably distributed in single and multimodule proteins. In each complex, a terminator function is present in a protein containing a characteristic coiled-coil molecular ruler, which determines glycan chain length. In serotype O4, we discovered a CMP-α-3-deoxy-ᴅ-manno-octulosonic acid-dependent chain-terminating glycosyltransferase that is the founding member of a new glycosyltransferase family (GT137) and potentially identifies a new glycosyltransferase fold. The O7 OPS is terminated by a methylphosphate moiety, like the K. pneumoniae O3 antigen, but the methyltransferase-kinase enzyme pairs responsible for termination in these serotypes differ in sequence and predicted structures. Together, the characterization of O4 and O7 has established unique enzyme activities and provided new insight into glycan-assembly strategies that are widely distributed in bacteria.
Collapse
Affiliation(s)
- Steven D Kelly
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Danielle M Williams
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Shawna Zhu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Taeok Kim
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Manas Jana
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jeremy Nothof
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| |
Collapse
|
46
|
Wang W, Ye C, Zhao B, Zheng Y, Zhang G, Su J, Huang H, Hao L, Chen M. Epidemiological and Molecular Characteristics of Hypermucoviscous and Hypervirulent Klebsiella pneumoniae Isolates in Community Patients in Shanghai, China. Infect Drug Resist 2024; 17:2685-2699. [PMID: 38953096 PMCID: PMC11216552 DOI: 10.2147/idr.s468482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
Background The occurrence and dissemination of hypermucoviscous and hypervirulent Klebsiella pneumoniae (hm-hvKp) isolates in clinical settings are a critical public health problem in the world. However, the data on these isolates in community populations are limited. This study aims to understand the prevalence and molecular characteristics of hm-hvKp isolates in community patients in Shanghai, China. Methods In 2018, an active surveillance system focused on hm-hvKp in community diarrhoeal cases was implemented in Pudong New Area, Shanghai, China, involving 12 sentinel hospitals. The antimicrobial susceptibility of hm-hvKp isolates from fecal samples was tested, and whole-genome sequencing (WGS) was performed to predict the serotypes and sequence types and to identify antimicrobial resistance determinants, virulence determinants, and phylogenetic clusters. Results The overall prevalence of hm K. pneumoniae isolates was 2.48% (31/1252), with the proportions of 1.76% (22/1252) for hm-hvKp and 0.72% (9/1252) for hm not hv K. pneumoniae. The prevalence of hm-hvKp isolates among different age groups and different months was statistically significant. All the 22 hm-hvKp isolates were susceptible to 20 antimicrobial agents and only carried bla SHV gene, and KL1 and KL2 accounted for eight (36.36%) cases and seven (31.82%) cases, respectively. The eight ST23/KL1 isolates belonged to the predominant CG23-I clade, which typically possessed the virulence determinants profile of rmpA/rmpA2-iro-iuc-ybt-irp-clb. The five ST86/KL2 isolates were assigned to the global clusters ST86/KL2-1 (n=2), ST86/KL2-2 (n=2), ST86/KL2-3 (n=1), all lack of the clb gene. Shanghai ST23/KL1 and ST86/KL2 isolates were closely related to the global isolates from liver abscesses, blood, and urine. Conclusion Hm-hvKp is carried by the community population of Shanghai, with ST23/KL1 and ST86/KL2 isolates predominant. Hm-hvKp isolates of different continents, different sources, and different virulence levels were closely related. Ongoing surveillance of hm-hvKp isolates in the community population is warranted.
Collapse
Affiliation(s)
- Wenqing Wang
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, People’s Republic of China
| | - Chuchu Ye
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, People’s Republic of China
- Department of Infectious Disease Control and Prevention, Pudong New Area Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Bing Zhao
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Yingjie Zheng
- Department of Epidemiology/Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning/Key Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai, People’s Republic of China
| | - Ge Zhang
- School of Public Health, Dali University, Yunnan, People’s Republic of China
| | - Jinghua Su
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Hong Huang
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Lipeng Hao
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Fudan University Pudong Institute of Preventive Medicine, Shanghai, People’s Republic of China
| | - Mingliang Chen
- Research and Translational Laboratory of Acute Injury and Secondary Infection, and Department of Laboratory Medicine, Minhang Hospital, Fudan University, Shanghai, People’s Republic of China
| |
Collapse
|
47
|
Wu J, Shen H, Lv Y, He J, Xie X, Xu Z, Yang P, Qian W, Bai T, Hou X. Age over sex: evaluating gut microbiota differences in healthy Chinese populations. Front Microbiol 2024; 15:1412991. [PMID: 38974029 PMCID: PMC11224521 DOI: 10.3389/fmicb.2024.1412991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
Age and gender have been recognized as two pivotal covariates affecting the composition of the gut microbiota. However, their mediated variations in microbiota seem to be inconsistent across different countries and races. In this study, 613 individuals, whom we referred to as the "healthy" population, were selected from 1,018 volunteers through rigorous selection using 16S rRNA sequencing. Three enterotypes were identified, namely, Escherichia-Shigella, mixture (Bacteroides and Faecalibacterium), and Prevotella. Moreover, 11 covariates that explain the differences in microbiota were determined, with age being the predominant factor. Furthermore, age-related differences in alpha diversity, beta diversity, and core genera were observed in our cohort. Remarkably, after adjusting for 10 covariates other than age, abundant genera that differed between age groups were demonstrated. In contrast, minimal differences in alpha diversity, beta diversity, and differentially abundant genera were observed between male and female individuals. Furthermore, we also demonstrated the age trajectories of several well-known beneficial genera, lipopolysaccharide (LPS)-producing genera, and short-chain fatty acids (SCFAs)-producing genera. Overall, our study further elucidated the effects mediated by age and gender on microbiota differences, which are of significant importance for a comprehensive understanding of the gut microbiome spectrum in healthy individuals.
Collapse
Affiliation(s)
- Jiacheng Wu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hexiao Shen
- School of Life Science, Hubei University, Wuhan, Hubei, China
| | - Yongling Lv
- School of Life Science, Hubei University, Wuhan, Hubei, China
| | - Jing He
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaotian Xie
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhiyue Xu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pengcheng Yang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Qian
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
48
|
Yu W, Huang C, Lian X, Jinag L, Li H, Shen P, Xiao Y. Genomic and immunocyte characterisation of bloodstream infection caused by Klebsiella pneumoniae. Ann Clin Microbiol Antimicrob 2024; 23:56. [PMID: 38902832 PMCID: PMC11191348 DOI: 10.1186/s12941-024-00721-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the characteristics of immunocyte associated with bloodstream infection (BSI) caused by Klebsiella pneumoniae (Kpn). METHODS Patients with BSI-Kpn were included from 2015 to 2022 in our hospital. Immunocyte subpopulations of enrolled BSI-Kpn patients were tested on the same day of blood culture using multicolor flow cytometry analysis. Antibiotic susceptibility test was determined by agar dilution or broth dilution method. All included isolates were subjected to whole genome sequencing and comparative genomics analysis. Clinical and genetic data were integrated to investigate the risk factors associated with clinical outcome. RESULTS There were 173 patients with non-duplicate BSI-Kpn, including 81 carbapenem-resistant Kpn (CRKP), 30 extended-spectrum β-lactamases producing Kpn (ESBL-Kpn), 62 none CRKP or ESBL-Kpn (S-Kpn). Among 68 ST11-CRKP isolates, ST11-O2v1:KL64 was the most common serotypes cluster (77.9%, 53/68), followed by ST11-OL101: KL47 (13.2%, 9/68). Compared with CSKP group, subpopulations of immunocyte in patients with CRKP were significantly lower (P < 0.01). In patients with ST11-O2v1:KL64 BSI-Kpn, the level of cytotoxic T lymphocytes (CD3 + CD8 +) is the highest, while the B lymphocytes (CD3-CD19 +) was the least. In addition, the level of immunocyte in patients with Kpn co-harbored clpV-ybtQ-qacE were lower than that in patients with Kpn harbored one of clpV, ybtQ or qacE and without these three genes. Furthermore, co-existence of clpV-ybtQ-qacE was independently associated with a higher risk for 30-day mortality. CONCLUSIONS The results demonstrate that patients with BSI-CRKP, especially for ST11-O2v1:KL64, exhibit lower leukomonocyte counts. In addition, BSI-Kpn co-harbored clpV-ybtQ-qacE is correlated to higher 30-day mortality.
Collapse
Affiliation(s)
- Wei Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Huang
- Department of Respiratory Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Xiang Lian
- Department of Infectious Diseases, The Affiliated Xiangshan Hospital of Wenzhou Medical University, Xiangshan First People's Hospital Medical and Health Group, Ningbo Fourth Hospital, Ningbo, China
| | - Lushun Jinag
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hong Li
- Department of Infectious Diseases, The Affiliated Xiangshan Hospital of Wenzhou Medical University, Xiangshan First People's Hospital Medical and Health Group, Ningbo Fourth Hospital, Ningbo, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|
49
|
Barber MF, Fitzgerald JR. Mechanisms of host adaptation by bacterial pathogens. FEMS Microbiol Rev 2024; 48:fuae019. [PMID: 39003250 PMCID: PMC11308195 DOI: 10.1093/femsre/fuae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 07/15/2024] Open
Abstract
The emergence of new infectious diseases poses a major threat to humans, animals, and broader ecosystems. Defining factors that govern the ability of pathogens to adapt to new host species is therefore a crucial research imperative. Pathogenic bacteria are of particular concern, given dwindling treatment options amid the continued expansion of antimicrobial resistance. In this review, we summarize recent advancements in the understanding of bacterial host species adaptation, with an emphasis on pathogens of humans and related mammals. We focus particularly on molecular mechanisms underlying key steps of bacterial host adaptation including colonization, nutrient acquisition, and immune evasion, as well as suggest key areas for future investigation. By developing a greater understanding of the mechanisms of host adaptation in pathogenic bacteria, we may uncover new strategies to target these microbes for the treatment and prevention of infectious diseases in humans, animals, and the broader environment.
Collapse
Affiliation(s)
- Matthew F Barber
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, United States
- Department of Biology, University of Oregon, Eugene, OR 97403, United States
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
| |
Collapse
|
50
|
Lee GY, Song J. Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi. Nat Commun 2024; 15:5258. [PMID: 38898034 PMCID: PMC11187135 DOI: 10.1038/s41467-024-49590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S. Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control Vi polymerization or acetylation is enough to result in different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper Vi capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo Vi capsule variants have primarily been identified in Africa, whereas the hyper Vi capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria.
Collapse
Affiliation(s)
- Gi Young Lee
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Jeongmin Song
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA.
| |
Collapse
|