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Sun C, Xu Y, Xu G, Ji X, Jiang P, He Y. Active fractions from Jingfang Baidu Powder alleviate Klebsiella-induced Pneumonia by inhibiting TLR4/Myd88-ERK signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118067. [PMID: 38636574 DOI: 10.1016/j.jep.2024.118067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/04/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Jingfang Baidu Powder (JFBDP) is a classic traditional Chinese medicine prescription. Although Jingfang Baidu powder obtained a general consensus on clinical efficacy in treating pneumonia, there were many Chinese herbal drugs in formula, complex components, and large oral dosage, which brings certain obstacles to clinical application. AIM OF THE STUDY Therefore, screening of the active fraction that exerts anti-pneumonia helps improve the pharmaceutical preparation, improve the treatment compliance of patients, and further contribute to the clinical application, and the screening of the new active ingredients with anti-pneumonia. The histopathological observation, real-time quantitative PCR, western blotting, and immunofluorescence were applied to evaluate the anti-pneumonia efficacy of active fractions from JFBDP. RESULTS Three fractions from JFBDP inhibit the gene expression of IL-1β, IL-10, CCL3, CCL5, and CCL22 in lung tissue infected by Klebsiella at various degrees, and presented a good dose-response relationship. JF50 showed stronger anti-inflammatory effects among three fractions including JF30, JF50, and JF75. Besides, JF50 significantly reduced the protein expression of TLR4 and Myd88 in lung tissue infected with Klebsiella, and it also significantly inhibited p-ERK and p-NF-κB p65. JF50 significantly inhibits the protein expression of Caspase 3, Caspase 8, and Caspase 9 in lung tissue infected with Klebsiella at the dose of 25 mg/kg and 50 mg/kg. CONCLUSION JF50 improves lung pathological damage in Klebsiella pneumonia mice by inhibiting the TLR4/Myd88/NF-κB-ERK signaling pathway, and inhibiting apoptosis of lung tissue cells. These findings provide a reference for further exploring the active substance basis of Jingfang Baidu Powder in treating bacterial pneumonia.
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Affiliation(s)
- Chuanbo Sun
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
| | - Yuting Xu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Guangpei Xu
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
| | - Xu Ji
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230001, China.
| | - Ping Jiang
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
| | - Yanfei He
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
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Mo Z, Lin S, Li T, Yu G, Sun Y, Zhou J, Xu Z. Native CRISPR-Cas-based programmable multiplex gene repression in Klebsiella variicola. Biotechnol Lett 2024:10.1007/s10529-024-03516-w. [PMID: 39066958 DOI: 10.1007/s10529-024-03516-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/12/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
Klebsiella variicola is a Gram-negative bacterium that is frequently isolated from a wide variety of natural niches. It is a ubiquitous opportunistic pathogen that can cause diverse infections in plants, animals, and humans. It also has significant biotechnological potential. However, due to the lack of efficient genetic tools, the molecular basis contributing to the pathogenesis and beneficial activities of K. variicola remains poorly understood. In this study, we found and characterized a native type I-E CRISPR-Cas system in a recently isolated K. variicola strain KV-1. The system cannot cleave target DNA sequences due to the inactivation of the Cas3 nuclease by a transposable element but retains the activity of the crRNA-guided Cascade binding to the target DNA sequence. A targeting plasmid carrying a mini-CRISPR to encode a crRNA was designed and introduced into the KV-1 strain, which successfully repurposed the native type I-E CRISPR-Cas system to inhibit the expression of the target gene efficiently and specifically. Moreover, by creating a mini-CRISPR to encode multiple crRNAs, multiplex gene repression was achieved by providing a single targeting plasmid. This work provides the first native CRISPR-Cas-based tool for programmable multiplex gene repression in K. variicola, which will facilitate studying the pathogenic mechanism of K. variicola and enable metabolic engineering to produce valuable bioproducts.
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Affiliation(s)
- Zhifeng Mo
- State Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Siying Lin
- State Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ting Li
- State Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Guohui Yu
- Key Laboratory of Green Prevention and Control On Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, 510225, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yunhao Sun
- Key Laboratory of Green Prevention and Control On Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, 510225, China
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jianuan Zhou
- State Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.
| | - Zeling Xu
- State Key Laboratory of Green Pesticide, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.
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Conte D, Mesa D, Krul D, Bail L, Ito CAS, Palmeiro JK, Dalla-Costa LM. Comparative genomics of IncQ1 plasmids carrying bla GES variants from clinical and environmental sources in Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105644. [PMID: 39038632 DOI: 10.1016/j.meegid.2024.105644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
IncQ-type plasmids have become important vectors in the dissemination of blaGES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different blaGES variants from human and environmental sources. The blaGES variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. A. veronii harbored blaGES-7 in a class 1 integron (In2061), recently described by our group, and K. variicola carried blaGES-5 in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS6100 truncating the 3'-conserved segment. The fused genes are transcribed together, although the attC site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of blaGES variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens.
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Affiliation(s)
- Danieli Conte
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil.
| | - Dany Mesa
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Damaris Krul
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Larissa Bail
- Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | | | - Jussara Kasuko Palmeiro
- Departamento de Análises Clínicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil; Laboratório de Microbiologia Molecular Aplicada, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Libera Maria Dalla-Costa
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
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Sundaresan AK, Gangwar J, Murugavel A, Malli Mohan GB, Ramakrishnan J. Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp. AMB Express 2024; 14:78. [PMID: 38965152 PMCID: PMC11224175 DOI: 10.1186/s13568-024-01737-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.
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Affiliation(s)
- Abhirami Krishnamoorthy Sundaresan
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Jaya Gangwar
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Aravind Murugavel
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Ganesh Babu Malli Mohan
- Microbial Omics Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Georgia, Athens, United States of America
| | - Jayapradha Ramakrishnan
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India.
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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.
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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
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Xue P, Xue M, Luo Y, Tang Q, Wang F, Sun R, Song Y, Chao Z, Fang M. Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of Short-Chain Fatty Acids in Local Pigs of Hainan. Microorganisms 2024; 12:1033. [PMID: 38930415 PMCID: PMC11205767 DOI: 10.3390/microorganisms12061033] [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: 03/30/2024] [Revised: 05/05/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding'an and DLY pigs high and low levels of dietary fiber, respectively, to investigate factors contributing to high dietary fiber adaption in Ding'an pigs. Twelve Ding'an pigs and DLY pigs were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 3). Compared with commercial pigs, Ding'an pigs have a stronger ability to digest dietary fiber. Prevotella was more prevalent in Ding'an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding'an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding'an pigs. Among them, Prevotella. sp. CAG:520 may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria (r > 0.7). We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding'an pigs after increasing the fiber content, which resulted in the downregulated expression of inflammatory factors in colonic mucosa. Spearman's correlation coefficient revealed a strong correlation between microbiota and the apparent digestibility of dietary fiber (r > 0.7). The mRNA expressions of SLC16A1, PYY, and GCG were significantly increased in the colonic mucosa of Ding'an pigs fed on high-fiber diets, which indicates that Ding'an pigs have an enhanced absorption of SCFAs. Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding'an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.
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Affiliation(s)
- Pengxiang Xue
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Mingming Xue
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Yabiao Luo
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Qiguo Tang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
| | - Feng Wang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571101, China; (F.W.); (R.S.); (Z.C.)
| | - Ruiping Sun
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571101, China; (F.W.); (R.S.); (Z.C.)
| | - Yanxia Song
- Sanya Institute, China Agricultural University, Sanya 572024, China;
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Science, Haikou 571101, China; (F.W.); (R.S.); (Z.C.)
| | - Meiying Fang
- National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (P.X.); (M.X.); (Y.L.); (Q.T.)
- Sanya Institute, China Agricultural University, Sanya 572024, China;
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Li L, Zhang Y, Wang W, Chen Y, He F, Yu Y. Global Emergence and Genomic Epidemiology of blaNDM-Carrying Klebsiella variicola. Infect Drug Resist 2024; 17:1893-1901. [PMID: 38766676 PMCID: PMC11102106 DOI: 10.2147/idr.s460569] [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: 02/26/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
Purpose Klebsiella variicola has emerged as a human pathogen in the past decade. Here, we present findings related to a K. variicola strain carrying the blaNDM-1 gene, which was isolated from a urinary tract infection in China. Global transmission dynamics and genomic epidemiology of blaNDM-carrying K. variicola were further investigated. Material and Methods The complete genome sequence of the strain was determined using the Illumina NovaSeq 6000 and Nanopore MinION sequencer. Genomic features and resistance mechanisms were analyzed through diverse bioinformatics approaches. Additionally, genome sequences of K. variicola strains carrying blaNDM were retrieved from the NCBI database, and a comprehensive analysis of the global dissemination trends of these strains was conducted. Results K. variicola strain 353 demonstrated resistance to multiple antimicrobials, including carbapenems. Within its genome, we identified fourteen antimicrobial resistance genes associated with β-lactam, aminoglycoside, fosfomycin, quinolone, trimethoprim, rifamycin, and sulfonamide resistance. The carbapenem-resistant gene blaNDM-1 was located on an IncU-type plasmid spanning 294,608 bp and flanked by ISCR1 and IS26. Downstream of blaNDM-1, we identified an Intl1 element housing numerous antibiotic resistance genes. A comprehensive search of the NCBI database revealed 72 K. variicola strains carrying blaNDM from twelve different countries, predominantly from clinical sources, with the highest prevalence observed in the USA and China. A total of 28 distinct sequence types (STs) were identified, with ST115 being the most prevalent, followed by ST60. Conclusion In summary, this study presents the genomic characterization of a K. variicola strain carrying blaNDM-1 on an IncU-type plasmid. The research highlights the global dissemination of blaNDM-carrying K. variicola, observed in both healthcare settings and natural environments. Our data have revealed a diverse array of antimicrobial resistance determinants in K. variicola, providing valuable insights that could aid in the development of strategies for the prevention, diagnosis, and treatment of K. variicola infections.
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Affiliation(s)
- Lirong Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yawen Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Weizhong Wang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yanmin Chen
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yan Yu
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
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Watanabe N, Watari T, Otsuka Y, Ito M, Yamagata K, Fujioka M. Antimicrobial resistance and AmpC production in ESBL-producing Klebsiella pneumoniae and Klebsiella quasipneumoniae: A retrospective study in Japanese clinical isolates. PLoS One 2024; 19:e0303353. [PMID: 38743684 PMCID: PMC11093370 DOI: 10.1371/journal.pone.0303353] [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: 02/01/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
INTRODUCTION The study of Klebsiella quasipneumoniae, Klebsiella variicola, and AmpC production in extended-spectrum β-lactamase (ESBL)-producing Klebsiella in Japan is limited, and existing data are insufficient. This study aims to characterize Klebsiella species, determine AmpC production rates, and analyze antimicrobial resistance patterns in ESBL-producing Klebsiella isolates in Japan. METHODS A total of 139 clinical isolates of ESBL-producing Klebsiella were collected in Japan, along with their corresponding antimicrobial susceptibility profiles. The isolates were identified using a web-based tool. ESBL genes within the isolates were identified using multiplex PCR. Screening for AmpC-producing isolates was performed using cefoxitin disks, followed by multiplex PCR to detect the presence of AmpC genes. Antimicrobial resistance patterns were analyzed across the predominant ESBL genotypes. RESULTS The web-based tool identified 135 isolates (97.1%) as Klebsiella pneumoniae and 4 (2.9%) as K. quasipneumoniae subsp. similipneumoniae, with no instances of K. variicola detected. Among K. pneumoniae, the CTX-M-1 group emerged as the predominant genotype (83/135, 61.5%), followed by K. quasipneumoniae subsp. similipneumoniae (3/4, 75.0%). The CTX-M-9 group was the second most prevalent genotype in K. pneumoniae (45/135, 33.3%). The high resistance rates were observed for quinolones (ranging from 46.7% to 63.0%) and trimethoprim/sulfamethoxazole (78.5%). The CTX-M-1 group exhibited higher resistance to ciprofloxacin (66/83, 79.5%) compared to the CTX-M-9 group (18/45, 40.0%), a trend also observed for levofloxacin and trimethoprim/sulfamethoxazole. Among the 16 isolates that tested positive during AmpC screening, only one K. pneumoniae isolates (0.7%) were confirmed to carry the AmpC gene. CONCLUSION Klebsiella pneumoniae with the CTX-M-1 group is the most common ESBL-producing Klebsiella in Japan and showed a low proportion of AmpC production. These isolates are resistant to quinolones and trimethoprim/sulfamethoxazole, highlighting the challenge of managing this pathogen. The findings underscore the importance of broader research and continuous monitoring to address the resistance patterns of ESBL-producing Klebsiella.
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Affiliation(s)
- Naoki Watanabe
- Department of Clinical Laboratory, Kameda Medical Center, Kamogawa, Chiba, Japan
- Graduate School of Health Sciences, Hirosaki University, Hirosaki, Aomori, Japan
| | - Tomohisa Watari
- Department of Clinical Laboratory, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Yoshihito Otsuka
- Department of Clinical Laboratory, Kameda Medical Center, Kamogawa, Chiba, Japan
| | - Masahiko Ito
- Sapporo Clinical Laboratory Inc., Chuo-ku, Sapporo, Hokkaido, Japan
| | - Kazufumi Yamagata
- Graduate School of Health Sciences, Hirosaki University, Hirosaki, Aomori, Japan
| | - Miyuki Fujioka
- Graduate School of Health Sciences, Hirosaki University, Hirosaki, Aomori, Japan
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9
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Das S, Pandey AK, Morris DE, Anderson R, Lim V, Wie CC, Yap IKS, Alattraqchi AG, Simin H, Abdullah R, Yeo CC, Clarke SC, Cleary DW. Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia. BMC Genomics 2024; 25:381. [PMID: 38632538 PMCID: PMC11025145 DOI: 10.1186/s12864-024-10276-4] [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: 10/03/2023] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is classified by the World Health Organisation (WHO) as a Priority One ESKAPE pathogen. South and Southeast Asian countries are regions where both healthcare associated infections (HAI) and community acquired infections (CAI) due to extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant K. pneumoniae (CRKp) are of concern. As K. pneumoniae can also exist as a harmless commensal, the spread of resistance genotypes requires epidemiological vigilance. However there has been no significant study of carriage isolates from healthy individuals, particularly in Southeast Asia, and specially Malaysia. Here we describe the genomic analysis of respiratory isolates of K. pneumoniae obtained from Orang Ulu and Orang Asli communities in Malaysian Borneo and Peninsular Malaysia respectively. The majority of isolates were K. pneumoniae species complex (KpSC) 1 K. pneumoniae (n = 53, 89.8%). Four Klebsiella variicola subsp. variicola (KpSC3) and two Klebsiella quasipneumoniae subsp. similipneumoniae (KpSC4) were also found. It was discovered that 30.2% (n = 16) of the KpSC1 isolates were ST23, 11.3% (n = 6) were of ST65, 7.5% (n = 4) were ST13, and 13.2% (n = 7) were ST86. Only eight of the KpSC1 isolates encoded ESBL, but importantly not carbapenemase. Thirteen of the KpSC1 isolates carried yersiniabactin, colibactin and aerobactin, all of which harboured the rmpADC locus and are therefore characterised as hypervirulent. Co-carriage of multiple strains was minimal. In conclusion, most isolates were KpSC1, ST23, one of the most common sequence types and previously found in cases of K. pneumoniae infection. A proportion were hypervirulent (hvKp) however antibiotic resistance was low.
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Affiliation(s)
- Souradeep Das
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Anish K Pandey
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Denise E Morris
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rebecca Anderson
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Victor Lim
- School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Chong Chun Wie
- Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ivan Kok Seng Yap
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ahmed Ghazi Alattraqchi
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Hafis Simin
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Ramle Abdullah
- Centre of Excellence in National Indigenous Pedagogy, Institute of Teacher Education Tengku, Ampuan Afzan Campus, Pahang, Malaysia
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Stuart C Clarke
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
- Global Health Research Institute, University of Southampton, Southampton, UK
| | - David W Cleary
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, University of Birmingham, UK.
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Lam M, Leung KM, Lai GKK, Leung FCC, Griffin SDJ. Complete genome sequence of Klebsiella variicola subsp. variicola ML.9ba2, an endophytic strain isolated from aerial roots of Philodendron erubescens. Microbiol Resour Announc 2024; 13:e0116323. [PMID: 38509053 PMCID: PMC11008176 DOI: 10.1128/mra.01163-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/02/2024] [Indexed: 03/22/2024] Open
Abstract
The endophytic strain Klebsiella variicola subsp. variicola ML.9ba2 was isolated from aerial roots of Philodendron erubescens in Hong Kong. Its complete genome of 5,682,083 bp (57.29% G+C), comprising a single chromosome and an IncF plasmid, was established through hybrid assembly.
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Affiliation(s)
- M. Lam
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - K. M. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - G. K. K. Lai
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - F. C. C. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - S. D. J. Griffin
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
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11
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Rodríguez-Medina N, Rodríguez-Santiago J, Alvarado-Delgado A, Sagal-Prado A, Silva-Sánchez J, De la Cruz MA, Ares MA, Sánchez-Arias M, Morfín-Otero R, Hernández-Castro R, Cornejo-Juárez P, Jiménez-Villanueva E, Sánchez-Francia D, Garza-Ramos U. Comprehensive study reveals phenotypic heterogeneity in Klebsiella pneumoniae species complex isolates. Sci Rep 2024; 14:5876. [PMID: 38467675 PMCID: PMC10928225 DOI: 10.1038/s41598-024-55546-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: 10/31/2023] [Accepted: 02/25/2024] [Indexed: 03/13/2024] Open
Abstract
Here, we conducted a comprehensive analysis of 356 Klebsiella pneumoniae species complex (KpSC) isolates that were classified as classical (cl), presumptive hypervirulent (p-hv) and hypermucoviscous-like (hmv-like). Overall, K. pneumoniae (82.3%), K. variicola (2.5%) and K. quasipneumoniae (2.5%) were identified. These isolates comprised 321 cl-KpSC, 7 p-hv-KpSC and 18 hmv-like-KpSC. A large proportion of cl-KpSC isolates were extended-spectrum-β-lactamases (ESBLs)-producers (64.4%) and 3.4% of isolates were colistin-resistant carrying carbapenemase and ESBL genes. All p-hv-KpSC showed an antibiotic susceptible phenotype and hmv-like isolates were found to be ESBL-producers (8/18). Assays for capsule production and capsule-dependent virulence phenotypes and whole-genome sequencing (WGS) were performed in a subset of isolates. Capsule amount differed in all p-hv strains and hmv-like produced higher capsule amounts than cl strains; these variations had important implications in phagocytosis and virulence. Murine sepsis model showed that most cl strains were nonlethal and the hmv-like caused 100% mortality with 3 × 108 CFUs. Unexpectedly, 3/7 (42.9%) of p-hv strains required 108 CFUs to cause 100% mortality (atypical hypervirulent), and 4/7 (57.1%) strains were considered truly hypervirulent (hv). Genomic analyses confirmed the diverse population, including isolates belonging to hv clonal groups (CG) CG23, CG86, CG380 and CG25 (this corresponded to the ST3999 a novel hv clone) and MDR clones such as CG258 and CG147 (ST392) among others. We noted that the hmv-like and hv-ST3999 isolates showed a close phylogenetic relationship with cl-MDR K. pneumoniae. The information collected here is important to understand the evolution of clinically important phenotypes such as hypervirulent and ESBL-producing-hypermucoviscous-like amongst the KpSC in Mexican healthcare settings. Likewise, this study shows that mgrB inactivation is the main mechanism of colistin resistance in K. pneumoniae isolates from Mexico.
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Affiliation(s)
- Nadia Rodríguez-Medina
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Jonathan Rodríguez-Santiago
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Alejandro Alvarado-Delgado
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Alan Sagal-Prado
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Miguel A De la Cruz
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel Angel Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Margarita Sánchez-Arias
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde", Instituto de Patología Infecciosa y Experimental, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | | | | | | | | | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico.
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12
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Chen H, Xu H, Liu R, Shen J, Zheng B, Li L. Coexistence of bla IMP-4 and bla SFO-1 in an IncHI5B plasmid harbored by tigecycline-non-susceptible Klebsiella variicola strain. Ann Clin Microbiol Antimicrob 2024; 23:24. [PMID: 38448920 PMCID: PMC10918965 DOI: 10.1186/s12941-024-00680-9] [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: 09/27/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Klebsiella variicola is considered a newly emerging human pathogen. Clinical isolates of carbapenemase and broad-spectrum β-lactamase-producing K. variicola remain relatively uncommon. A strain of K. variicola 4253 was isolated from a clinical sample, and was identified to carry the blaIMP-4 and blaSFO-1 genes. This study aims to discern its antibiotic resistance phenotype and genomic characteristics. METHODS Species identification was conducted using MALDI-TOF/MS. PCR identification confirmed the presence of the blaIMP-4 and blaSFO-1 genes. Antibiotic resistance phenotype and genomic characteristics were detected by antimicrobial susceptibility testing and whole-genome sequencing. Plasmid characterization was carried out through S1-PFGE, conjugation experiments, Southern blot, and comparative genomic analysis. RESULTS K. variicola 4253 belonged to ST347, and demonstrated resistance to broad-spectrum β-lactamase drugs and tigecycline while being insensitive to imipenem and meropenem. The blaIMP-4 and blaSFO-1 genes harbored on the plasmid p4253-imp. The replicon type of p4253-imp was identified as IncHI5B, representing a multidrug-resistant plasmid capable of horizontal transfer and mediating the dissemination of drug resistance. The blaIMP-4 gene was located on the In809-like integrative element (Intl1-blaIMP-4-aacA4-catB3), which circulates in Acinetobacter and Enterobacteriaceae. CONCLUSIONS This study reports the presence of a strain of K. variicola, which is insensitive to tigecycline, carrying a plasmid harboring blaIMP-4 and blaSFO-1. It is highly likely that the strain acquired this plasmid through horizontal transfer. The blaIMP-4 array (Intl1-blaIMP-4-aacA4-catB3) is also mobile in Acinetobacter and Enterobacteriaceae. So it is essential to enhance clinical awareness and conduct epidemiological surveillance on multidrug-resistant K. variicola, conjugative plasmids carrying blaIMP-4, and the In809 integrative element.
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Affiliation(s)
- Hui Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Ruishan Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Jian Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China.
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13
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Puljko A, Barišić I, Dekić Rozman S, Križanović S, Babić I, Jelić M, Maravić A, Udiković-Kolić N. Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia. ENVIRONMENT INTERNATIONAL 2024; 185:108554. [PMID: 38479059 DOI: 10.1016/j.envint.2024.108554] [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: 12/19/2023] [Revised: 01/30/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study was to isolate CRE from treated wastewater from the Zagreb wastewater treatment plant and to determine their phenotypic and genomic characteristics. A total of 200 suspected CRE were isolated, 148 of which were confirmed as Enterobacterales by MALDI-TOF MS. The predominant species was Klebsiella spp. (n = 47), followed by Citrobacter spp. (n = 40) and Enterobacter cloacae complex (cplx.) (n = 35). All 148 isolates were carbapenemase producers with a multidrug-resistant phenotype. Using multi-locus sequence typing and whole-genome sequencing (WGS), 18 different sequence types were identified among these isolates, 14 of which were associated with human-associated clones. The virulence gene analysis of the sequenced Klebsiella isolates (n = 7) revealed their potential pathogenicity. PCR and WGS showed that the most frequent carbapenemase genes in K. pneumoniae were blaOXA-48 and blaNDM-1, which frequently occurred together, while blaKPC-2 together with blaNDM-1 was mainly detected in K. oxytoca, E. cloacae cplx. and Citrobacter spp. Colistin resistance was observed in 40% of Klebsiella and 57% of Enterobacter isolates. Underlying mechanisms identified by WGS include known and potentially novel intrinsic mechanisms (point mutations in the pmrA/B, phoP/Q, mgrB and crrB genes) and acquired mechanisms (mcr-4.3 gene). The mcr-4.3 gene was identified for the first time in K. pneumoniae and is probably located on the conjugative IncHI1B plasmid. In addition, WGS analysis of 13 isolates revealed various virulence genes and resistance genes to other clinically relevant antibiotics as well as different plasmids possibly associated with carbapenemase genes. Our study demonstrates the important role that treated municipal wastewater plays in harboring and spreading enterobacterial pathogens that are resistant to last-resort antibiotics.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210 Vienna, Austria
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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14
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Lim TW, Huang S, Jiang Y, Zhang Y, Burrow MF, McGrath C. Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing. J Oral Microbiol 2024; 16:2317059. [PMID: 38410192 PMCID: PMC10896157 DOI: 10.1080/20002297.2024.2317059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/03/2024] [Indexed: 02/28/2024] Open
Abstract
Background The microbiomes on the surface of unclean removable prostheses are complex and yet largely underexplored using metagenomic sequencing technology. Objectives To characterize the microbiome of removable prostheses with different levels of cleanliness using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M) sequencing and compare the Microbial Index of Pathogenic Bacteria (MIP) between clean and unclean prostheses. Materials and Methods Ninety-seven removable prostheses were classified into 'clean' and 'unclean' groups. All prosthesis plaque samples underwent 2bRAD metagenomic sequencing to characterize the species-resolved microbial composition. MIPs for clean and unclean prostheses were calculated based on the sum of the relative abundance of pathogenic bacteria in a microbiome using a reference database that contains opportunistic pathogenic bacteria and disease-associated information. Results Beta diversity analyses based on Jaccard qualitative and Bray-Curtis quantitative distance matrices identified significant differences between the two groups (p < 0.05). There was a significant enrichment of many pathogenic bacteria in the unclean prosthesis group. The MIP for unclean prostheses (0.47 ± 0.25) was significantly higher than for clean prostheses (0.37 ± 0.29), p = 0.029. Conclusions The microbial community of plaque samples from 'unclean' prostheses demonstrated compositional differences compared with 'clean' prostheses. In addition, the pathogenic microbiome in the 'unclean' versus 'clean' group differed.
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Affiliation(s)
- Tong Wah Lim
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shi Huang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yuesong Jiang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yufeng Zhang
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Michael Francis Burrow
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Colman McGrath
- Division of Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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15
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Aggarwal R, Mahajan P, Pandiya S, Bajaj A, Verma SK, Yadav P, Kharat AS, Khan AU, Dua M, Johri AK. Antibiotic resistance: a global crisis, problems and solutions. Crit Rev Microbiol 2024:1-26. [PMID: 38381581 DOI: 10.1080/1040841x.2024.2313024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/28/2024] [Indexed: 02/23/2024]
Abstract
Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.
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Affiliation(s)
- Rupesh Aggarwal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Mahajan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sameeksha Pandiya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aayushi Bajaj
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shailendra Kumar Verma
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Arun S Kharat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Asad Ullah Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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16
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Sękowska A. In Vitro Activity of "Old" and "New" Antimicrobials against the Klebsiella pneumoniae Complex. Antibiotics (Basel) 2024; 13:126. [PMID: 38391512 PMCID: PMC10886291 DOI: 10.3390/antibiotics13020126] [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: 12/19/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
The Klebsiella pneumoniae complex is a commonly isolated bacteria in human infections. These opportunistic pathogens pose a serious threat to public health due to their potential transmission to the human population. Resistance to carbapenems is a significant antimicrobial resistance mechanism, leading to limited therapeutic options. Therefore, the aim of this study was to evaluate the in vitro activity of fosfomycin, colistin, ceftazidime-avibactam, and meropenem-vaborbactam against multidrug-resistant K. pneumoniae complex strains. This study involved 160 strains of Gram-negative rods, comprising 138 K. pneumoniae and 22 K. variicola. The minimal inhibitory concentration of fosfomycin was estimated using the agar dilution method, and for colistin, the microdilution method was employed. Susceptibility to ceftazidime-avibactam and meropenem-vaborbactam was determined using the gradient strip method. All analyzed K. pneumoniae complex isolates produced extended-spectrum β-lactamases, and 60.0% exhibited carbapenemases. The majority of the analyzed strains were susceptible to fosfomycin and colistin (62.5%). Among pandrug-resistant K. pneumoniae complex isolates, the highest susceptibility was observed with colistin (43.9%). Fosfomycin demonstrated good activity against ESβLs- and VIM-positive isolates from this complex. Colistin also exhibited satisfactory in vitro activity against VIM- and KPC-positive isolates from the K. pneumoniae complex. Ceftazidime-avibactam displayed good activity against K. pneumoniae complex strains producing ESβLs, KPC, and OXA enzymes. Additionally, meropenem-vaborbactam showed satisfactory in vitro activity against ESβLs- and KPC-positive isolates from this complex.
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Affiliation(s)
- Alicja Sękowska
- Microbiology Department, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 9 Maria Skłodowska-Curie St., 85-094 Bydgoszcz, Poland
- Clinical Microbiology Department, Dr. A. Jurasz University Hospital No. 1, 85-094 Bydgoszcz, Poland
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17
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Wang Y, Xie Y, Mahara G, Xiong Y, Xiong Y, Zheng Q, Chen J, Zhang W, Zhou H, Li Q. Intestinal microbiota and metabolome perturbations in ischemic and idiopathic dilated cardiomyopathy. J Transl Med 2024; 22:89. [PMID: 38254195 PMCID: PMC10804607 DOI: 10.1186/s12967-023-04605-6] [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: 06/17/2023] [Accepted: 10/06/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Various clinical similarities are present in ischemic (ICM) and idiopathic dilated cardiomyopathy (IDCM), leading to ambiguity on some occasions. Previous studies have reported that intestinal microbiota appeared dysbiosis in ICM, whether implicating in the IDCM remains unclear. The aim of this study was to assess the alterations in intestinal microbiota and fecal metabolites in ICM and IDCM. METHODS ICM (n = 20), IDCM (n = 22), and healthy controls (HC, n = 20) were enrolled in this study. Stool samples were collected for 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. RESULTS Both ICM and IDCM exhibited reduced alpha diversity and altered microbial community structure compared to HC. At the genus level, nine taxa including Blautia, [Ruminococcus]_torques_group, Christensenellaceae_R-7_group, UCG-002, Corynebacterium, Oceanobacillus, Gracilibacillus, Klebsiella and Citrobacter was specific to ICM, whereas one taxa Alistipes uniquely altered in IDCM. Likewise, these changes were accompanied by significant metabolic differences. Further differential analysis displayed that 18 and 14 specific metabolites uniquely changed in ICM and IDCM, respectively. The heatmap was generated to display the association between genera and metabolites. Receiver operating characteristic curve (ROC) analysis confirmed the predictive value of the distinct microbial-metabolite features in disease status. The results showed that microbial (area under curve, AUC = 0.95) and metabolic signatures (AUC = 0.84) were effective in discriminating ICM from HC. Based on the specific microbial and metabolic features, the patients with IDCM could be separated from HC with an AUC of 0.80 and 0.87, respectively. Furthermore, the gut microbial genus (AUC = 0.88) and metabolite model (AUC = 0.89) were comparable in predicting IDCM from ICM. Especially, the combination of fecal microbial-metabolic features improved the ability to differentiate IDCM from ICM with an AUC of 0.96. CONCLUSION Our findings highlighted the alterations of gut microbiota and metabolites in different types of cardiomyopathies, providing insights into the pathophysiological mechanisms of myocardial diseases. Moreover, multi-omics analysis of fecal samples holds promise as a non-invasive tool for distinguishing disease status.
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Affiliation(s)
- Yusheng Wang
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yandan Xie
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Gehendra Mahara
- Clinical Research Center, Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yanling Xiong
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yalan Xiong
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qifang Zheng
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Jianqin Chen
- Department of Cardiovascular Internal Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Metcalf R, Messer LF, White HL, Ormsby MJ, Matallana-Surget S, Quilliam RS. Evidence of interspecific plasmid uptake by pathogenic strains of Klebsiella isolated from microplastic pollution on public beaches. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132567. [PMID: 37741206 DOI: 10.1016/j.jhazmat.2023.132567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Microplastic beads are becoming a common feature on beaches, and there is increasing evidence that such microplastics can become colonised by potential human pathogens. However, whether the concentrations and pathogenicity of these pathogens pose a public health risk are still unclear. Therefore, the aim of this study was to determine realistic environmental concentrations of potential pathogens colonising microplastic beads, and quantify the expression of virulence and antimicrobial resistance genes (ARGs). Microplastic beads were collected from beaches and a culture-dependent approach was used to determine the concentrations of seven target bacteria (Campylobacter spp.; E. coli; intestinal enterococci; Klebsiella spp.; Pseudomonas aeruginosa; Salmonella spp.; Vibrio spp.). All seven target bacteria were detected without the need for a pre-enrichment step; urban sites had higher bacterial concentrations, whilst polymer type had no influence on bacterial concentrations. Klebsiella was the most abundant target bacteria and possessed virulence and ARGs, some of which were present on plasmids from other species, and showed pathogenicity in a Galleria melonella infection model. Our findings demonstrate how pathogen colonised microplastic beads can pose a heightened public health risk at the beach, and highlights the urgency for improved monitoring and enforcement of regulations on the release of microplastics into the environment.
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Affiliation(s)
- Rebecca Metcalf
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK.
| | - Lauren F Messer
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Hannah L White
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Michael J Ormsby
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Sabine Matallana-Surget
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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Zhang PJ, Lu ZH, Cao LJ, Chen H, Sun Y. Successful treatment of invasive liver abscess syndrome caused by Klebsiella variicola with intracranial infection and septic shock: A case report. World J Gastrointest Surg 2023; 15:2938-2944. [PMID: 38222021 PMCID: PMC10784832 DOI: 10.4240/wjgs.v15.i12.2938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/11/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023] Open
Abstract
BACKGROUND Klebsiella variicola (K. variicola) is a member of the Klebsiella genus and is often misidentified as Klebsiella pneumoniae. In this report, we present a rare case of invasive liver abscess caused by K. variicola. CASE SUMMARY We report a rare case of liver abscess due to K. variicola. A 57-year-old female patient presented with back pain for a month. She developed a high-grade fever associated with chills, and went into a coma and developed shock. The clinical examinations and tests after admission confirmed a diagnosis of primary liver abscess caused by K. variicola complicated by intracranial infection and septic shock. The patient successfully recovered following early percutaneous drainage of the abscess, prompt appropriate antibiotic administration, and timely open surgical drainage. CONCLUSION This is a case of successful treatment of invasive liver abscess syndrome caused by K. variicola, which has rarely been reported. The findings of this report point to the need for further study of this disease.
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Affiliation(s)
- Pin-Jie Zhang
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Zhong-Hua Lu
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Li-Jun Cao
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Hu Chen
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Yun Sun
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
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20
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Matsuda N, Aung MS, Urushibara N, Kawaguchiya M, Ohashi N, Taniguchi K, Kudo K, Ito M, Kobayashi N. Prevalence, clonal diversity, and antimicrobial resistance of hypervirulent Klebsiella pneumoniae and Klebsiella variicola clinical isolates in northern Japan. J Glob Antimicrob Resist 2023; 35:11-18. [PMID: 37604276 DOI: 10.1016/j.jgar.2023.08.009] [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: 06/16/2023] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
OBJECTIVES Hypervirulent Klebsiella pneumoniae (hvKp) and Klebsiella variicola (hvKv) cause hospital/community-acquired infections, often associated with antimicrobial resistance (AMR). This study aimed to investigate the molecular epidemiology of hvKp and hvKv in northern Japan. METHODS A total of 500 K. pneumoniae and 421 K. variicola clinical isolates collected from August to December 2021 were studied. Prevalence of virulence factor-encoding genes, wzi sequence and associated K/KL type, sequence type (ST), and beta-lactamases and their types were characterized. RESULTS Any virulence gene (rmpA, rmpA2, peg-344, iucA, iutA, and iroB) and/or magA was detected in 25% (n = 125) of K. pneumoniae and 1% (n = 5) of K. variicola. Among these hvKp/hvKv, 22 wzi types (18 and 4 types, respectively) and 24 STs (20 and 4 STs, respectively) were identified. Sequence types of hvKp were classified into some clonal groups (CGs), among which CG35, including six STs, was the most common (n = 59; 47%), followed by CG23, and CG65. ST268 (CG35) associated with wzi95-K20 or wzi720 was the dominant lineage (n = 43, 34%), while K1:ST23/ST249 and K2:ST65/ST86 accounted for 26% and 13% of hvKp, respectively. Extended-spectrum beta-lactamase (ESBL) genes (blaCTX-M-2, blaCTX-M-3, blaCTX-M-15, and blaCTX-M-27) were detected in only ST23 and CG35 (ST268 and ST412) hvKp. No isolate was resistant to carbapenems, without detection of the ESBL gene in K. variicola. Phylogenetically, wzi was differentiated into two main clusters of K. pneumoniae and K. variicola. A major clonal group CG347 was identified in K. variicola. CONCLUSION Clonal structures were revealed for hvKp and hvKv clinical isolates with their AMR status in northern Japan.
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Affiliation(s)
- Norifumi Matsuda
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan.
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Nobuhide Ohashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | | | - Kenji Kudo
- Sapporo Clinical Laboratory, Inc., Sapporo, Hokkaido, Japan
| | - Masahiko Ito
- Sapporo Clinical Laboratory, Inc., Sapporo, Hokkaido, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
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21
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Duran-Bedolla J, Rodríguez-Medina N, Dunn M, Mosqueda-García D, Barrios-Camacho H, Aguilar-Vera A, Aguilar-Vera E, Suárez-Rodríguez R, Ramírez-Trujillo JA, Garza-Ramos U. Plasmids of the incompatibility group FIB K occur in Klebsiella variicola from diverse ecological niches. Int Microbiol 2023; 26:917-927. [PMID: 36971854 DOI: 10.1007/s10123-023-00346-0] [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: 01/23/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Plasmids play a fundamental role in the evolution of bacteria by allowing them to adapt to different environments and acquire, through horizontal transfer, genes that confer resistance to different classes of antibiotics. Using the available in vitro and in silico plasmid typing systems, we analyzed a set of isolates and public genomes of K. variicola to study its plasmid diversity. The resistome, the plasmid multilocus sequence typing (pMLST), and molecular epidemiology using the MLST system were also studied. A high frequency of IncF plasmids from human isolates but lower frequency from plant isolates were found in our strain collection. In silico detection revealed 297 incompatibility (Inc) groups, but the IncFIBK (216/297) predominated in plasmids from human and environmental samples, followed by IncFIIK (89/297) and IncFIA/FIA(HI1) (75/297). These Inc groups were associated with clinically important ESBL (CTX-M-15), carbapenemases (KPC-2 and NDM-1), and colistin-resistant genes which were associated with major sequence types (ST): ST60, ST20, and ST10. In silico MOB typing showed 76% (311/404) of the genomes contained one or more of the six relaxase families with MOBF being most abundant. We identified untypeable plasmids carrying blaKPC-2, blaIMP-1, and blaSHV-187 but for which a relaxase was found; this may suggest that novel plasmid structures could be emerging in this bacterial species. The plasmid content in K. variicola has limited diversity, predominantly composed of IncFIBK plasmids dispersed in different STs. Plasmid detection using the replicon and MOB typing scheme provide a broader context of the plasmids in K. variicola. This study showed that whole-sequence-based typing provides current insights of the prevalence of plasmid types and their association with antimicrobial resistant genes in K. variicola obtained from humans and environmental niches.
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Affiliation(s)
- Josefina Duran-Bedolla
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Nadia Rodríguez-Medina
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Michael Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Dalila Mosqueda-García
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Edgar Aguilar-Vera
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Ramón Suárez-Rodríguez
- Laboratorio de Fisiología Molecular de Plantas, Centro de Investigación en Biotecnología (CEIB), Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - José Augusto Ramírez-Trujillo
- Laboratorio de Fisiología Molecular de Plantas, Centro de Investigación en Biotecnología (CEIB), Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México.
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Yin L, Shen X, Yin D, Hou H, Wang J, Zhao R, Dai Y, Pan X, Qi K. Integrated analysis of noncoding RNAs and mRNAs reveals their potential roles in chicken spleen response to Klebsiella variicola infection. Res Vet Sci 2023; 164:105029. [PMID: 37769515 DOI: 10.1016/j.rvsc.2023.105029] [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: 06/29/2023] [Revised: 09/09/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023]
Abstract
Klebsiella variicola is an emerging pathogen that has become a threat to human and animal health. There is evidence that long noncoding RNAs (lncRNAs) are involved in a host cell's response to microbial infections. However, no study has defined the link between K. variicola pathogenesis and lncRNAs until now. We used RNA sequencing to comprehensively analyze the lncRNAs and mRNAs in the chicken spleen after K. variicola infection. In total, we identified 2896 differentially expressed mRNAs and 578 differentially expressed lncRNAs. To examine the potential functions of these lncRNAs, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analyses were performed on the target mRNAs of these differently expressed lncRNAs. The results suggested that lncRNAs play essential roles in modulating mRNA expression and triggering downstream immune signaling pathways to regulate the immune response in the chicken spleen. Using previous microRNA sequencing data, we constructed lncRNA-miRNA-mRNA regulatory networks to clarify the regulatory mechanisms in the chicken immune system. Several potential regulatory pairs related to K. variicola infection were found, involving XR_001467769.2, TCONS_00018386, gga-miR-132a-3p, gga-miR-132b-5p, gga-miR-2954, and novel62_mature. In conclusion, our findings make a significant contribution towards understanding the role of lncRNA in chicken spleen cells during K. variicola infection, thereby establishing a solid foundation for future research in this area.
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Affiliation(s)
- Lei Yin
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xuehuai Shen
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Dongdong Yin
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Hongyan Hou
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Jieru Wang
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Ruihong Zhao
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Yin Dai
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xiaocheng Pan
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China.
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
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23
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Hernández-Salmerón JE, Irani T, Moreno-Hagelsieb G. Fast genome-based delimitation of Enterobacterales species. PLoS One 2023; 18:e0291492. [PMID: 37708115 PMCID: PMC10501659 DOI: 10.1371/journal.pone.0291492] [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: 05/22/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Average Nucleotide Identity (ANI) is becoming a standard measure for bacterial species delimitation. However, its calculation can take orders of magnitude longer than similarity estimates based on sampling of short nucleotides, compiled into so-called sketches. These estimates are widely used. However, their variable correlation with ANI has suggested that they might not be as accurate. For a where-the-rubber-meets-the-road assessment, we compared two sketching programs, mash and dashing, against ANI, in delimiting species among Esterobacterales genomes. Receiver Operating Characteristic (ROC) analysis found Area Under the Curve (AUC) values of 0.99, almost perfect species discrimination for all three measures. Subsampling to avoid over-represented species reduced these AUC values to 0.92, still highly accurate. Focused tests with ten genera, each represented by more than three species, also showed almost identical results for all methods. Shigella showed the lowest AUC values (0.68), followed by Citrobacter (0.80). All other genera, Dickeya, Enterobacter, Escherichia, Klebsiella, Pectobacterium, Proteus, Providencia and Yersinia, produced AUC values above 0.90. The species delimitation thresholds varied, with species distance ranges in a few genera overlapping the genus ranges of other genera. Mash was able to separate the E. coli + Shigella complex into 25 apparent phylogroups, four of them corresponding, roughly, to the four Shigella species represented in the data. Our results suggest that fast estimates of genome similarity are as good as ANI for species delimitation. Therefore, these estimates might suffice for covering the role of genomic similarity in bacterial taxonomy, and should increase confidence in their use for efficient bacterial identification and clustering, from epidemiological to genome-based detection of potential contaminants in farming and industry settings.
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Affiliation(s)
| | - Tanya Irani
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
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24
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Nucci A, Janaszkiewicz J, Rocha EPC, Rendueles O. Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola. MICROLIFE 2023; 4:uqad038. [PMID: 37781688 PMCID: PMC10540941 DOI: 10.1093/femsml/uqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Juliette Janaszkiewicz
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
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25
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Nikapitiya C, Chandrarathna HPSU, Dias MKHM, Lee J, De Zoysa M. Characterization and biocontrol efficacy of lytic phage (KPP-1) that infects multidrug resistant Klebsiella variicola. Braz J Microbiol 2023; 54:2509-2520. [PMID: 37368195 PMCID: PMC10484831 DOI: 10.1007/s42770-023-01037-8] [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: 09/02/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Klebsiella variicola strain was identified from a natural water stream. Novel phage (KPP-1) infecting K. variicola was isolated and characterized. The biocontrol efficacy of KPP-1 against K. variicola-infected adult zebrafish was also investigated. The host K. variicola strain was resistant to six of the antibiotics tested and comprised the virulence genes kfuBC, fim, ureA, and Wza-Wzb-Wzccps. Morphological analysis by transmission electron microscopy revealed that KPP-1 has icosahedron head and tail structures. The latent period and burst size of KPP-1 were 20 min and 88 PFU per infected cell, respectively, at a multiplicity of infection of 0.1. KPP-1 was stable over a broad pH range (3-11), temperature (4-50 °C), and salinity (0.1-3%). KPP-1 inhibits the growth of K. variicola in vitro and in vivo. In the zebrafish infection model, treatment with KPP-1-infected K. variicola demonstrated 56% of cumulative survival. This suggests the possibility of developing KPP-1 as a potential biocontrol agent against multidrug-resistant K. variicola that belongs to the K. pneumoniae complex.
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Affiliation(s)
- Chamilani Nikapitiya
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - H P S U Chandrarathna
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | | | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea.
- Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea.
| | - Mahanama De Zoysa
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Xi Y, Zhao J, Zhang J, Jin Y, Yang H, Duan G, Chen S, Long J. Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola. Lett Appl Microbiol 2023; 76:ovad108. [PMID: 37715312 DOI: 10.1093/lambio/ovad108] [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: 04/27/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023]
Abstract
Klebsiella variicola, an emerging human pathogen, poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver of the emergence of multiple antibiotic-resistant K. variicola. Clustered regularly interspersed short palindromic repeats (CRISPR) coupled with CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, and can provide acquired immunity against HGT. However, the information about the CRISPR/Cas system in K. variicola is still limited. In this study, 487 genomes of K. variicola obtained from the National Center for Biotechnology Information database were used to analyze the characteristics of CRISPR/Cas systems. Approximately 21.56% of genomes (105/487) harbor at least one confirmed CRISPR array. Three types of CRISPR/Cas systems, namely the type I-E, I-E*, and IV-A systems, were identified among 105 strains. Spacer origin analysis further revealed that approximately one-third of spacers significantly match plasmids or phages, which demonstrates the implication of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tend to target mobile genetic elements from K. pneumoniae. This finding provides new evidence of the interaction of K. variicola and K. pneumoniae during their evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.
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Affiliation(s)
- Yanyan Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
| | - Jiaxue Zhao
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
| | - Jiangfeng Zhang
- Henan Provincial People's Hospital, Zhengzhou, Henan 450001, People's Republic of China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
- Henan Key Laboratory of Molecular Medicine, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
| | - Jinzhao Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
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Yuan T, Qazi IH, Li J, Yang P, Yang H, Zhang X, Liu W, Liu J. Analysis of changes in bacterial diversity in healthy and bacterial wilt mulberry samples using metagenomic sequencing and culture-dependent approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1206691. [PMID: 37680359 PMCID: PMC10481342 DOI: 10.3389/fpls.2023.1206691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023]
Abstract
Introduction Mulberry bacterial wilt is a serious destructive soil-borne disease caused by a complex and diverse group of pathogenic bacteria. Given that the bacterial wilt has been reported to cause a serious damage to the yield and quality of mulberry, therefore, elucidation of its main pathogenic groups is essential in improving our understanding of this disease and for the development of its potential control measures. Methods In this study, combined metagenomic sequencing and culture-dependent approaches were used to investigate the microbiome of healthy and bacterial wilt mulberry samples. Results The results showed that the healthy samples had higher bacterial diversity compared to the diseased samples. Meanwhile, the proportion of opportunistic pathogenic and drug-resistant bacterial flora represented by Acinetobacter in the diseased samples was increased, while the proportion of beneficial bacterial flora represented by Proteobacteria was decreased. Ralstonia solanacearum species complex (RSSC), Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, K. quasipneumoniae, K. michiganensis, K. oxytoca, and P. ananatis emerged as the main pathogens of the mulberry bacterial wilt. Discussion In conclusion, this study provides a valuable reference for further focused research on the bacterial wilt of mulberry and other plants.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiping Liu
- South China Agriculture University, College of Animal Science, Regional Sericulture Training Center for Asia-Pacific, Guangzhou, Guangdong, China
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Sun Y, Zheng C, Zhou J, Zhen M, Wei X, Yan X, Guo X, Zheng L, Shao M, Li C, Qin D, Zhang J, Xiong L, Xing J, Huang B, Dong Z, Cheng P, Yu G. Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot. PLANT DISEASE 2023; 107:2325-2334. [PMID: 37596715 DOI: 10.1094/pdis-09-22-2018-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yunhao Sun
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Chuanyuan Zheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Meng Zhen
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xingying Wei
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xun Yan
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xiaojian Guo
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Li Zheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Mingwei Shao
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Chunji Li
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Di Qin
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jie Zhang
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Lina Xiong
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Juejun Xing
- Laboratory and Equipment Management Department, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Bingzhi Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510000, China
| | - Zhangyong Dong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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Kosikowska U, Dłuski DF, Pietras-Ożga D, Leszczyńska-Gorzelak B, Andrzejczuk S. Prevalence of Culturable Bacteria and Yeasts in the Nasopharynx Microbiota during the Physiological Course of Pregnancy. J Clin Med 2023; 12:4447. [PMID: 37445482 DOI: 10.3390/jcm12134447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The aim of the study was to compare the prevalence of the nasopharyngeal carriage of culturable microorganisms in the microbiota of asymptomatic women with a physiological pregnancy (PW) and nonpregnant women (NPW). Nasopharyngeal swabs were collected from 53 PW and 30 NPW to detect bacterial and fungal colonization. Isolates were identified using the culture method and the MALDI-TOF MS technique. The nasopharyngeal microbiota (NPM) partially differed between PW and NPW. These differences in the frequency of nasopharyngeal colonization between the PW and NPW groups were not statistically significant (p > 0.05); all cases were colonized by bacteria and only two cases in the PW group were colonized by yeasts, namely, Rhodotorula spp. High levels of staphylococcal colonization, including predominantly coagulase-negative staphylococci and S. aureus in the nasopharyngeal sample, were present in both groups. The reduced number of Gram-negative rods colonized in the cases studied was seen in samples from the NPW group, particularly with Enterobacterales, and anaerobic Cutibacterium spp. were isolated only in the PW group (p < 0.05). Moreover, a higher carriage rate of Enterobacter aerogenes colonization was statistically significant (p < 0.05) and correlated with the NPW group. Pregnancy may disturb the composition of the NPM represented by commensals and opportunistic bacteria and promote yeast colonization as compared to nonpregnant women.
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Affiliation(s)
- Urszula Kosikowska
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland
| | | | - Dorota Pietras-Ożga
- Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | | | - Sylwia Andrzejczuk
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland
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Pandey S, Whitlock KB, Test MR, Hodor P, Pope CE, Limbrick DD, McDonald PJ, Hauptman JS, Hoffman LR, Simon TD. Characterization of cerebrospinal fluid (CSF) microbiota at the time of initial surgical intervention for children with hydrocephalus. PLoS One 2023; 18:e0280682. [PMID: 37342995 PMCID: PMC10284395 DOI: 10.1371/journal.pone.0280682] [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: 10/03/2022] [Accepted: 01/05/2023] [Indexed: 06/23/2023] Open
Abstract
OBJECTIVE To characterize the microbiota of the cerebrospinal fluid (CSF) from children with hydrocephalus at the time of initial surgical intervention. STUDY DESIGN CSF was obtained at initial surgical intervention. One aliquot was stored in skim milk-tryptone-glucose-glycerol (STGG) medium and the second was unprocessed; both were then stored at -70°C. Bacterial growth for CSF samples stored in STGG were subsequently characterized using aerobic and anaerobic culture on blood agar and MALDI-TOF sequencing. All unprocessed CSF samples underwent 16S quantitative polymerase chain reaction (qPCR) sequencing, and a subset underwent standard clinical microbiological culture. CSF with culture growth (either after storage in STGG or standard clinical) were further analyzed using whole-genome amplification sequencing (WGAS). RESULTS 11/66 (17%) samples stored in STGG and 1/36 (3%) that underwent standard clinical microbiological culture demonstrated bacterial growth. Of the organisms present, 8 were common skin flora and 4 were potential pathogens; only 1 was also qPCR positive. WGAS findings and STGG culture findings were concordant for only 1 sample, identifying Staphylococcus epidermidis. No significant difference in time to second surgical intervention was observed between the STGG culture-positive and negative groups. CONCLUSION(S) Using high sensitivity methods, we detected the presence of bacteria in a subset of CSF samples at the time of first surgery. Therefore, the true presence of bacteria in CSF of children with hydrocephalus cannot be ruled out, though our findings may suggest these bacteria are contaminants or false positives of the detection methods. Regardless of origin, the detection of microbiota in the CSF of these children may not have any clinical significance.
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Affiliation(s)
- Shailly Pandey
- University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kathryn B. Whitlock
- New Harmony Statistical Consulting, Clinton, Washington, United States of America
| | - Matthew R. Test
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Paul Hodor
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Christopher E. Pope
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - David D. Limbrick
- Department of Neurosurgery, Washington University in St. Louis, St. Louis, Missouri, United States of America
- St. Louis Children’s Hospital, St. Louis, Missouri, United States of America
| | - Patrick J. McDonald
- Section of Neurosurgery, University of Manitoba, Winnipeg, Manitoba, Canada
- Winnipeg Children’s Hospital, Winnipeg, Manitoba, Canada
| | - Jason S. Hauptman
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Neurosurgery, University of Washington, Seattle, Washington, United States of America
- Seattle Children’s Hospital, Seattle, Washington, United States of America
| | - Lucas R. Hoffman
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Seattle Children’s Hospital, Seattle, Washington, United States of America
| | - Tamara D. Simon
- Department of Pediatrics, University of Southern California, Los Angeles, California, United States of America
- The Saban Research Institute, Los Angeles, California, United States of America
- Children’s Hospital Los Angeles, Los Angeles, California, United States of America
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Li L, Jiang Y, Zhu Q, Liu D, Chang M, Wang Y, Xi R, Wang W. Hyaluronan with Different Molecular Weights Can Affect the Gut Microbiota and Pathogenetic Progression of Post-Intensive Care Syndrome Mice in Different Ways. Int J Mol Sci 2023; 24:ijms24119757. [PMID: 37298710 DOI: 10.3390/ijms24119757] [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: 04/28/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Post-intensive care syndrome (PICS) poses a serious threat to the health of intensive care unit (ICU) survivors, and effective treatment options are currently lacking. With increasing survival rates of ICU patients worldwide, there is a rising interest in developing methods to alleviate PICS symptoms. This study aimed to explore the potential of using Hyaluronan (HA) with different molecular weights as potential drugs for treating PICS in mice. Cecal ligation and puncture (CLP) were used to establish a PICS mice model, and high molecular weight HA (HMW-HA) or oligo-HA were used as therapeutic agents. Pathological and physiological changes of PICS mice in each group were monitored. 16S rRNA sequencing was performed to dissect gut microbiota discrepancies. The results showed that both molecular weights of HA could increase the survival rate of PICS mice at the experimental endpoint. Specifically, 1600 kDa-HA can alleviate PICS in a short time. In contrast, 3 kDa-HA treatment decreased PICS model survivability in the early stages of the experiment. Further, via 16S rRNA sequence analysis, we observed the changes in the gut microbiota in PICS mice, thereby impairing intestinal structure and increasing inflammation. Additionally, both types of HA can reverse this change. Moreover, compared to 1600 kDa-HA, 3 kDa-HA can significantly elevate the proportion of probiotics and reduce the abundance of pathogenic bacteria (Desulfovibrionaceae and Enterobacteriaceae). In conclusion, HA holds the advantage of being a potential therapeutic drug for PICS, but different molecular weights can lead to varying effects. Moreover, 1600 kDa-HA showed promise as a protective agent in PICS mice, and caution should be taken to its timing when considering using 3 kDa-HA.
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Affiliation(s)
- Lu Li
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yuanyuan Jiang
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qianqian Zhu
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Dawei Liu
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingkai Chang
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yongzhe Wang
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Ruitong Xi
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Wenfei Wang
- Biopharmaceutical Lab., College of Life Science, Northeast Agricultural University, Harbin 150030, China
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Kim SJ, Jo J, Ko KS. Lipid A modification-induced colistin-resistant Klebsiella variicola from healthy adults. J Med Microbiol 2023; 72. [PMID: 37261959 DOI: 10.1099/jmm.0.001680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Background. Klebsiella variicola was once recognised as a benign plant-endosymbiont but recent case reports suggest that it is a newly emerging Gram-negative pathogen related to opportunistic infection of multiple sites in humans.Methods. Antimicrobial susceptibility testing was performed using broth microdilution method. To identify colistin resistance mechanisms, phoPQ, pmrAB, and mgrB were sequenced and their mRNA expression was analysed using quantitative real-time PCR. In addition, we tried to detect crrAB and mcr. The lipid A moieties of colistin-susceptible and -resistant isolates were analysed using MALDI-TOF.Results. Among the two K. variicola isolates, one is colistin-resistant, and another is colistin-susceptible. The colistin-resistant K. variicola isolate showed no mutations in phoPQ, pmrAB, and mgrB, and crrAB and mcr were not identified. However, its phoQ and pbgP expression was significantly higher and amino-arabinosylated lipid A with hexa-acylated species in lipopolysaccharide was identified.Conclusions. We found that colistin resistance in K. variicola was mediated by the modification of lipid A. Although the isolate was obtained from faecal samples of healthy adults, colistin-resistant K. variicola challenges public health as an opportunistic pathogen.
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Affiliation(s)
- Sun Ju Kim
- Department of Pharmacy, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jeongwoo Jo
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kwan Soo Ko
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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Tanii R, Harada S, Saito H, Okamoto K, Doi Y, Suzuki M. A case report of fatal COVID-19 complicated by rapidly progressive sepsis caused by Klebsiella variicola. BMC Infect Dis 2023; 23:184. [PMID: 36991335 DOI: 10.1186/s12879-023-08128-9] [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: 07/24/2022] [Accepted: 02/27/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND There is a growing interest in Klebsiella variicola as a causative pathogen in humans, though its clinical features and the impact of co-infection or secondary infection with COVID-19 remain unknown. CASE PRESENTATION A 71-year-old man presented with fever, altered mental status and generalized weakness and was admitted to ICU due to severe COVID-19 pneumonia. He was newly diagnosed with type II diabetes mellitus upon admission. On hospital day 3, his respiratory status deteriorated, requiring invasive mechanical ventilation. On hospital day 10, superimposed bacterial pneumonia was suspected and subsequently, broad-spectrum antibiotics were administered for the associated bloodstream infection. On hospital day 13, despite administration of active antibiotics and appropriate source control, he decompensated and died. The causative organism isolated from blood cultures was initially reported as K. pneumoniae, but it was identified as K. variicola by a genetic analysis. A representative isolate (FUJ01370) had a novel multilocus sequence typing allelic profile (gapA-infB-mdh-pgi-phoE-rpoB-tonB: 16-24-21-27-52-17-152), to which sequence type 5794 was assigned (GenBank assembly accession: GCA_019042755.1). CONCLUSIONS We report a fatal case of respiratory and bloodstream infection due to K. variicola complicating severe COVID-19. Co-infection or secondary infection of K. variicola in COVID-19 is likely under-recognized and can be fulminant as in this case.
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Affiliation(s)
- Rimi Tanii
- Department of Emergency and Critical Care Medicine, St. Marianna University Yokohama Seibu Hospital, 1197-1, Yasashi-cho, Asahi-ku, Yokohama, Kanagawa, Japan.
| | - Sohei Harada
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroki Saito
- Department of Emergency and Critical Care Medicine, St. Marianna University Yokohama Seibu Hospital, 1197-1, Yasashi-cho, Asahi-ku, Yokohama, Kanagawa, Japan
| | - Koh Okamoto
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Fructooligosaccharides attenuate non-alcoholic fatty liver disease by remodeling gut microbiota and association with lipid metabolism. Biomed Pharmacother 2023; 159:114300. [PMID: 36696803 DOI: 10.1016/j.biopha.2023.114300] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is a common liver disease highly associated with metabolic diseases and gut dysbiosis. Several clinical trials have confirmed that fructooligosaccharides (FOSs) are a viable alternative treatment for NAFLD. However, the mechanisms underlying the activities of FOSs remain unclear. METHODS In this study, the effects of FOSs were investigated with the use of two C57BL/6 J mouse models of NAFLD induced by a high-fat, high-cholesterol (HFHC) diet and a methionine- and choline-deficient (MCD) diet, respectively. The measured metabolic parameters included body, fat, and liver weights; and blood glucose, glucose tolerance, and serum levels of glutamate transaminase, aspartate transaminase, and triglycerides. Liver tissues were collected for histological analysis. In addition, 16 S rRNA sequencing was conducted to investigate the effects of FOSs on the composition of the gut microbiota of mice in the HFHC and MCD groups and treated with FOSs. RESULTS FOS treatment attenuated severe metabolic changes and hepatic steatosis caused by the HFHC and MCD diets. In addition, FOSs remodeled the structure of gut microbiota in mice fed the HFHC and MCD diets, as demonstrated by increased abundances of Bacteroidetes (phylum level), Klebsiella variicola, Lactobacillus gasseri, and Clostridium perfringens (species level); and decreased abundances of Verrucomicrobia (phylum level) and the Fissicatena group (genus level). Moreover, the expression levels of genes associated with lipid metabolism and inflammation (i.e., ACC1, PPARγ, CD36, MTTP, APOC3, IL-6, and IL-1β) were down-regulated after FOS treatment. CONCLUSION FOSs alleviated the pathological phenotype of NAFLD via remodeling of the gut microbiota composition and decreasing hepatic lipid metabolism, suggesting that FOSs as functional dietary supplements can potentially reduce the risk of NAFLD.
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Ge H, Qiao J, Xu H, Liu R, Zhao J, Chen R, Li C, Chen M, Guo X. Emergence of OXA-484-Producing Klebsiella variicola in China. Infect Drug Resist 2023; 16:1767-1775. [PMID: 37008750 PMCID: PMC10065429 DOI: 10.2147/idr.s404551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Purpose The frequent and inappropriate use of antibiotics has caused a dramatic rise in the number, species, and degree of multi-drug resistant bacteria, making them more prevalent and difficult to treat. In this context, the aim of the present study was to characterize the OXA-484-producing strains isolated from a perianal swab of a patient by using whole-genome analysis. Patients and Methods In this study, carbapenemase-producing Klebsiella variicola was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), average nucleotide identity (ANI) and PCR. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting were utilized to characterize the plasmid profiles of K. variicola 4717. In particular, WGS was performed to obtain genomic information on this clinical isolate, and assemble all the plasmids of the bla OXA-484-harboring strain. Results The antimicrobial susceptibility pattern of K. variicola 4717 revealed that it was resistant to a range of antibiotics, including aztreonam, imipenem, meropenem, ceftriaxone, cefotaxime, ceftazidime, levofloxacin, ciprofloxacin, piperacillin-tazobactam, methylene-sulfamer oxazole, amoxicillin-clavulanic acid, cefepime, and tigecycline. Its susceptibility to chloromycin was intermediate, while it was still susceptible to amikacin, gentamicin, fosfomycin, and polymyxin B. The presence of two companion plasmids, p4717_1 and p4717_2, together with a plasmid carrying the bla OXA-484 gene was observed. An in-depth investigation of p4717-OXA-484 uncovered that it is an IncX3-type plasmid and shares a similar segment encoded by IS26. Given the similar genetic background, it was conceivable that bla OXA-484 could have developed from bla OXA-181 through a series of mutations. Conclusion Herein, we described the first genome sequence of K. variicola strain harbouring the class D β-actamase bla OXA-484 in an Inc-X3-type plasmid. Our work also uncovered the genetic characterization of K. variicola 4717 and the importance of initiating antimicrobial detection promptly.
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Affiliation(s)
- Haoyu Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jie Qiao
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Junhui Zhao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Ruyan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Chenyu Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Mantao Chen
- Department of Neurosurgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Correspondence: Xiaobing Guo, Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Jianshe East Road, Zhengzhou, Henan Province, 450000, People’s Republic of China, Tel +86 371 6627 8237, Fax +86 371 6691 3569, Email
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Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications. Pharmaceutics 2023; 15:pharmaceutics15020434. [PMID: 36839755 PMCID: PMC9960720 DOI: 10.3390/pharmaceutics15020434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
In recent years, multidrug-resistant (MDR) strains of Klebsiella pneumoniae have spread globally, being responsible for the occurrence and severity of nosocomial infections. The NDM-1-kp, VIM-1 carbapenemase-producing isolates as well as extended-spectrum beta lactamase-producing (ESBL) isolates along with Klebsiella oxytoca strains have become emerging pathogens. Due to the growing problem of antibiotic resistance, bacteriophage therapy may be a potential alternative to combat such multidrug-resistant Klebsiella strains. Here, we present the results of a long-term study on the isolation and biology of bacteriophages active against K. pneumoniae, as well as K. oxytoca strains. We evaluated biological properties, morphology, host specificity, lytic spectrum and sensitivity of these phages to chemical agents along with their life cycle parameters such as adsorption, latent period, and burst size. Phages designated by us, vB_KpnM-52N (Kpn52N) and VB_KpnM-53N (Kpn53N), demonstrated relatively broad lytic spectra among tested Klebsiella strains, high burst size, adsorption rates and stability, which makes them promising candidates for therapeutic purposes. We also examined selected Klebsiella phages from our historical collection. Notably, one phage isolated nearly 60 years ago was successfully used in purulent cerebrospinal meningitis in a new-born and has maintained lytic activity to this day. Genomic sequences of selected phages were determined and analyzed. The phages of the sequenced genomes belong to the Slopekvirus and Jiaodavirus genus, a group of phages related to T4 at the family level. They share several features of T4 making them suitable for antibacterial therapies: the obligatorily lytic lifestyle, a lack of homologs of known virulence or antibiotic resistance genes, and a battery of enzymes degrading host DNA at infection.
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Magnúsdóttir S, Saraiva JP, Bartholomäus A, Soheili M, Toscan RB, Zhang J, Nunes da Rocha U. Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa. Front Microbiol 2023; 14:1037845. [PMID: 36760505 PMCID: PMC9905122 DOI: 10.3389/fmicb.2023.1037845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/02/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Every year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization of the global population, the spread of ARGs in urban bacteria has become a more severe threat to human health. Methods In this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 urban metagenomes in multiple urban locations to investigate the fate and occurrence of ARGs in urban bacteria. Additionally, we analyzed the occurrence of these ARGs on plasmids and estimated the virulence of the bacterial species. Results Our results showed that multidrug and glycopeptide ARGs are ubiquitous among urban bacteria. Additionally, we analyzed the deterministic effects of phylogeny on the spread of these ARGs and found ARG classes that have a non-random distribution within the phylogeny of our recovered MAGs. However, few ARGs were found on plasmids and most of the recovered MAGs contained few virulence factors. Discussion Our results suggest that the observed non-random spreads of ARGs are not due to the transfer of plasmids and that most of the bacteria observed in the study are unlikely to be virulent. Additional research is needed to evaluate whether the ubiquitous and widespread ARG classes will become entirely prevalent among urban bacteria and how they spread among phylogenetically distinct species.
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Affiliation(s)
- Stefanía Magnúsdóttir
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany,*Correspondence: Stefanía Magnúsdóttir, ✉
| | - Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | | | - Majid Soheili
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Rodolfo Brizola Toscan
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Junya Zhang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany,Ulisses Nunes da Rocha, ✉
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Bi L, Han LL, Du S, Yu DT, He JZ, Zhang LM, Hu HW. Cross-biome soil viruses as an important reservoir of virulence genes. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130111. [PMID: 36209605 DOI: 10.1016/j.jhazmat.2022.130111] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Viruses can significantly influence the composition and functions of their host communities and enhance host pathogenicity via the transport of virus-encoded virulence genes. However, the contribution of viral communities to the dissemination of virulence genes across various biomes across a large scale is largely unknown. Here, we constructed 29,283 soil viral contigs (SVCs) from viral size fraction metagenomes and public databases. A total of 1310 virulence genes were identified from 1164 SVCs in a wide variety of soil biomes, including grassland, agricultural and forest soils. The virulence gene gmd was the most abundant one, followed by csrA, evpJ, and pblA. A great proportion of viruses encoding virulence genes were uncharacterized. Virus-host linkage analysis revealed that most viruses were linked to only one bacterial genus, whereas several SVCs were associated with more than one bacterial genus and even two bacterial phyla, suggesting the potential risk of spreading virulence genes across different bacterial communities via viruses. Altogether, we provided new evidence for the prevalence of virulence genes in soil viruses across biomes, which advanced our understanding of the potential role of soil viruses in driving the pathogenesis of their hosts in terrestrial ecosystems.
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Affiliation(s)
- Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Ting Yu
- School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Genome Characterization of Bacteriophage KPP-1, a Novel Member in the Subfamily Vequintavirinae, and Use of Its Endolysin for the Lysis of Multidrug-Resistant Klebsiella variicola In Vitro. Microorganisms 2023; 11:microorganisms11010207. [PMID: 36677499 PMCID: PMC9862379 DOI: 10.3390/microorganisms11010207] [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: 10/31/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug-resistant members of the Klebsiella pneumoniae complex have become a threat to human lives and animals, including aquatic animals, owing to the limited choice of antimicrobial treatments. Bacteriophages are effective natural tools available to fight against multidrug-resistant bacteria. The bacteriophage KPP-1 was found to be strictly lytic against K. variicola, a multidrug-resistant isolate, producing clear plaques. The genome sequence analysis of KPP-1 revealed that it comprised 143,369 base pairs with 47% overall GC content. A total of 272 genes (forward 161, complementary 111) encode for 17 tRNAs and 255 open reading frames (ORFs). Among them, 32 ORFs could be functionally annotated using the National Center for Biotechnology Information (NCBI) Protein Basic Local Alignment Search Tool (BLASTp) algorithm while 223 were found to code for hypothetical proteins. Comparative genomic analysis revealed that the closest neighbor of KPP-1 can be found in the genus Mydovirus of the subfamily Vequintavirinae. KPP-1 not only markedly suppressed the growth of the host but also worked synergistically with ampicillin. Useful genes for pathogen control such as endolysin (locus tag: KPP_11591) were found to have activity against multidrug-resistant isolate of K. variicola. Further studies are necessary to develop a strategy to control the emerging pathogen K. variicola using bacteriophages such as KPP-1.
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Yadav B, Mohanty S, Behera B. Occurrence and Genomic Characteristics of Hypervirulent Klebsiella pneumoniae in a Tertiary Care Hospital, Eastern India. Infect Drug Resist 2023; 16:2191-2201. [PMID: 37077254 PMCID: PMC10108904 DOI: 10.2147/idr.s405816] [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: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 04/21/2023] Open
Abstract
Purpose This study was conducted to find out the occurrence of hypervirulent Klebsiella pneumoniae (hvKP) isolates from different clinical specimens in a tertiary care hospital of eastern India and investigate the distribution of virulence factors, capsular serotypes and antibiogram profile. The distribution of carbapenemase-encoding genes in convergent (hvKP and carbapenem-resistant) isolates was also studied. Materials and methods A total of 1004 K. pneumoniae isolates were obtained from different clinical specimens from August 2019 to June 2021 and hvKP isolates were identified using the string test. Genes of capsular serotypes K1, K2, K5, K20, K54 and K57, virulence-associated genes, rmpA, rmpA2, mrkD, allS, iroN, iutA, iuc, kfuB and ybtS, and carbapenemase-encoding genes, NDM-1, OXA-48, OXA-181, and KPC, were evaluated by polymerase chain reaction. Antimicrobial susceptibility was determined primarily by the VITEK-2 Compact automated platform (bioMérieux, Marcy-l'Étoile, France) and supplemented by disc-diffusion/EzyMIC (HiMedia, Mumbai, India) wherever needed. Results Out of 1004 isolates, 33 (3.3%) were hvKP. Most frequent capsular serotype was K2 in 11 (33.3%). Amongst virulence genes, mrkD, iutA and kfuB were detected most frequently in 93.9%, 84.8% and 63.6% isolates respectively. Classical Klebsiella pneumoniae isolates were significantly more resistant than hvKP to cephalosporins, amoxicillin-clavulanic acid, and fluoroquinolones (p < 0.05). Carbapenem resistance was seen in 10 hvKP convergent isolates with the most prevalent carbapenemase-encoding gene being OXA-48 and OXA-181 in 50% isolates. Conclusion There is a need for continued surveillance of hvKP strains in view of the impending threat of a global spread of convergent strains.
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Affiliation(s)
- Bhuvan Yadav
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India
| | - Srujana Mohanty
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India
- Correspondence: Srujana Mohanty, Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India, Tel +9438884124, Email
| | - Bijayini Behera
- Department of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, 751019, India
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Wang L, Zhu M, Yan C, Zhang Y, He X, Wu L, Xu J, Lu J, Bao Q, Hu Y, Xu T, Liang J. Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China. Front Microbiol 2023; 14:985102. [PMID: 36950157 PMCID: PMC10026359 DOI: 10.3389/fmicb.2023.985102] [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: 07/03/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Background The emergence of highly drug-resistant K. pneumoniae, has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical Klebsiella isolates and to characterize the prevalence and structure of class 1 integrons. Methods Based on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for K. pneumoniae and K. variicola. Integron characterization and comparative genomic analysis were performed using various bioinformatic tools. Results Species identification showed that the 167 isolates belonged to four species: K. pneumoniae, K. variicola subsp. variicola, K. quasipneumoniae and K. aerogenes. Thirty-six known and 5 novel STs were identified in K. pneumoniae, and 10 novel STs were identified in K. variicola subsp. variicola. Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene (bla IPM-4) and class D β-lactamases gene (bla OXA-1 and bla OXA-10), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS26-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment. Conclusion The results of this work demonstrated that the species and STs of the clinical Klebsiella isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.
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Affiliation(s)
- Lan Wang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Chunxia Yan
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Yanfang Zhang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Xuying He
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Lin Wu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Jiefeng Xu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yunliang Hu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
- *Correspondence: Teng Xu,
| | - Jialei Liang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Jialei Liang,
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Legese MH, Asrat D, Swedberg G, Hasan B, Mekasha A, Getahun T, Worku M, Shimber ET, Getahun S, Ayalew T, Gizachew B, Aseffa A, Mihret A. Sepsis: emerging pathogens and antimicrobial resistance in Ethiopian referral hospitals. Antimicrob Resist Infect Control 2022; 11:83. [PMID: 35698179 PMCID: PMC9195281 DOI: 10.1186/s13756-022-01122-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/29/2022] [Indexed: 12/22/2022] Open
Abstract
Background Sepsis due to multidrug resistant (MDR) bacteria is a growing public health problem mainly in low-income countries.
Methods A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. A total of 1416 patients clinically investigated for sepsis were enrolled. The number of patients from Tikur Anbessa, Yekatit 12, Dessie and Hawassa hospital was 501, 298, 301 and 316, respectively. At each study site, blood culture was performed from all patients and positive cultures were characterized by their colony characteristics, gram stain and conventional biochemical tests. Each bacterial species was confirmed using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF). Antimicrobial resistance pattern of bacteria was determined by disc diffusion. Logistic regression analysis was used to assess associations of dependent and independent variables. A p-value < 0.05 was considered as statistically significant. The data was analyzed using SPSS version 25.
Results Among 1416 blood cultures performed, 40.6% yielded growth. Among these, 27.2%, 0.3% and 13.1%, were positive for pathogenic bacteria, yeast cells and possible contaminants respectively. Klebsiella pneumoniae (26.1%), Klebsiella variicola (18.1%) and E. coli (12.4%) were the most frequent. Most K. variicola were detected at Dessie (61%) and Hawassa (36.4%). Almost all Pantoea dispersa (95.2%) were isolated at Dessie. Rare isolates (0.5% or 0.2% each) included Leclercia adecarboxylata, Raoultella ornithinolytica, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia, Kosakonia cowanii and Lelliottia amnigena. Enterobacteriaceae most often showed resistance to ampicillin (96.2%), ceftriaxone (78.3%), cefotaxime (78%), cefuroxime (78%) and ceftazidime (76.4%). MDR frequency of Enterobacteriaceae at Hawassa, Tikur Anbessa, Yekatit 12 and Dessie hospital was 95.1%, 93.2%, 87.3% and 67.7%, respectively. Carbapenem resistance was detected in 17.1% of K. pneumoniae (n = 111), 27.7% of E. cloacae (n = 22) and 58.8% of Acinetobacter baumannii (n = 34).
Conclusion Diverse and emerging gram-negative bacterial etiologies of sepsis were identified. High multidrug resistance frequency was detected. Both on sepsis etiology types and MDR frequencies, substantial variation between hospitals was determined. Strategies to control MDR should be adapted to specific hospitals. Standard bacteriological services capable of monitoring emerging drug-resistant sepsis etiologies are essential for effective antimicrobial stewardship.
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Liang Z, Wang Y, Lai Y, Zhang J, Yin L, Yu X, Zhou Y, Li X, Song Y. Host defense against the infection of Klebsiella pneumoniae: New strategy to kill the bacterium in the era of antibiotics? Front Cell Infect Microbiol 2022; 12:1050396. [PMID: 36506034 PMCID: PMC9730340 DOI: 10.3389/fcimb.2022.1050396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a typical gram-negative iatrogenic bacterium that often causes bacteremia, pneumonia and urinary tract infection particularly among those with low immunity. Although antibiotics is the cornerstone of anti-infections, the clinical efficacy of β-lactamase and carbapenems drugs has been weakened due to the emergence of drug-resistant K. pneumoniae. Recent studies have demonstrated that host defense plays a critical role in killing K. pneumoniae. Here, we summarize our current understanding of host immunity mechanisms against K. pneumoniae, including mechanical barrier, innate immune cells, cellular immunity and humoral immunity, providing a theoretical basis and the new strategy for the clinical treatment of K. pneumoniae through improving host immunity.
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Affiliation(s)
- Zihan Liang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Yiyao Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Yixiang Lai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Jingyi Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Lanlan Yin
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Xiang Yu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Yongqin Zhou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Xinzhi Li
- College of Basic Medical Science, China Three Gorges University, Yichang, China,Affiliated Renhe Hospital of China Three Gorges University, Yichang, China,*Correspondence: Yinhong Song, ; Xinzhi Li,
| | - Yinhong Song
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China,Institute of Infection and Inflammation, China Three Gorges University, Yichang, China,College of Basic Medical Science, China Three Gorges University, Yichang, China,*Correspondence: Yinhong Song, ; Xinzhi Li,
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Morgado S, Fonseca E, Vicente AC. Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources. Microorganisms 2022; 10:2281. [PMID: 36422351 PMCID: PMC9697336 DOI: 10.3390/microorganisms10112281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/03/2023] Open
Abstract
The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen.
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Affiliation(s)
| | | | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Av. Brasil, 4365—Manguinhos, Rio de Janeiro 21040-900, Brazil
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Voellmy IK, Lang C, Gasser M, Kronenberg A. Antibiotic resistance surveillance of Klebsiella pneumoniae complex is affected by refined MALDI-TOF identification, Swiss data, 2017 to 2022. Euro Surveill 2022; 27. [PMID: 36367012 PMCID: PMC9650708 DOI: 10.2807/1560-7917.es.2022.27.45.2200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Modern laboratory methods such as next generation sequencing and MALDI-TOF allow identification of novel bacterial species. This can affect surveillance of infections and antimicrobial resistance. From 2017, increasing numbers of medical microbiology laboratories in Switzerland differentiated Klebsiella variicola from Klebsiella pneumoniae complex using updated MALDI-TOF databases, whereas many laboratories still report them as K. pneumoniae or K. pneumoniae complex. Aim Our study explored whether separate reporting of K. variicola and the Klebsiella pneumoniae complex affected the ANRESIS surveillance database. Methods We analysed antibiotic susceptibility rates and specimen types of K. variicola and non-K. variicola-K. pneumoniae complex isolates reported by Swiss medical laboratories to the ANRESIS database (Swiss Centre for Antibiotic Resistance) from January 2017 to June 2022. Results Analysis of Swiss antimicrobial resistance data revealed increased susceptibility rates of K. variicola compared with species of the K. pneumoniae complex other than K. variicola in all six antibiotic classes tested. This can lead to underestimated resistance rates of K. pneumoniae complex in laboratories that do not specifically identify K. variicola. Furthermore, K. variicola strains were significantly more often reported from blood and primarily sterile specimens than isolates of the K. pneumoniae complex other than K. variicola, indicating increased invasiveness of K. variicola. Conclusion Our data suggest that refined differentiation of the K. pneumoniae complex can improve our understanding of its taxonomy, susceptibility, epidemiology and clinical significance, thus providing more precise information to clinicians and epidemiologists.
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Affiliation(s)
- Irene Katharina Voellmy
- Swiss Centre for Antibiotic Resistance ANRESIS, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Michael Gasser
- Swiss Centre for Antibiotic Resistance ANRESIS, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andreas Kronenberg
- Swiss Centre for Antibiotic Resistance ANRESIS, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Accurate Identification of Klebsiella variicola by MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories. Microbiol Spectr 2022; 10:e0284422. [PMID: 36125293 PMCID: PMC9603720 DOI: 10.1128/spectrum.02844-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Klebsiella variicola is a pathogen that is increasingly recognized as being associated with human infections, but the methods available to clinical microbiology laboratories for accurate identification are limited. In this study, we assessed the accuracy of identification of K. variicola by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry using genetic identification with multiplex PCR as the reference method. Antimicrobial susceptibilities and virulence of K. variicola strains were also investigated. Fifty-five Klebsiella pneumoniae, 26 K. variicola, and 2 Klebsiella quasipneumoniae clinical strains were used for evaluation. Both MALDI Biotyper with library version 9 and Klebsiella MALDI TypeR, a web-based species identification tool using MALDI-TOF data, accurately identified all K. variicola strains. In addition, two strains of K. quasipneumoniae were accurately identified with Klebsiella MALDI TypeR. Whole-genome sequencing confirmed the accurate identification to the subspecies level by Klebsiella MALDI TypeR for four strains (two strains each of K. variicola subsp. variicola and K. quasipneumoniae subsp. similipneumoniae). While 13 strains, 3 strains, and 1 strain of K. pneumoniae showed nonsusceptibility to ampicillin-sulbactam, ceftriaxone, and meropenem, respectively, all strains of K. variicola were susceptible to all tested antimicrobial agents. Although two K. variicola strains were positive for the string test, no K. variicola strains harbored any of the genes associated with hypervirulence of K. pneumoniae. Accurate identification of the K. pneumoniae complex, including K. variicola, by MALDI-TOF in clinical microbiology laboratories is expected to clarify the clinical characteristics of each species in the future. IMPORTANCE Recent widespread use of bacterial whole-genome sequencing analysis has resulted in the proposal of novel bacterial species and reclassification of taxonomy. Accurate methods for identification of bacterial species in clinical microbiology laboratories are essential to accumulate information on the clinical characteristics of each bacterial species. Klebsiella variicola is a member of the Klebsiella pneumoniae complex, and its association with human infections has been increasingly recognized, but accurate identification methods approved for use in clinical microbiology laboratories have been limited thus far. The findings of the present study suggest that K. variicola can be accurately identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry using updated library or web-based identification tools. Accurate identification will promote exploration of clinical characteristics of K. variicola.
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Bioconversion of Glycerol into Lactic Acid by a New Bacterial Strain from the Brazilian Cerrado Soil. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8100477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A lactic-acid-producing strain was isolated from the Brazilian Cerrado soil (Brazilian savanna). Glycerol, a byproduct of the biodiesel industry, can be converted into various chemical intermediates of industrial value by biotechnological routes. Klebsiella pneumoniae can metabolize glycerol in environments with or without oxygen and bioconvert it into several chemicals with high value-added, such as lactic acid, 3-hydroxypropionic acid and 1,3 propanediol. The wild-type bacterial strain (2GPP) isolated from a soil sample from the Brazilian Cerrado was determined to be a K. pneumoniae complex that was capable of successfully metabolizing glycerol. Fermentations were performed with different temperatures, pH, and inoculum concentrations to evaluate the best lactic acid production. At first, 1,3-propanediol and L-(+)-lactic acid were produced in mini reactors. A lactic acid production of 3.8 g·L−1 and a decrease in 1,3-propanediol output were observed. Thus, by adjusting process variables such as pH and temperature during fermentation, it was possible to maximize the production of lactic acid and decrease the formation of 1,3-propanediol by utilizing experimental design strategies.
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48
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Zhang Z, Peng H, Yang D, Zhang G, Zhang J, Ju F. Polyvinyl chloride degradation by a bacterium isolated from the gut of insect larvae. Nat Commun 2022; 13:5360. [PMID: 36097154 PMCID: PMC9468159 DOI: 10.1038/s41467-022-32903-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
Evidence for microbial degradation of polyvinyl chloride (PVC) has previously been reported, but little is known about the degrading strains and enzymes. Here, we isolate a PVC-degrading bacterium from the gut of insect larvae and shed light on the PVC degradation pathway using a multi-omic approach. We show that the larvae of an insect pest, Spodoptera frugiperda, can survive by feeding on PVC film, and this is associated with enrichment of Enterococcus, Klebsiella and other bacteria in the larva’s gut microbiota. A bacterial strain isolated from the larval intestine (Klebsiella sp. EMBL-1) is able to depolymerize and utilize PVC as sole energy source. We use genomic, transcriptomic, proteomic, and metabolomic analyses to identify genes and proteins potentially involved in PVC degradation (e.g., catalase-peroxidase, dehalogenases, enolase, aldehyde dehydrogenase and oxygenase), and propose a PVC biodegradation pathway. Furthermore, enzymatic assays using the purified catalase-peroxidase support a role in PVC depolymerization. Microbial degradation of polyvinyl chloride (PVC) has previously been reported, but little is known about the degrading strains and enzymes. Here, Zhe et al. isolate a PVC-degrading bacterium from the gut of insect larvae and shed light on the PVC degradation pathway using a multi-omic approach.
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Affiliation(s)
- Zhe Zhang
- Research Center for Industries of the Future (RCIF), School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China.,Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China.,Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China.,Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Haoran Peng
- Research Center for Industries of the Future (RCIF), School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China.,Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China
| | - Dongchen Yang
- College of Plant Protection, Hebei Agricultural University, Baoding, 071000, China
| | - Guoqing Zhang
- Research Center for Industries of the Future (RCIF), School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China.,Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China
| | - Jinlin Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding, 071000, China
| | - Feng Ju
- Research Center for Industries of the Future (RCIF), School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China. .,Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China. .,Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, 310024, Zhejiang Province, China. .,Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China. .,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China.
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Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. Nat Commun 2022; 13:5235. [PMID: 36068270 PMCID: PMC9446638 DOI: 10.1038/s41467-022-32991-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression. Here, using whole-metagenome shotgun sequencing data from patients with COVID-19 and controls, the authors reconstruct 11,584 microbial metagenome-assembled genomes (MAGs) including 5,403 non-redundant MAGs, revealing microbiota and metabolic pathways associations with SARS-CoV-2 infection at strain-level resolution.
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Bray JE, Correia A, Varga M, Jolley KA, Maiden MCJ, Rodrigues CMC. Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation. Microb Genom 2022; 8. [PMID: 36098501 PMCID: PMC9676034 DOI: 10.1099/mgen.0.000849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Bacterial genomics is making an increasing contribution to the fields of medicine and public health microbiology. Consequently, accurate species identification of bacterial genomes is an important task, particularly as the number of genomes stored in online databases increases rapidly and new species are frequently discovered. Existing database entries require regular re-evaluation to ensure that species annotations are consistent with the latest species definitions. We have developed an automated method for bacterial species identification that is an extension of ribosomal multilocus sequence typing (rMLST). The method calculates an ‘rMLST nucleotide identity’ (rMLST-NI) based on the nucleotides present in the protein-encoding ribosomal genes derived from bacterial genomes. rMLST-NI was used to validate the species annotations of 11839 publicly available Klebsiella and Raoultella genomes based on a comparison with a library of type strain genomes. rMLST-NI was compared with two whole-genome average nucleotide identity methods (OrthoANIu and FastANI) and the k-mer based Kleborate software. The results of the four methods agreed across a dataset of 11839 bacterial genomes and identified a small number of entries (n=89) with species annotations that required updating. The rMLST-NI method was 3.5 times faster than Kleborate, 4.5 times faster than FastANI and 1600 times faster than OrthoANIu. rMLST-NI represents a fast and generic method for species identification using type strains as a reference.
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Affiliation(s)
- James E Bray
- Department of Zoology, University of Oxford, Oxford, UK
| | - Annapaula Correia
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | - Charlene M C Rodrigues
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Paediatrics, Imperial College Healthcare NHS Trust, London, UK
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