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McDonald JB, Wade B, Andrews DM, Van TTH, Moore RJ. Development of tools for the genetic manipulation of Campylobacter and their application to the N-glycosylation system of Campylobacter hepaticus, an emerging pathogen of poultry. mBio 2024:e0110124. [PMID: 39072641 DOI: 10.1128/mbio.01101-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024] Open
Abstract
Various species of campylobacters cause significant disease problems in both humans and animals. The continuing development of tools and methods for genetic and molecular manipulation of campylobacters enables the detailed study of bacterial virulence and disease pathogenesis. Campylobacter hepaticus is an emerging pathogen that causes spotty liver disease (SLD) in poultry. SLD has a significant economic and animal welfare impact as the disease results in elevated mortalities and significant decreases in egg production. Although potential virulence genes of C. hepaticus have been identified, they have not been further studied and characterized, as appropriate genetic tools and methods to transform and perform mutagenesis studies in C. hepaticus have not been available. In this study, the genetic manipulation of C. hepaticus is reported, with the development of novel plasmid vectors, methods for transformation, site-specific mutagenesis, and mutant complementation. These tools were used to delete the pglB gene, an oligosaccharyltransferase, a central enzyme of the N-glycosylation pathway, by allelic exchange. In the mutant strain, N-glycosylation was completely abolished. The tools and methods developed in this study represent innovative approaches that can be applied to further explore important virulence factors of C. hepaticus and other closely related Campylobacter species. IMPORTANCE Spotty liver disease (SLD) of layer chickens, caused by infection with Campylobacter hepaticus, is a significant economic and animal welfare burden on an important food production industry. Currently, SLD is controlled using antibiotics; however, alternative intervention methods are needed due to increased concerns associated with environmental contamination with antibiotics, and the development of antimicrobial resistance in many bacterial pathogens of humans and animals. This study has developed methods that have enabled the genetic manipulation of C. hepaticus. To validate the methods, the pglB gene was inactivated by allelic exchange to produce a C. hepaticus strain that could no longer N-glycosylate proteins. Subsequently, the mutation was complemented by reintroduction of the gene in trans, on a plasmid vector, to demonstrate that the phenotypic changes noted were caused by the mutation of the targeted gene. The tools developed enable ongoing studies to understand other virulence mechanisms of this important emerging pathogen.
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Affiliation(s)
- Jamieson B McDonald
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Ben Wade
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Daniel M Andrews
- Bioproperties Pty Ltd, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
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Ye L, Zhang L, Li X, Huang Y, Zhang B, Yang X, Tan W, Li X, Zhang X. De novo genome assembly and functional insights of the first commercial pink Auricularia cornea. Genomics 2024; 116:110902. [PMID: 39053612 DOI: 10.1016/j.ygeno.2024.110902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
A pioneering pink cultivar of Auricularia cornea, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink A. cornea Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink A. cornea genome and provides a comprehensive insight into its complex functions.
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Affiliation(s)
- Lei Ye
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Lingzi Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Huang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co., Ltd, Luzhou 646000, China
| | - Bo Zhang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xuezhen Yang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Wei Tan
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xiaolin Li
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co., Ltd, Luzhou 646000, China.
| | - Xiaoping Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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Pilati GVT, Salles GBC, Savi BP, Dahmer M, Muniz EC, Filho VB, Elois MA, Souza DSM, Fongaro G. Isolation and Characterization of Escherichia coli from Brazilian Broilers. Microorganisms 2024; 12:1463. [PMID: 39065231 PMCID: PMC11279037 DOI: 10.3390/microorganisms12071463] [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: 06/19/2024] [Revised: 07/03/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) causes colibacillosis, one of the main diseases leading to economic losses in industrial poultry farming due to high morbidity and mortality and its role in the condemnation of chicken carcasses. This study aimed to isolate and characterize APEC obtained from necropsied chickens on Brazilian poultry farms. Samples from birds already necropsied by routine inspection were collected from 100 batches of broiler chickens from six Brazilian states between August and November 2021. Three femurs were collected per batch, and characteristic E. coli colonies were isolated on MacConkey agar and characterized by qualitative PCR for minimal predictive APEC genes, antimicrobial susceptibility testing, and whole genome sequencing to identify species, serogroups, virulence genes, and resistance genes. Phenotypic resistance indices revealed significant resistance to several antibiotics from different antimicrobial classes. The isolates harbored virulence genes linked to APEC pathogenicity, including adhesion, iron acquisition, serum resistance, and toxins. Aminoglycoside resistance genes were detected in 79.36% of isolates, 74.6% had sulfonamide resistance genes, 63.49% showed β-lactam resistance genes, and 49.2% possessed at least one tetracycline resistance gene. This study found a 58% prevalence of avian pathogenic E. coli in Brazilian poultry, with strains showing notable antimicrobial resistance to commonly used antibiotics.
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Affiliation(s)
- Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Gleidson Biasi Carvalho Salles
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
- Zoetis Industry of Veterinary Products LTDA, São Paulo 04709-111, Brazil;
| | - Beatriz Pereira Savi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Mariane Dahmer
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | | | - Vilmar Benetti Filho
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Doris Sobral Marques Souza
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil; (G.V.T.P.); (G.B.C.S.); (B.P.S.); (M.D.); (M.A.E.); (D.S.M.S.)
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Camacho-Beltrán E, Morales-Aguilar JJ, López-Meyer M, Rincón-Enríquez G, Quiñones-Aguilar EE. Complete genome sequence of the Exiguobacterium bacteriophage. Microbiol Resour Announc 2024; 13:e0034224. [PMID: 38860812 PMCID: PMC11256790 DOI: 10.1128/mra.00342-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
We purified a lytic bacteriophage from soil collected in Guasave, Sinaloa: phiExGM16. This bacteriophage was isolated using the host, Exiguobacterium acetilycum. Its 17.6 kb genome contains 33 putative genes and shows a cover of 64% with 76.37% of nucleotide identity to Microbacterium phage Noelani.
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Affiliation(s)
- Erika Camacho-Beltrán
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Zapopan, Jalisco, Mexico
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Guasave, Sinaloa, Mexico
| | - Juan José Morales-Aguilar
- Universidad Autónoma de Occidente, Unidad Regional Guasave. Avenida Universidad S/N Colonia Villa Universidad, Guasave, Sinaloa, Mexico
| | - Melina López-Meyer
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Guasave, Sinaloa, Mexico
| | - Gabriel Rincón-Enríquez
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Zapopan, Jalisco, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Zapopan, Jalisco, Mexico
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Lyytinen OL, Dapuliga C, Wallinger D, Patpatia S, Audu BJ, Kiljunen SJ. Three novel Enterobacter cloacae bacteriophages for therapeutic use from Ghanaian natural waters. Arch Virol 2024; 169:156. [PMID: 38967872 PMCID: PMC11226500 DOI: 10.1007/s00705-024-06081-9] [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: 11/24/2023] [Accepted: 05/15/2024] [Indexed: 07/06/2024]
Abstract
Infections caused by multidrug-resistant (MDR) bacteria are a growing global concern. Enterobacter cloacae complex (ECC) species are particularly adept at developing antibiotic resistance. Phage therapy is proposed as an alternative treatment for pathogens that no longer respond to antibiotics. Unfortunately, ECC phages are understudied when compared to phages of many other bacterial species. In this Ghanaian-Finnish study, we isolated two ECC strains from ready-to-eat food samples and three novel phages from natural waters against these strains. We sequenced the genomic DNA of the novel Enterobacter phages, fGh-Ecl01, fGh-Ecl02, and fGh-Ecl04, and assessed their therapeutic potential. All of the phages were found to be lytic, easy to propagate, and lacking any toxic, integrase, or antibiotic resistance genes and were thus considered suitable for therapy purposes. They all were found to be related to T4-type viruses: fGh-Ecl01 and fGh-Ecl04 to karamviruses and fGh-Ecl02 to agtreviruses. Testing of Finnish clinical ECC strains showed promising susceptibility to these novel phages. As many as 61.1% of the strains were susceptible to fGh-Ecl01 and fGh-Ecl04, and 7.4% were susceptible to fGh-Ecl02. Finally, we investigated the susceptibility of the newly isolated ECC strains to three antibiotics - meropenem, ciprofloxacin, and cefepime - in combination with the novel phages. The use of phages and antibiotics together had synergistic effects. When using an antibiotic-phage combination, even low concentrations of antibiotics fully inhibited the growth of bacteria.
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Affiliation(s)
- O L Lyytinen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - C Dapuliga
- Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - D Wallinger
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - S Patpatia
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - B J Audu
- National Veterinary Research Institute, Vom, Nigeria
| | - S J Kiljunen
- Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
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Zhang Y, Chai J, Yang Z, Luo J. The complete mitochondrial genome and phylogenetic analysis of Pealius mori (Hemiptera: Aleyrodidae). Mitochondrial DNA B Resour 2024; 9:856-860. [PMID: 38979131 PMCID: PMC11229734 DOI: 10.1080/23802359.2024.2373229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/22/2024] [Indexed: 07/10/2024] Open
Abstract
The complete mitochondrial genome of Pealius mori (Hemiptera: Aleyrodidae) was determined in this study. The mitogenome was 15,654 bp long with 37 typical Insecta mitochondrial genes and one non-coding control region. Its gene content and order were different to other Hemiptera mitochondrial genomes. The overall nucleotide composition of the mitogenome was 42.62% A, 32.73% T, 11.12% G and 13.54% C, with an A + T bias of 75.34%. Phylogenetic analyses of 14 species in Aleyrodidae, 2 species in Lepidoptera and 1 species in Thysanoptera by Maximum Likelihood showed that P. mori China had been more closely related to P. mori France, closely related to Pealius machili. This result well supported the taxonomic position of Aleyrodidae and their close relationship with the Pealius category.
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Affiliation(s)
- Yonghong Zhang
- Sericulture and Apiculture Research Institute, Yunnan Academy of Agricultural Science, Mengzi, Yunnan, China
| | - Jianping Chai
- Sericulture and Apiculture Research Institute, Yunnan Academy of Agricultural Science, Mengzi, Yunnan, China
| | - Zhenguo Yang
- Sericulture and Apiculture Research Institute, Yunnan Academy of Agricultural Science, Mengzi, Yunnan, China
| | - Jiafu Luo
- Sericulture and Apiculture Research Institute, Yunnan Academy of Agricultural Science, Mengzi, Yunnan, China
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Su Z, Xu Y, Xiao Y, Chen B, Qiu X, Ye J, Tang K. Mesobacterium hydrothermale sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island. Antonie Van Leeuwenhoek 2024; 117:93. [PMID: 38954062 DOI: 10.1007/s10482-024-01994-6] [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: 03/18/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
A Gram-negative, rod-shaped, non-motile, aerobic bacterium, designated as strain TK19101T, was isolated from the intermediate seawater of yellow vent in the shallow-sea hydrothermal system located near Kueishantao Island. The strain was found to grow at 10-40 °C (optimum, 35 °C), at pH 6.0-8.0 (optimum, 7.0), and in 0-5% (w/v) NaCl (optimum, 1%). Strain TK19101T was catalase-positive and oxidase-positive. The predominant fatty acids (> 10%) in strain TK19101T cells were C16:0, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), and C18:0. The predominant isoprenoid quinone of strain TK19101T was ubiquinone-10. The polar lipids of strain TK19101T comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and unknown polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TK19101T belonged to the genus Mesobacterium. Strain TK19101T exhibited highest 16S rRNA gene sequence similarity value to Mesobacterium pallidum MCCC M24557T (97.48%). The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain TK19101T and the closest related species Mesobacterium pallidum MCCC M24557T were 74.88% and 20.30%, respectively. The DNA G + C content was 63.49 mol%. On the basis of the analysis of 16S rRNA gene sequences, genotypic and phylogenetic data, strain TK19101T has a unique phylogenetic status and represents a novel species of genus Mesobacterium, for which the name Mesobacterium hydrothermale sp. nov. is proposed. The type strain is TK19101T (= MCCC 1K08936T = KCTC 8354T).
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Affiliation(s)
- Zhiyi Su
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Yue Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Yuhang Xiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xuanyun Qiu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People's Republic of China.
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Ranta K, Skurnik M, Kiljunen S. fENko-Kae01 is a flagellum-specific jumbo phage infecting Klebsiella aerogenes. BMC Microbiol 2024; 24:234. [PMID: 38951769 PMCID: PMC11218385 DOI: 10.1186/s12866-024-03387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Klebsiella aerogenes is an opportunistic pathogen that causes a wide variety of infections. Due to the rising problem of antibiotic resistance, novel antibiotics and strategies to combat bacterial infections are needed. Host-specific bacteriophages are natural enemies of bacteria and can be used in phage therapy as an alternative form of treatment against bacterial infections. Jumbo phages are defined as phages with genomes larger than 200 kb. Relatively few studies have been done on jumbo phages compared to smaller phages. RESULTS A novel phage, fENko-Kae01, was isolated from a commercial phage cocktail. Genomic analysis revealed that fENko-Kae01 is a lytic jumbo phage with a 360 kb genome encoding 578 predicted genes. No highly similar phage genomes were identified and fENko-Kae01 may be a completely new genus representative. No known genes associated with lysogenic life cycle, bacterial virulence, or antibiotic resistance were identified. The phage had myovirus morphology and a narrow host range. Phage resistant bacterial mutants emerged under phage selection. Whole genome sequencing revealed that the biogenesis of the flagellum was affected in four mutants and the lack of functional flagellum was confirmed in motility assays. Furthermore, phage fENKo-Kae01 failed to adsorb on the non-motile mutants indicating that the bacterial flagellum is the phage-binding receptor. CONCLUSIONS fENko-Kae01 is a novel jumbo bacteriophage that is considered safe for phage therapy. fENko-Kae01 uses the flagellum as the phage-binding receptor and may represent a completely novel genus.
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Affiliation(s)
- Kira Ranta
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Skurnik
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Saija Kiljunen
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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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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Li S, Xu M, Yang D, Yang M, Wu H, Li X, Yang C, Fang Z, Wu Q, Tan L, Xiao W, Weng Q. Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae. Front Microbiol 2024; 15:1400700. [PMID: 38993489 PMCID: PMC11236537 DOI: 10.3389/fmicb.2024.1400700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.
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Affiliation(s)
- Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Deying Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mei Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hejing Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuelian Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Changzhou Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, Yunnan International Joint Laboratory of Virology and Immunology, Yunnan University, Kunming, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
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Gao F, Li X, Wang X, Liu H, Zhang W, Zhang Y, Jia Y, Zhao Z, Bai G. Differences between Chronically Hepatitis B Virus-Infected Pregnant Women with and without Intrafamilial Infection: From Viral Gene Sequences to Clinical Manifestations. Intervirology 2024; 67:72-82. [PMID: 38934174 DOI: 10.1159/000539994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION This study aimed to investigate the differences between pregnant women with chronic hepatitis B virus (HBV) infection and intrafamilial infection and those without intrafamilial infection. METHODS HBV-DNA was extracted from the sera of 16 pregnant women with chronic hepatitis B (CHB) and their family members for gene sequencing and phylogenetic analyses. A total of 74 pregnant women with CHB were followed up from the second trimester to 3 months postpartum. Viral markers and other laboratory indicators were compared between pregnant women with CHB with and without intrafamilial infection. RESULTS The phylogenetic tree showed that HBV lines in the mother-spread pedigree shared a node, whereas there was an unrelated genetic background for HBV lines in individuals without intrafamilial infection. From delivery to 3 months postpartum, compared with those without intrafamilial infection, pregnant women with intrafamilial infection were related negatively to HBV-DNA (β = -0.43, 95% confidence interval [CI]: -0.76 to -0.12, p = 0.009), HBeAg (β = -195.15, 95% CI: -366.35 to -23.96, p = 0.027), and hemoglobin changes (β = -8.09, 95% CI: -15.54 to -0.64, p = 0.035) and positively to changes in the levels of alanine aminotransferase (β = 73.9, 95% CI: 38.92-108.95, p < 0.001) and albumin (β = 2.73, 95% CI: 0.23-5.23, p = 0.033). CONCLUSION The mother-spread pedigree spread model differs from that of non-intrafamilial infections. Pregnant women with intrafamilial HBV infection have less hepatitis flares and liver damage, but their HBV-DNA and HBeAg levels rebound faster after delivery, than those without intrafamilial infection by the virus.
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Affiliation(s)
- Fan Gao
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xia Li
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaona Wang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hankui Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wentao Zhang
- Department of Gynaecology and Obstetrrics, Xi'an No. 3 Hospital, Xi'an, China
| | - Yidan Zhang
- Department of Gynaecology and Obstetrrics, Xi'an Fourth Hospital, Xi'an, China
| | - Yanju Jia
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ziyan Zhao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Guiqin Bai
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Gene Joint Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Yuan Z, Liu P, Lu X, Zhu D, Liu J, Guo Q, Zhang W, Duan Y. Complete Mitochondrial Genome and Phylogenetic Analysis of the Blue Whistling Thrush ( Myophonus caeruleus). Genes (Basel) 2024; 15:830. [PMID: 39062609 PMCID: PMC11275496 DOI: 10.3390/genes15070830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The blue whistling thrush (Myophonus caeruleus) is a bird belonging to the order Passeriformes and family Muscicapidae. M. caeruleus is widely distributed in China, Pakistan, India, and Myanmar and is a resident bird in the southern part of the Yangtze River in China and summer migratory bird in the northern part of the Yangtze River. At present, there are some controversies about the classification of M. caeruleus. We use complete mitochondrial genomes to provide insights into the phylogenetic position of M. caeruleus and its relationships among Muscicapidae. The mitochondrial genome (GenBank: MN564936) is 16,815 bp long and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region (D-loop). The thirteen PCGs started with GTG and ATG and ended with five types of stop codons. The nucleotide composition of T was 23.71%, that of C was 31.45%, that of A was 30.06%, and that of G was 14.78%. The secondary structures of 22 tRNAs were predicted, all of which could form typical cloverleaf structures. There were 24 mismatches, mainly G-U mismatches. Through phylogenetic tree reconstruction, it was found that Saxicola, Monticola, Oenanthe, and Phoenicurus were clustered into one clade, together with the sister group of Myophonus.
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Affiliation(s)
- Zhenfeng Yuan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (Z.Y.); (P.L.); (D.Z.); (Q.G.)
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China; (X.L.); (J.L.)
| | - Peng Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (Z.Y.); (P.L.); (D.Z.); (Q.G.)
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Kunming 650224, China
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Xi Lu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China; (X.L.); (J.L.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Dong Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (Z.Y.); (P.L.); (D.Z.); (Q.G.)
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China; (X.L.); (J.L.)
| | - Jun Liu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China; (X.L.); (J.L.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Qiang Guo
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (Z.Y.); (P.L.); (D.Z.); (Q.G.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
| | - Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China
| | - Yubao Duan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China; (X.L.); (J.L.)
- College of Forestry, Southwest Forestry University, Kunming 650224, China
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Liu H, Wang C, He Y, Wei X, Cheng J, Yang W, Shi K, Si H. Assessing a respiratory toxic infectious bronchitis virus (IBV) strain: isolation, identification, pathogenicity, and immunological failure insights. Microbiol Spectr 2024:e0399023. [PMID: 38904372 DOI: 10.1128/spectrum.03990-23] [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: 11/20/2023] [Accepted: 05/10/2024] [Indexed: 06/22/2024] Open
Abstract
Infectious bronchitis virus (IBV) is caused by avian coronavirus and poses a global economic threat to the poultry industry. In 2023, a highly pathogenic IBV strain, IBV/CN/GD20230501, was isolated and identified from chickens vaccinated with IBV-M41 in Guangdong, China. This study comprehensively investigated the biological characteristics of the isolated IBV strain, including its genotype, whole genome sequence analysis of its S1 gene, pathogenicity, host immune response, and serum non-targeted metabolomics. Through the analysis of the S1 gene sequence, serum neutralization tests, and comparative genomics, it was proven that IBV/CN/GD20230501 belongs to the GI-I type of strain and is serotype II. One alanine residue in the S1 subunit of the isolated strain was mutated into serine, and some mutations were observed in the ORF1ab gene and the terminal region of the genome. Animal challenge experiments using the EID50 and TCID50 calculations showed that IBV/CN/GD20230501 possesses strong respiratory pathogenicity, with early and long-term shedding of viruses and rapid viral spread. Antibody detection indicated that chickens infected with IBV/CN/GD20230501 exhibited delayed expression of early innate immune genes, while those infected with M41 showed rapid gene induction and effective viral control. Metabolomics analysis demonstrated that this virus infection led to differential expression of 291 ions in chicken serum, mainly affecting the citric acid cycle (tricarboxylic acid cycle).IMPORTANCEThis study identified an infectious bronchitis virus (IBV) strain isolated from vaccinated chickens in an immunized population that had certain sequence differences compared to IBV-M41, resulting in significantly enhanced pathogenicity and host defense. This strain has the potential to replace M41 as a more suitable challenge model for drug research. The non-targeted metabolomics analysis highlighting the citric acid cycle provides a new avenue for studying this highly virulent strain.
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Affiliation(s)
- Huixin Liu
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
| | - Chenchen Wang
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
| | - Yang He
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
| | - Xiaofang Wei
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
| | - Junze Cheng
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
| | - Wenwen Yang
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
| | - Kaichuang Shi
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
- Poultry Disease Diagnosis Division, Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Hongbin Si
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi grass station, Nanning, China
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Han W, Zhou P, Chen C, Wu C, Shen L, Wan C, Xiao Y, Zhang J, Wang B, Shi J, Yuan X, Gao H, Wang H, Zhou Y, Yu F. Characteristic of KPC-12, a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in the Carbapenem-Resistant Klebsiella pneumoniae ST11-KL47 Clone Background. Infect Drug Resist 2024; 17:2541-2554. [PMID: 38933778 PMCID: PMC11199322 DOI: 10.2147/idr.s465699] [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: 04/07/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections are a great threat to public health worldwide. Ceftazidime-avibactam (CZA) is an effective β-lactam/β-lactamase inhibitors against CRKP. However, reports of resistance to CZA, mainly caused by Klebsiella pneumoniae carbapenemase (KPC) variants, have increased in recent years. In this study, we aimed to describe the resistance characteristics of KPC-12, a novel KPC variant identified from a CZA resistant K. pneumoniae. Methods The K. pneumoniae YFKP-97 collected from a patient with respiratory tract infection was performed whole-genome sequencing (WGS) on the Illumina NovaSeq 6000 platform. Genomic characteristics were analyzed using bioinformatics methods. Antimicrobial susceptibility testing was conducted by the broth microdilution method. Induction of resistant strain was carried out in vitro as previously described. The G. mellonella killing assay was used to evaluate the pathogenicity of strains, and the conjugation experiment was performed to evaluate plasmid transfer ability. Results Strain YFKP-97 was a multidrug-resistant clinical ST11-KL47 K. pneumoniae confers high-level resistance to CZA (16/4 μg/mL). WGS revealed that a KPC variant, KPC-12, was carried by the IncFII (pHN7A8) plasmids (pYFKP-97_a and pYFKP-97_b) and showed significantly decreased activity against carbapenems. In addition, there was a dose-dependent effect of bla KPC-12 on its activity against ceftazidime. In vitro inducible resistance assay results demonstrated that the KPC-12 variant was more likely to confer resistance to CZA than the KPC-2 and KPC-3 variants. Discussion Our study revealed that patients who was not treated with CZA are also possible to be infected with CZA-resistant strains harbored a novel KPC variant. Given that the transformant carrying bla KPC-12 was more likely to exhibit a CZA-resistance phenotype. Therefore, it is important to accurately identify the KPC variants as early as possible.
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Affiliation(s)
- Weihua Han
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Peiyao Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Chun Chen
- Cancer Center, Department of Pulmonary and Critical Care Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, People’s Republic of China
| | - Chunyang Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Li Shen
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Cailing Wan
- School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Yanghua Xiao
- School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Jiao Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Bingjie Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Junhong Shi
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Xinru Yuan
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Haojin Gao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Hongxiu Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Ying Zhou
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
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15
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Kagambèga A, Ramadan H, Dione M, Bouda SC, Hiott LM, McMillan EA, Sharma P, Gupta SK, Barro N, Jackson CR, Frye JG. Genome analysis of Salmonella enterica serovar enteritis strains isolated from poultry and humans in Burkina Faso. Microbiol Resour Announc 2024; 13:e0102423. [PMID: 38700349 PMCID: PMC11237741 DOI: 10.1128/mra.01024-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
Whole-genome sequencing (WGS) was used to characterize four Salmonella enterica Enteritidis isolates from poultry (n=2) and human (n=2) from Ouagadougou, Burkina Faso. Antimicrobial resistance genes, chromosomal mutations, and mobile genetic elements were identified by analysis of WGS data using sequence homology.
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Affiliation(s)
- Assèta Kagambèga
- United States Department of Agriculture, Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA
- Laboratoire de Biologie Moléculaire, D'épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Ecole Doctorale Sciences et Technologies (EDST)/Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso, Burkina Faso
- Ecole Normale Supérieure, Ministère des Enseignement Supérieur, de la Recherche Scientifique et de L'innovation, Ouagadougou, Burkina Faso, Burkina Faso
| | - Hazem Ramadan
- United States Department of Agriculture, Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Michel Dione
- Animal and Human Health program, International Livestock Research Institute, Ouakam, Dakar, Senegal
| | - Soutongnooma C. Bouda
- Laboratoire de Biologie Moléculaire, D'épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Ecole Doctorale Sciences et Technologies (EDST)/Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso, Burkina Faso
| | - Lari M. Hiott
- United States Department of Agriculture, Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA
| | - Elizabeth A. McMillan
- United States Department of Agriculture, Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA
| | - Poonam Sharma
- Department of Biochemistry and Molecular Biology, Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sushim K. Gupta
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire, D'épidémiologie et de Surveillance des Bactéries et Virus Transmissibles par les Aliments (LaBESTA)/Ecole Doctorale Sciences et Technologies (EDST)/Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso, Burkina Faso
| | - Charlene R. Jackson
- United States Department of Agriculture, Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA
| | - Jonathan G. Frye
- United States Department of Agriculture, Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Athens, Georgia, USA
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Camacho-Beltrán E, Morales-Aguilar JJ, López-Meyer M, Rincón-Enríquez G, Quiñones-Aguilar EE. Complete genome sequence of the Microbacterium enclense bacteriophage phiMiGM15. Microbiol Resour Announc 2024; 13:e0030224. [PMID: 38700345 PMCID: PMC11237405 DOI: 10.1128/mra.00302-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
We characterized the complete genome sequence of phiMiGM15, a lytic bacteriophage with siphovirus morphology that infects Microbacterium enclense. Its 48.6 kb genome contains 81 putative genes and shows coverage of 28% with 82.26% of nucleotide identity to Microbacterium phage Caron accession number OQ190481.1.
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Affiliation(s)
- Erika Camacho-Beltrán
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Juan de Dios Bátiz Paredes 250, Guasave, Sinaloa, Mexico
| | - Juan José Morales-Aguilar
- Universidad Autónoma de Occidente, Unidad Regional Guasave. Avenida Universidad S/N Colonia Villa Universidad, Guasave, Sinaloa, Mexico
| | - Melina López-Meyer
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR-Unidad Sinaloa), Juan de Dios Bátiz Paredes 250, Guasave, Sinaloa, Mexico
| | - Gabriel Rincón-Enríquez
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología, Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
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Cao X, Huang X, Lin Y, Sun J, Liu P, Dong X, He G, Feng S, Luo K. Prevalence and genomic-based antimicrobial resistance analysis of Avibacterium paragallinarum isolates in Guangdong Province, China. Poult Sci 2024; 103:103751. [PMID: 38652951 PMCID: PMC11063509 DOI: 10.1016/j.psj.2024.103751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Infectious coryza (IC) is an acute infectious respiratory disease in chickens that is caused by Avibacterium paragallinarum (A. paragallinarum). A. paragallinarum poses a significant threat to poultry health due to its virulence and multidrug resistance. This study isolated and identified 21 A. paragallinarum isolates from Guangdong between 2022 and 2023. Biochemical tests showed that 100% of A. paragallinarum isolates fermented glucose but did not ferment alginate and galactose, and only YZ18 was nicotinamide adenine dinucleotide independent. To determine the genetic relatedness between these isolates and NCBI reference strains, whole-genome-based phylogenetic analysis was employed. In addition, analysis of the 2,000 bp-length hmtp210 gene showed that the hmtp210 gene was strongly associated with A. paragallinarum serotypes. Meanwhile, a PCR assay for serotyping A. paragallinarum was developed based on the hmtp210 gene, this assay has high sensitivity and specificity. The antimicrobial susceptibility of isolates was assessed using the disk diffusion method. The antibiotic resistance genes of isolates were analyzed using the genomic method. Phenotypic resistance to ampicillin (95.2%), streptomycin (95.2%), methotrexate-sulfamethoxazole (90.5%), and tetracycline (85.7%) was most frequent among the isolates. All of the isolates exhibited resistance to multiple drugs, and furthermore, the isolates possessed a collective total of 14 genes associated with antibiotic resistance. This study will contribute to advancing our knowledge of A. paragallinarum antibiotic resistance and provide a scientific basis for the prophylaxis and treatment of IC, and the subsequent rational design of potential clinical therapeutics.
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Affiliation(s)
- Xuewei Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiuqin Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yizhen Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Juan Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Peiqi Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinying Dong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ge He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, Guangzhou, China; Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture and Rural Affairs, Guangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
| | - Kaijian Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, Guangzhou, China; Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture and Rural Affairs, Guangzhou, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China.
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18
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Wu Q, An N, Fang Z, Li S, Xiang L, Liu Q, Tan L, Weng Q. Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave. Virus Genes 2024; 60:295-308. [PMID: 38594490 PMCID: PMC11139720 DOI: 10.1007/s11262-024-02064-9] [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: 03/17/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.
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Affiliation(s)
- Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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19
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Momose Y, Sasaki Y, Yonemitsu K, Kuroda M, Ikeda T, Uema M, Furuya Y, Toyofuku H, Igimi S, Asai T. Changes in the Phenotypes of Salmonella spp. in Japanese Broiler Flocks. Food Saf (Tokyo) 2024; 12:25-33. [PMID: 39036747 PMCID: PMC11257683 DOI: 10.14252/foodsafetyfscj.d-24-00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/19/2024] [Indexed: 07/23/2024] Open
Abstract
Salmonella infections represent a leading cause of foodborne illnesses; resistance to third-generation cephalosporins (TGCs), which are a first-choice antimicrobial for treating human Salmonella enteritis, has become a serious public health concern worldwide. Because the consumption of undercooked chicken meat products is a major cause of foodborne salmonellosis in Japan, we conducted three surveys at different periods between 2017 and 2022, with the cooperation of four abattoirs (two in Eastern and two in Western Japan). The first survey was conducted at abattoir A, which is located in Eastern Japan. Salmonella was detected in 84.4% of broiler flocks tested (27/32); among them, all the TGC-resistant isolates obtained from one farm (farm FA) were identified as S. Infantis. Salmonella was recovered from 62.5% of breast meat samples (20/32), with one case suggesting cross-contamination. The second survey was conducted at three other abattoirs to examine the prevalence of TGC-resistant Salmonella, in both Western (abattoirs B and C) and Eastern (abattoir D) Japan. Salmonella was detected in 90.6% of broiler flocks examined (29/32). TGC-resistant S. Infantis was isolated from 2 flocks until 2018 and not thereafter. Subsequently, isolates were identified as TGC-susceptible S. Schwarzengrund in both regions. The third survey was performed at abattoir A to elucidate whether there were changes in the phenotypes. Of the 11 broiler flocks introduced from farm FA, 10 were positive for Salmonella (90.9%); all the isolates were S. Schwarzengrund susceptible to TGC. This study shows that TGC-susceptible S. Schwarzengrund has replaced the resistant phenotypes among broiler flocks in both Eastern and Western Japan. Although chicken meat products could be cross-contaminated with Salmonella during the slaughtering process, reducing the prevalence of Salmonella in broiler flocks remains important to decrease Salmonella enteritis in humans.
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Affiliation(s)
- Yoshika Momose
- Division of Biomedical Food Research, National Institute of
Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Yoshimasa Sasaki
- Division of Biomedical Food Research, National Institute of
Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
- Division of Veterinary Science, Department of Veterinary
Medicine, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro,
Hokkaido 080-8555, Japan
| | - Kenzo Yonemitsu
- Management Department of Biosafety, Laboratory Animal, and
Pathogen Bank, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashimurayama,
Tokyo 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious
Diseases, 1-23-1 Toyama, Shinjuku-ku,Tokyo 162-8640, Japan
| | - Tetsuya Ikeda
- Department of Infectious Diseases, Hokkaido Institute of
Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
| | - Masashi Uema
- Division of Biomedical Food Research, National Institute of
Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Yoko Furuya
- Japan Food Safety Verification Organization, 1-7-5,
Sekiguchi, Bunkyo-ku, Tokyo 112-0014, Japan
| | - Hajime Toyofuku
- The United Graduate School of Veterinary Science, Yamaguchi
University, 1677-1 Yoshida,Yamaguchi 753–8515, Japan
| | - Shizunobu Igimi
- Department of Applied Biology and Chemistry, Tokyo University
of Agriculture, 1-1-1, Sakuragaoka,Setagaya-ku, Tokyo 156-8502, Japan
| | - Tetsuo Asai
- The United Graduate School of Veterinary Science, Gifu
University, 1-1, Yanagido, Gifu, Gifu 501-1193, Japan
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20
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Yao X, Nie W, Chen X, Zhang J, Wei J, Qiu Y, Liu K, Shao D, Liu H, Ma Z, Li Z, Li B. Two Enterococcus faecium Isolates Demonstrated Modulating Effects on the Dysbiosis of Mice Gut Microbiota Induced by Antibiotic Treatment. Int J Mol Sci 2024; 25:5405. [PMID: 38791443 PMCID: PMC11121104 DOI: 10.3390/ijms25105405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Broad-spectrum antibiotics are frequently used to treat bacteria-induced infections, but the overuse of antibiotics may induce the gut microbiota dysbiosis and disrupt gastrointestinal tract function. Probiotics can be applied to restore disturbed gut microbiota and repair abnormal intestinal metabolism. In the present study, two strains of Enterococcus faecium (named DC-K7 and DC-K9) were isolated and characterized from the fecal samples of infant dogs. The genomic features of E. faecium DC-K7 and DC-K9 were analyzed, the carbohydrate-active enzyme (CAZyme)-encoding genes were predicted, and their abilities to produce short-chain fatty acids (SCFAs) were investigated. The bacteriocin-encoding genes in the genome sequences of E. faecium DC-K7 and DC-K9 were analyzed, and the gene cluster of Enterolysin-A, which encoded a 401-amino-acid peptide, was predicted. Moreover, the modulating effects of E. faecium DC-K7 and DC-K9 on the gut microbiota dysbiosis induced by antibiotics were analyzed. The current results demonstrated that oral administrations of E. faecium DC-K7 and DC-K9 could enhance the relative abundances of beneficial microbes and decrease the relative abundances of harmful microbes. Therefore, the isolated E. faecium DC-K7 and DC-K9 were proven to be able to alter the gut microbiota dysbiosis induced by antibiotic treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (X.Y.); (W.N.); (X.C.); (J.Z.); (J.W.); (Y.Q.); (K.L.); (D.S.); (H.L.); (Z.M.)
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (X.Y.); (W.N.); (X.C.); (J.Z.); (J.W.); (Y.Q.); (K.L.); (D.S.); (H.L.); (Z.M.)
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21
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Li J, Du J, Ding G, Zhang W, Zhou Y, Xu Y, Zhou D, Sun Y, Liu X, Shen B. Isolation, characterization and functional analysis of a bacteriophage targeting Culex pipiens pallens resistance-associated Aeromonas hydrophila. Parasit Vectors 2024; 17:222. [PMID: 38745242 PMCID: PMC11094981 DOI: 10.1186/s13071-024-06281-x] [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: 11/17/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Culex pipiens pallens is a well-known mosquito vector for several diseases. Deltamethrin, a commonly used pyrethroid insecticide, has been frequently applied to manage adult Cx. pipiens pallens. However, mosquitoes can develop resistance to these insecticides as a result of insecticide misuse and, therefore, it is crucial to identify novel methods to control insecticide resistance. The relationship between commensal bacteria and vector resistance has been recently recognized. Bacteriophages (= phages) are effective tools by which to control insect commensal bacteria, but there have as yet been no studies using phages on adult mosquitoes. In this study, we isolated an Aeromonas phage vB AhM-LH that specifically targets resistance-associated symbiotic bacteria in mosquitoes. We investigated the impact of Aeromonas phage vB AhM-LH in an abundance of Aeromonas hydrophila in the gut of Cx. pipiens pallens and its effect on the status of deltamethrin resistance. METHODS Phages were isolated on double-layer agar plates and their biological properties analyzed. Phage morphology was observed by transmission electron microscopy (TEM) after negative staining. The phage was then introduced into the mosquito intestines via oral feeding. The inhibitory effect of Aeromonas phage vB AhM-LH on Aeromonas hydrophila in mosquito intestines was assessed through quantitative real-time PCR analysis. Deltamethrin resistance of mosquitoes was assessed using WHO bottle bioassays. RESULTS An Aeromonas phage vB AhM-LH was isolated from sewage and identified as belonging to the Myoviridae family in the order Caudovirales using TEM. Based on biological characteristics analysis and in vitro antibacterial experiments, Aeromonas phage vB AhM-LH was observed to exhibit excellent stability and effective bactericidal activity. Sequencing revealed that the Aeromonas phage vB AhM-LH genome comprises 43,663 bp (51.6% CG content) with 81 predicted open reading frames. No integrase-related gene was detected in the vB AH-LH genome, which marked it as a potential biological antibacterial. Finally, we found that Aeromonas phage vB AhM-LH could significantly reduce deltamethrin resistance in Cx. pipiens pallens, in both the laboratory and field settings, by decreasing the abundance of Aeromonas hydrophila in their midgut. CONCLUSIONS Our findings demonstrate that Aeromonas phage vB AhM-LH could effectively modulate commensal bacteria Aeromonas hydrophila in adult mosquitoes, thus representing a promising strategy to mitigate mosquito vector resistance.
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Affiliation(s)
- Jinze Li
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiajia Du
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guangshuo Ding
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenxing Zhang
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yinghui Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yidan Xu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dan Zhou
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yan Sun
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoqiu Liu
- Department of Pathogen Biology, China Medical University, Shenyang, China.
| | - Bo Shen
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China.
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22
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Mo R, Zhu D, Sun J, Yuan Q, Guo F, Duan Y. Molecular identification and phylogenetic analysis of the mitogenome in endangered giant nuthatch Sitta magna ( Passeriformes, Sittidae). Heliyon 2024; 10:e30513. [PMID: 38765151 PMCID: PMC11098796 DOI: 10.1016/j.heliyon.2024.e30513] [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: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
The Giant Nuthatch Sitta magna (family Sittidae) is a passerine bird, the quantification of the number of habitats and species on a global scale remains low. Most species are restricted to low elevations in southwest China, eastern Myanmar, and northern Thailand. To characterize the mitochondrial genome sequence of S. magna and its phylogenetic relationships with other members within the genus Sitta, the mitochondrial genome of S. magna was sequenced using the whole genome shotgun method. The sequencing results showed that the mitochondrial genome was 16,829 bp long and consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (D-loop). All tRNAs were predicted to form a typical clover secondary structure. Among the 13 PCGs, only the start codon in COI was ATC, the start codon by the remaining 12 PCGs was ATG, and the stop codons were TAG, TAA, AGG, AGA, and TA. Bayesian inference and maximum likelihood phylogenetic analysis of the sequences of 17 species generated consistent well-supported phylogenies. The family Polioptilidae and the family Troglodytidae were closely related, and the family Sittidae was confined to a single branch. The genus Sitta in the family Sittidae was mainly clustered into three branches. Our findings provide new mitochondrial genomic data that could be used for phylogenetic and taxonomic studies; our results also certificate into the phylogenetic relationships within the genus Sitta ((S. himalayensi+(S. nagaensis + S. europaea))+(S. villosa + S. yunnanensis))+(S. carolinensis + S. magna).
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Affiliation(s)
- Ruixin Mo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Dong Zhu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Jing Sun
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Feng Guo
- Administration of Zixi Mountain Provincial Nature Reserve, Chuxiong, 675008, China
| | - Yubao Duan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
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23
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An N, Wu Q, Fang Z, Xiang L, Liu Q, Tan L, Weng Q. Genome analysis and classification of Xanthomonas bacteriophage AhaSv, a new member of the genus Salvovirus. Arch Virol 2024; 169:117. [PMID: 38739272 DOI: 10.1007/s00705-024-06047-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Xanthomonas phage AhaSv was isolated from lake water. Genome sequencing showed that its genome is a linear dsDNA molecule with a length of 55,576 bp and a G+C content of 63.23%. Seventy-one open reading frames (ORFs) were predicted, and no tRNAs were found in the genome. Phylogenetic analysis showed that AhaSv is closely related to members of the genus Salvovirus of the family Casjensviridae. Intergenomic similarity values between phage AhaSv and homologous phages were up to 90.6%, suggesting that phage AhaSv should be considered a member of a new species in the genus Salvovirus.
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Affiliation(s)
- Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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24
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Wang X, Zhao W, Cui S, Su B, Huang Y, Chen H. Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers. Animals (Basel) 2024; 14:1454. [PMID: 38791671 PMCID: PMC11117285 DOI: 10.3390/ani14101454] [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: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of Dendrocerus (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of Dendrocerus and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of D. bellus and D. anisodontus were 15,445 bp and 15,373 bp, respectively, with the trnG of D. bellus missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (D. bellus) and 82.4% (D. anisodontus). Using Ceraphron sp. (Ceraphronidae) as reference, the Ka/Ks values of NAD4L and NAD6 in D. anisodontus were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with Ceraphon sp. gene order, nine operations were identified in D. anisodontus, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the COX1 genes in Megaspilidae and a 60% rate of success was achieved in the genus Dendrocerus.
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Affiliation(s)
- Xu Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100000, China;
| | - Wenjing Zhao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
| | - Shanshan Cui
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (X.W.); (W.Z.); (S.C.)
| | - Baoshan Su
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China;
| | - Yixin Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100000, China;
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China;
| | - Huayan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Chinese Academy of Sciences, Guangzhou 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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25
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Tang S, Zhang X, Du C, Jiang D, Yang X. The complete mitochondrial genome of Rhipicephalus haemaphysaloides and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:551-556. [PMID: 38686316 PMCID: PMC11057557 DOI: 10.1080/23802359.2024.2345136] [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: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
We conducted an analysis of the complete mitochondrial genome of Rhipicephalus haemaphysaloides, a tick species known for transmitting various bacteria and viruses. The mitochondrial genome of R. haemaphysaloides has a length of 14,739 bp and consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 2 control regions. By utilizing the maximum likelihood method, we established the phylogenetic relationship among R. haemaphysaloides and other species within the Rhipicephalus genus of the Ixodidae family. This analysis revealed that R. haemaphysaloides and other Rhipicephalus species belong to the same clade, further affirming the taxonomic placement of R. haemaphysaloides within the Rhipicephalus genus. Furthermore, we compared the mitochondrial genomes of R. haemaphysaloides isolates from Changning, Yunnan Province, China, with isolates from Yangxin, Ganzhou, and Yingtan, Hubei Province, China. In summary, our investigation offers genetic proof endorsing the taxonomic categorization and phylogenetic placement of Ixodidae by assessing the entire mitochondrial genome of R. haemaphysaloides.
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Affiliation(s)
- Shaobo Tang
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, P.R. China
| | - Xiaoyun Zhang
- School of Public Health, Dali University, Dali, P.R. China
| | - Chunhong Du
- Yunan Institute of Eudemic Diseases Control and Prevention, Dali, P.R. China
| | - Dandan Jiang
- School of Public Health, Dali University, Dali, P.R. China
| | - Xing Yang
- Integrated Laboratory of Pathogenic Biology, College of Preclinical Medicine, Dali University, Dali, P.R. China
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26
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Garrido-Palazuelos LI, Aguirre-Sánchez JR, Castro-Del Campo N, López-Cuevas O, González-Torres B, Chaidez C, Medrano-Félix JA. Genomic characteristics of Salmonella Montevideo and Pomona: impact of isolation source on antibiotic resistance, virulence and metabolic capacity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-16. [PMID: 38576268 DOI: 10.1080/09603123.2024.2336597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Salmonella enterica is known for its disease-causing serotypes, including Montevideo and Pomona. These serotypes have been found in various environments, including river water, sediments, food, and animals. However, the global spread of these serotypes has increased, leading to many reported infections and outbreaks. The goal of this study was the genomic analysis of 48 strains of S. Montevideo and S. Pomona isolated from different sources, including clinical. Results showed that environmental strains carried more antibiotic resistance genes than the clinical strains, such as genes for resistance to aminoglycosides, chloramphenicol, and sulfonamides. Additionally, the type 4 secretion system, was only found in environmental strains. .Also many phosphotransferase transport systems were identified and the presence of genes for the alternative pathway Entner-Doudoroff. The origin of isolation may have a significant impact on the ability of Salmonella isolates to adapt and survive in different environments, leading to genomic flexibility and a selection advantage.
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Affiliation(s)
- Lennin Isaac Garrido-Palazuelos
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Roberto Aguirre-Sánchez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Osvaldo López-Cuevas
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Berenice González-Torres
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Cristóbal Chaidez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Andrés Medrano-Félix
- Investigadoras e investigadores por México Centro de Investigación En Alimentación y Desarrollo A.C. Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán, México
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Bhandare S, Lawal OU, Colavecchio A, Cadieux B, Zahirovich-Jovich Y, Zhong Z, Tompkins E, Amitrano M, Kukavica-Ibrulj I, Boyle B, Wang S, Levesque RC, Delaquis P, Danyluk M, Goodridge L. Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species. Microorganisms 2024; 12:695. [PMID: 38674639 PMCID: PMC11052255 DOI: 10.3390/microorganisms12040695] [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: 03/08/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.
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Affiliation(s)
- Sudhakar Bhandare
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham LE12 5RD, UK
| | - Opeyemi U. Lawal
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Anna Colavecchio
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Brigitte Cadieux
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Yella Zahirovich-Jovich
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Zeyan Zhong
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Elizabeth Tompkins
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Margot Amitrano
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC H9X 3V9, Canada or (S.B.)
| | - Irena Kukavica-Ibrulj
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Brian Boyle
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Siyun Wang
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Roger C. Levesque
- Institute for Integrative Systems Biology (IBIS), Laval University, Québec, QC G1V 0A6, Canada (R.C.L.)
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada
| | - Michelle Danyluk
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Lawrence Goodridge
- Canadian Research Institute for Food Safety, Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
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Xi H, Fu B, Sheng Q, Luo M, Sun L. Isolation and Characterization of a Lytic Bacteriophage RH-42-1 of Erwinia amylovora from Orchard Soil in China. Viruses 2024; 16:509. [PMID: 38675852 PMCID: PMC11054837 DOI: 10.3390/v16040509] [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: 01/30/2024] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Fire blight, caused by the bacterium Erwinia amylovora, is a major threat to pear production worldwide. Bacteriophages, viruses that infect bacteria, are a promising alternative to antibiotics for controlling fire blight. In this study, we isolated a novel bacteriophage, RH-42-1, from Xinjiang, China. We characterized its biological properties, including host range, plaque morphology, infection dynamics, stability, and sensitivity to various chemicals. RH-42-1 infected several E. amylovora strains but not all. It produced clear, uniform plaques and exhibited optimal infectivity at a multiplicity of infection (MOI) of 1, reaching a high titer of 9.6 × 109 plaque-forming units (PFU)/mL. The bacteriophage had a short latent period (10 min), a burst size of 207 PFU/cell, and followed a sigmoidal one-step growth curve. It was stable at temperatures up to 60 °C but declined rapidly at higher temperatures. RH-42-1 remained viable within a pH range of 5 to 9 and was sensitive to extreme pH values. The bacteriophage demonstrates sustained activity upon exposure to ultraviolet radiation for 60 min, albeit with a marginal reduction. In our assays, it exhibited a certain level of resistance to 5% chloroform (CHCl3), 5% isopropanol (C3H8O), and 3% hydrogen peroxide (H2O2), which had little effect on its activity, whereas it showed sensitivity to 75% ethanol (C2H5OH). Electron microscopy revealed that RH-42-1 has a tadpole-shaped morphology. Its genome size is 14,942 bp with a GC content of 48.19%. Based on these characteristics, RH-42-1 was identified as a member of the Tectiviridae family, Alphatectivirus genus. This is the first report of a bacteriophage in this genus with activity against E. amylovora.
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Affiliation(s)
- Haishen Xi
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Benzhong Fu
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Qiang Sheng
- Xinjiang Bayingolin Mongolian Autonomous Prefecture Academy of Agricultural Sciences, Korla 841003, China;
| | - Ming Luo
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Liying Sun
- The Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling 712100, China
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Tang W, Li X, Ye B, Shi B, Zhang H, Dang Z, Sun Y, Danqu L, Xia C, Quzhen D, Zhao X, Chui W, Huang F. Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae). Ticks Tick Borne Dis 2024; 15:102311. [PMID: 38262211 DOI: 10.1016/j.ttbdis.2024.102311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.
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Affiliation(s)
- Wenqiang Tang
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bin Shi
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases at China CDC/Chinese Center for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory for Parasite and Vector Biology, Shanghai 200025, China
| | - Yuexiang Sun
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Lamu Danqu
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Chenyang Xia
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Danzeng Quzhen
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xialing Zhao
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China.
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30
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Wang Y, Wang J, Zhu X, Wang W. Genome and transcriptome sequencing of Trichoderma harzianum T4, an important biocontrol fungus of Rhizoctonia solani, reveals genes related to mycoparasitism. Can J Microbiol 2024; 70:86-101. [PMID: 38314685 DOI: 10.1139/cjm-2023-0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Trichoderma harzianum is a well-known biological control strain and a mycoparasite of Rhizoctonia solani. To explore the mechanisms of mycoparasitism, the genome and transcriptome of T. harzianum T4 were both assembled and analyzed in this study. The genome of T. harzianum T4 was assembled into 106 scaffolds, sized 41.25 Mb, and annotated with a total of 8118 predicted genes. We analyzed the transcriptome of T. harzianum T4 against R. solani in a dual culture in three culture periods: before contact (BC), during contact (C), and after contact (AC). Transcriptome sequencing identified 1092, 1222, and 2046 differentially expressed genes (DEGs), respectively. These DEGs, which are involved in pathogen recognition and signal transduction, hydrolase, transporters, antibiosis, and defense-related functional genes, are significantly upregulated in the mycoparasitism process. The results of genome and transcriptome analysis indicated that the mycoparasitism process of T. harzianum T4 was very complex. T. harzianum successfully recognizes and invades host cells and kills plant pathogens by regulating various DEGs at different culture periods. The relative expression levels of the 26 upregulated DEGs were confirmed by RT-qPCR to validate the reliability of the transcriptome data. The results provide insight into the molecular mechanisms underlying T. harzianum T4's mycoparasitic processes, and they provide a potential molecular target for the biological control mechanism of T. harzianum T4.
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Affiliation(s)
- Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiaochong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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31
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Seo B, Jeon K, Kim WK, Jang YJ, Cha KH, Ko G. Strain-Specific Anti-Inflammatory Effects of Faecalibacterium prausnitzii Strain KBL1027 in Koreans. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10213-7. [PMID: 38411865 DOI: 10.1007/s12602-024-10213-7] [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] [Accepted: 01/04/2024] [Indexed: 02/28/2024]
Abstract
Faecalibacterium prausnitzii is one of the most dominant commensal bacteria in the human gut, and certain anti-inflammatory functions have been attributed to a single microbial anti-inflammatory molecule (MAM). Simultaneously, substantial diversity among F. prausnitzii strains is acknowledged, emphasizing the need for strain-level functional studies aimed at developing innovative probiotics. Here, two distinct F. prausnitzii strains, KBL1026 and KBL1027, were isolated from Korean donors, exhibiting notable differences in the relative abundance of F. prausnitzii. Both strains were identified as the core Faecalibacterium amplicon sequence variant (ASV) within the healthy Korean cohort, and their MAM sequences showed a high similarity of 98.6%. However, when a single strain was introduced to mice with dextran sulfate sodium (DSS)-induced colitis, KBL1027 showed the most significant ameliorative effects, including alleviation of colonic inflammation and restoration of gut microbial dysbiosis. Moreover, the supernatant from KBL1027 elevated the secretion of IL-10 cytokine more than that of KBL1026 in mouse bone marrow-derived macrophage (BMDM) cells, suggesting that the strain-specific, anti-inflammatory efficacy of KBL1027 might involve effector compounds other than MAM. Through analysis of the Faecalibacterium pan-genome and comparative genomics, strain-specific functions related to extracellular polysaccharide biosynthesis were identified in KBL1027, which could contribute to the observed morphological disparities. Collectively, our findings highlight the strain-specific, anti-inflammatory functions of F. prausnitzii, even within the same core ASV, emphasizing the influence of their human origin.
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Affiliation(s)
- Boram Seo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
- Personalized Diet Research Group, Food Functionality Research Division, Korea Food Research Institute, Jeollabuk-do, Republic of Korea
| | - Kyungchan Jeon
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Woon-Ki Kim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - You Jin Jang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.
- N-Bio, Seoul National University, Seoul, Republic of Korea.
- Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
- KoBioLabs Inc., Seoul, Republic of Korea.
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32
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Palevich F, Gardner A, Ross C, Mills J, Brightwell G, Palevich N. Multiple genome sequences of lactic acid bacteria, Carnobacterium divergens and Carnobacterium maltaromaticum strains, isolated from vacuum-packaged lamb meat. Microbiol Resour Announc 2024; 13:e0105823. [PMID: 38197696 PMCID: PMC10868225 DOI: 10.1128/mra.01058-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Here, we report the whole-genome sequences of 11 Carnobacterium divergens and 2 Carnobacterium maltaromaticum bacteria isolated from vacuum-packed chill-stored lamb meat in New Zealand. Examination of these lactic acid bacteria (LAB) genomes will improve our knowledge of their potential antimicrobial activities and spoilage mechanisms of importance to the meat industry.
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Affiliation(s)
- Faith Palevich
- Food System Integrity, Hopkirk Research Institute, AgResearch Ltd, Palmerston North, New Zealand
| | - Amanda Gardner
- Food System Integrity, Hopkirk Research Institute, AgResearch Ltd, Palmerston North, New Zealand
| | - Colleen Ross
- Food System Integrity, Hopkirk Research Institute, AgResearch Ltd, Palmerston North, New Zealand
| | - John Mills
- Food System Integrity, Hopkirk Research Institute, AgResearch Ltd, Palmerston North, New Zealand
| | - Gale Brightwell
- Food System Integrity, Hopkirk Research Institute, AgResearch Ltd, Palmerston North, New Zealand
| | - Nikola Palevich
- Rumen Microbiology, Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
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33
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Aguirre-Sanchez JR, Vega-Lopez IF, Castro Del Campo N, Medrano-Felix JA, Martínez-Urtaza J, Chaidez-Quiroz C. Genomic-wide analysis approach revealed genomic similarity for environmental Mexican S. Oranienburg genomes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:956-967. [PMID: 36946386 DOI: 10.1080/09603123.2023.2191312] [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: 01/09/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
As the human population grows, an increase in food trade is needed. This elevates the risk of epidemiological outbreaks. One of the prevalent pathogens associated with food production in Mexico has been Salmonella Oranienburg. Effective surveillance systems require microbial genetic knowledge. The objective of this work is to describe the genetic composition of Mexican S. Oranienburg genomes. For that, 53 strains from different environmental sources were isolated and sequenced. Additionally, 109 S. Oranienburg genomes were downloaded. Bioinformatic analyses were used to explore the clonal complex and genomic relatedness. A major clonal group formed by ST23 was identified comprising four STs. 202 SNPs were found the maximum difference among isolates. Virulence genes for host invasion and colonization as rpoS, fimbria type 1, and, T3SS were found common for all isolates. This study suggests that Mexican S. Oranienburg strains are potential pathogens circulating continuously in the region between host and non-host environments.
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Affiliation(s)
- J R Aguirre-Sanchez
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
| | - I F Vega-Lopez
- Laboratorio en Ciencia y Mineria de Datos, Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacán, México
| | - N Castro Del Campo
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
| | - J A Medrano-Felix
- Inocuidad Alimentaria, Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo A.C, Culiacán, México
| | - J Martínez-Urtaza
- Departement of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - C Chaidez-Quiroz
- Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo, Culiacán, México
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Dou T, Gao F, Zhu J, Wang Z, Yang X, Hao Y, Song N, An S, Yin X, Liu X. Evolutionary analysis and biological characterization of a novel alphabaculovirus isolated from Mythimna separata. J Gen Virol 2024; 105. [PMID: 38376497 DOI: 10.1099/jgv.0.001958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Baculoviruses are insect-specific pathogens. Novel baculovirus isolates provide new options for the biological control of pests. Therefore, research into the biological characteristics of newly isolated baculoviruses, including accurate classification and nomenclature, is important. In this study, a baculovirus was isolated from Mythimna separata and its complete genome sequence was determined by next-generation sequencing. The double-stranded DNA genome was 153 882 bp in length, encoding 163 open reading frames. The virus was identified as a variant of Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) and designated Mamestra brassicae multiple nucleopolyhedrovirus CHN1 (MbMNPV-CHN1) according to ultrastructural analysis, genome comparison and phylogenetic analysis. Phylogenetic inference placed MbMNPV-CHN1 in a clade containing isolates of MacoNPV-A, MacoNPV-B and MbMNPV, which we have designated the Mb-McNPV group. The genomes of isolates in the Mb-McNPV group exhibited a high degree of collinearity with relatively minor differences in the content of annotated open reading frames. The development of codon usage bias in the Mb-McNPV group was affected mainly by natural selection. MbMNPV-CHN1 shows high infectivity against seven species of Lepidoptera. The yield of MbMNPV-CHN1 in the fourth- and fifth-instar M. separata larvae was 6.25×109-1.23×1010 OBs/cadaver. Our data provide insights into the classification, host range and virulence differences among baculoviruses of the Mb-McNPV group, as well as a promising potential new baculoviral insecticide.
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Affiliation(s)
- Tao Dou
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Futao Gao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Junhua Zhu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Zihao Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Xifa Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Youwu Hao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Shiheng An
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Xiangyang Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
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35
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Zhou Y, Wu X, Wu C, Zhou P, Yang Y, Wang B, Xu Y, Zhao H, Guo Y, Yu J, Yu F. Emergence of KPC-2 and NDM-5-coproducing hypervirulent carbapenem-resistant Klebsiella pneumoniae with high-risk sequence types ST11 and ST15. mSphere 2024; 9:e0061223. [PMID: 38193656 PMCID: PMC10826354 DOI: 10.1128/msphere.00612-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
The emergence of Klebsiella pneumoniae carbapenemase-2 (KPC-2) and New Delhi metallo-β-lactamase (NDM)-coproducing hypervirulent carbapenem-resistant Klebsiella pneumoniae (KPC-2-NDM-hv-CRKP) poses a certain threat to public health. Currently, only a few sporadic reports of such double-positive hv-CRKPs were available. In this study, we isolated two KPC-2-NDM-5-hv-CRKPs from elderly patients with serious underlying diseases and poor prognoses. We found both FK3122 and FK3127 were typical multidrug-resistant (MDR) isolates, exhibiting high-level resistance to both carbapenems and novel β-lactamase inhibitors ceftazidime/avibactam. Notably, FK3122 is even resistant to cefiderocol due to multiple blaNDM-5 elements. Besides the MDR phenotype, A549 human lung epithelial cells and Galleria mellonella infection model all indicated that FK3122 and FK3127 were highly pathogenic. According to the whole-genome sequencing analysis, we observed over 10 resistant elements, and the uncommon co-existence of blaKPC-2, blaNDM-5, and virulence plasmids in both two isolates. Both virulence plasmids identified in FK3122 and FK3127 shared a high identity with classical virulence plasmid pK2044, harboring specific hypervirulent factors: rmpA and iuc operon. We also found that the resistance and virulence plasmids in FK3127 could not only be transferred to Escherichia coli EC600 independently but also together as a co-transfer, which was additionally confirmed by the S1-pulsed-field gel electrophoresis plasmid profile. Moreover, polymorphic mobile genetic elements were found surrounding resistance genes, which may stimulate the mobilization of resistance genes and result in the duplication of these elements. Considering the combination of high pathogenicity, limited therapy options, and easy transmission of KPC-2-NDM-5-hv-CRKP, our study emphasizes the need for underscores the imperative for ongoing surveillance of these pathogens.IMPORTANCEHypervirulent Klebsiella pneumoniae drug resistance has increased gradually with the emergence of carbapenem-resistant hypervirulent K. pneumoniae (hv-CRKP). However, little information is available on the virulence characteristics of the New Delhi metallo-β-lactamase (NDM) and Klebsiella pneumoniae carbapenemase-2 (KPC-2) co-producing K. pneumoniae strains. In this study, we obtained two KPC-2-NDM-hv-CRKPs from elderly patients, each with distinct capsule types and sequence types: ST11-KL64 and ST15-KL24; these ST-type lineages are recognized as classical multidrug-resistant (MDR) K. pneumoniae. We found these KPC-2-NDM-hv-CRKPs were not only typical MDR isolates, including resistance to ceftazidime/avibactam and cefiderocol, but also displayed exceptionally high levels of pathogenicity. In addition, these high-risk factors can also be transferred to other isolates. Consequently, our study underscores the need for ongoing surveillance of these isolates due to their heightened pathogenicity, limited therapeutic options, and potential for easy transmission.
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Affiliation(s)
- Ying Zhou
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaocui Wu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyang Wu
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Peiyao Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yang Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Bingjie Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanlei Xu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huilin Zhao
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jingyi Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Zhang C, van der Heijden MGA, Dodds BK, Nguyen TB, Spooren J, Valzano-Held A, Cosme M, Berendsen RL. A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization. MICROBIOME 2024; 12:13. [PMID: 38243337 PMCID: PMC10799531 DOI: 10.1186/s40168-023-01726-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/18/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis. RESULTS Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization. CONCLUSIONS Our results highlight that AM fungi do not function in isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.
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Affiliation(s)
- Changfeng Zhang
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Bethany K Dodds
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Thi Bich Nguyen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Jelle Spooren
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alain Valzano-Held
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marco Cosme
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
- Plants and Ecosystems, Biology Department, University of Antwerp, Antwerp, Belgium
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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Zhao K, Qiu L, Tao X, Zhang Z, Wei H. Genome Analysis for Cholesterol-Lowing Action and Bacteriocin Production of Lactiplantibacillus plantarum WLPL21 and ZDY04 from Traditional Chinese Fermented Foods. Microorganisms 2024; 12:181. [PMID: 38258009 PMCID: PMC10820322 DOI: 10.3390/microorganisms12010181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Lactiplantibacillus plantarum, a typical ecological species against pathogens, used due to its bacteriocin yield in fermented foods, was proven to have the capacity to lower cholesterol. In this study, using L. plantarum ATCC8014 as the control, L. plantarum WLPL21 and ZDY04 were probed with whole-genome sequencing to ascertain their potential ability to lower cholesterol and yield bacteriocins, as well as to further evaluate their survival capacity in vitro. Our results showed 386 transport-system genes in both L. plantarum WLPL21 and ZDY04. Correspondingly, the in vitro results showed that L. plantarum WLPL21 and ZDY04 could remove cholesterol at 49.23% and 41.97%, respectively, which is 1.89 and 1.61 times that of L. plantarum ATCC8014. The survival rates of L. plantarum WLPL21 and ZDY04 in 1% H2O2, pH 3.0, and 0.3% bile salt were higher than those of L. plantarum ATCC8014. Our results exhibited a complete gene cluster for bacteriocin production encoded by L. plantarum WLPL21 and ZDY04, including plnJKR, plnPQAB, plnEFI, plnSUVWY, and plnJK; and plnMN, plnPQA and plnEFI, respectively, compared with only plnEF in L. plantarum ATCC8014. The present study suggests that the combination of genomic analysis with in vitro evaluations might be useful for exploring the potential functions of probiotics.
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Affiliation(s)
- Kui Zhao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Liang Qiu
- Centre for Translational Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, China;
| | - Xueying Tao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Zhihong Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
| | - Hua Wei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China; (K.Z.); (X.T.); (Z.Z.)
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Wan X, Skurnik M. Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets. Methods Mol Biol 2024; 2793:237-256. [PMID: 38526734 DOI: 10.1007/978-1-0716-3798-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation. Moreover, steps are provided to predict protein-protein interactions and visualizing these using PyMOL. The culmination of these methods equips researchers with an effective pipeline to identify and analyze toxHPUFs and their potential targets, laying the groundwork for future experimental confirmations.
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Affiliation(s)
- Xing Wan
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Huq M, Wahid SUH, Istivan T. Biofilm Formation in Campylobacter concisus: The Role of the luxS Gene. Microorganisms 2023; 12:46. [PMID: 38257873 PMCID: PMC10820981 DOI: 10.3390/microorganisms12010046] [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: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Campylobacter concisus is a bacterium that inhabits human oral cavities and is an emerging intestinal tract pathogen known to be a biofilm producer and one of the bacterial species found in dental plaque. In this study, biofilms of oral and intestinal C. concisus isolates were phenotypically characterized. The role of the luxS gene, which is linked to the regulation of biofilm formation in other pathogens, was assessed in relation to the pathogenic potential of this bacterium. Biofilm formation capacity was assessed using phenotypic assays. Oral strains were shown to be the highest producers. A luxS mutant was created by inserting a kanamycin cassette within the luxS gene of the highest biofilm-forming isolate. The loss of the polar flagellum was observed with scanning and transmission electron microscopy (SEM and TEM). Furthermore, the luxS mutant exhibited a significant reduction (p < 0.05) in biofilm formation, motility, and its expression of flaB, in addition to the capability to invade intestinal epithelial cells, compared to the parental strain. The study concluded that C. concisus oral isolates are significantly higher biofilm producers than the intestinal isolates and that LuxS plays a role in biofilm formation, invasion, and motility in this bacterium.
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Affiliation(s)
- Mohsina Huq
- School of Science, STEM College, RMIT University, Bundoora, Melbourne, VIC 3083, Australia
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | | | - Taghrid Istivan
- School of Science, STEM College, RMIT University, Bundoora, Melbourne, VIC 3083, Australia
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Huang F, Li X, Ye B, Zhou Y, Dang Z, Tang W, Wang L, Zhang H, Chui W, Kui J. Characterization of the Complete Mitochondrial Genome and Phylogenetic Analyses of Eurytrema coelomaticum (Trematoda: Dicrocoeliidae). Genes (Basel) 2023; 14:2199. [PMID: 38137020 PMCID: PMC10743053 DOI: 10.3390/genes14122199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Eurytrema coelomaticum, a pancreatic fluke, is recognized as a causative agent of substantial economic losses in ruminants. This infection, commonly referred to as eurytrematosis, is a significant concern due to its detrimental impact on livestock production. However, there is a paucity of knowledge regarding the mitochondrial genome of E. coelomaticum. In this study, we performed the initial sequencing of the complete mitochondrial genome of E. coelomaticum. Our findings unveiled that the mitochondrial genome of E. coelomaticum spans a length of 15,831 bp and consists of 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. The A+T content constituted 62.49% of the genome. Moreover, all 12 protein-coding genes of E. coelomaticum exhibit the same arrangement as those of E. pancreaticum and other published species belonging to the family Dicrocoeliidae. The presence of a short string of additional amino acids (approximately 20~23 aa) at the N-terminal of the cox1 protein in both E. coelomaticum and E. pancreaticum mitochondrial genomes has contributed to the elongation of the cox1 gene in genus Eurytrema, surpassing that of all previously sequenced Dicrocoeliidae. The phylogenetic analysis displayed a close relationship between E. coelomaticum and E. pancreaticum, along with a genus-level association between Eurytrema and Lyperosomum. These findings underscore the importance of mitochondrial genomic data for comparative studies of Dicrocoeliidae and even Digenea, offering valuable DNA markers for future investigations in the systematic, epidemiological, and population genetic studies of this parasite and other digenean trematodes.
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Affiliation(s)
- Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Yule Zhou
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People’s Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850009, China
| | - Long Wang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, Xining 810003, China
| | - Jun Kui
- Huangzhong District Animal Husbandry and Veterinary Station, Xining 811600, China
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Niu BY, Ren DJ, Zhang FB, Zhu HT, Wei HL, Ma MC, Gao M. Lysobacter changpingensis sp. nov., a novel species of the genus Lysobacter isolated from a rhizosphere soil of strawberry in China. Folia Microbiol (Praha) 2023; 68:991-998. [PMID: 37266892 PMCID: PMC10689546 DOI: 10.1007/s12223-023-01058-8] [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: 11/11/2022] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
In the present work, we characterized in detail strain CM-3-T8T, which was isolated from the rhizosphere soil of strawberries in Beijing, China, in order to elucidate its taxonomic position. Cells of strain CM-3-T8T were Gram-negative, non-spore-forming, aerobic, short rod. Growth occurred at 25-37 °C, pH 5.0-10.0, and in the presence of 0-8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CM-3-T8T formed a stable clade with Lysobacter soli DCY21T and Lysobacter panacisoli CJ29T, with the 16S rRNA gene sequence similarities of 98.91% and 98.50%. The average nucleotide identity and digital DNA-DNA hybridization values between strain SG-8 T and the two reference type strains listed above were 76.3%, 79.6%, and 34.3%, 27%, respectively. The DNA G + C content was 68.4% (mol/mol). The major cellular fatty acids were comprised of C15:0 iso (36.15%), C17:0 iso (8.40%), and C11:0 iso 3OH (8.28%). The major quinone system was ubiquinone Q-8. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylethanolamine (PME), diphosphatidylglycerol (DPG), and aminophospholipid (APL). On the basis of phenotypic, genotypic, and phylogenetic evidence, strain CM-3-T8T (= ACCC 61714 T = JCM 34576 T) represents a new species within the genus Lysobacter, for which the name Lysobacter changpingensis sp. nov. is proposed.
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Affiliation(s)
- Bang-Yan Niu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Dong-Jun Ren
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Fang-Bo Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Hong-Tu Zhu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Hai-Lei Wei
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Ming-Chao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Miao Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences/Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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Khurana S, Katiyar A, Puraswani M, Sharma D, Walia K, Malhotra R, Mathur P. Molecular mechanisms of colistin- and multidrug-resistance in bacteria among patients with hospital-acquired infections. Future Sci OA 2023; 9:FSO896. [PMID: 37753358 PMCID: PMC10518808 DOI: 10.2144/fsoa-2022-0055] [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: 08/12/2022] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
Aim The increasing burden of resistance in Gram-negative bacteria (GNB) is becoming a major issue for hospital-acquired infections. Therefore, understanding the molecular mechanisms is important. Methodology Resistance genes of phenotypically colistin-resistant GNB (n = 60) were determined using whole genome sequencing. Antimicrobial susceptibility patterns were detected by Vitek®2 & broth microdilution. Results Of these phenotypically colistin-resistant isolates, 78% were also genetically resistant to colistin. Activation of efflux pumps, and point-mutations in pmrB, and MgrB genes conferred colistin resistance among GNB. Eight different strains of K. pneumoniae were identified and ST43 was the most prominent strain with capsular type-specific (cps) gene KL30. Discussion These results, in combination with rapid diagnostic methods, will help us better advice appropriate antimicrobial regimens.
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Affiliation(s)
- Surbhi Khurana
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Centre, All India Institute of Medical Sciences, New Delhi
| | - Amit Katiyar
- Centralized Core Research Facility, Bioinformatics Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Mamta Puraswani
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Centre, All India Institute of Medical Sciences, New Delhi
| | - Divya Sharma
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Centre, All India Institute of Medical Sciences, New Delhi
| | - Kamini Walia
- Epidemiology & Communicable Diseases, Indian Council of Medical Research
| | - Rajesh Malhotra
- Department of Orthopedics, Chief, JPNA Trauma Centre, All India Institute of Medical Sciences, New Delhi
| | - Purva Mathur
- Department of Laboratory Medicine, Jai Prakash Narayan Apex Trauma Centre, All India Institute of Medical Sciences, New Delhi
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Martins IM, Seribelli AA, Machado Ribeiro TR, da Silva P, Lustri BC, Hernandes RT, Falcão JP, Moreira CG. Invasive non-typhoidal Salmonella (iNTS) aminoglycoside-resistant ST313 isolates feature unique pathogenic mechanisms to reach the bloodstream. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105519. [PMID: 37890808 DOI: 10.1016/j.meegid.2023.105519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Invasive non-typhoidal Salmonella (iNTS) from the clonal type ST313 (S. Typhimurium ST313) is the primary cause of invasive salmonellosis in Africa. Recently, in Brazil, iNTS ST313 strains have been isolated from different sources, but there is a lack of understanding of the mechanisms behind how these gut bacteria can break the gut barrier and reach the patient's bloodstream. Here, we compare 13 strains of S. Typhimurium ST313, previously unreported isolates, from human blood cultures, investigating aspects of virulence and mechanisms of resistance. Initially, RNAseq analyses between ST13-blood isolate and SL1344 (ST19) prototype revealed 15 upregulated genes directly related to cellular invasion and replication, such as sopD2, sifB, and pipB. Limited information is available about S. Typhimurium ST313 pathogenesis and epidemiology, especially related to the global distribution of strains. Herein, the correlation of strains isolated from different sources in Brazil was employed to compare clinical and non-clinical isolates, a total of 22 genomes were studied by single nucleotide polymorphism (SNPs). The epidemiological analysis of 22 genomes of S. Typhimurium ST313 strains grouped them into three distinct clusters (A, B, and C) by SNP analysis, where cluster A comprised five, group B six, and group C 11. The 13 clinical blood isolates were all resistant to streptomycin, 92.3% of strains were resistant to ampicillin and 15.39% were resistant to kanamycin. The resistance genes acrA, acrB, mdtK, emrB, emrR, mdsA, and mdsB related to the production of efflux pumps were detected in all (100%) strains studied, similar to pathogenic traits investigated. In conclusion, we evidenced that S. Typhimurium ST313 strains isolated in Brazil have unique epidemiology. The elevated frequencies of virulence genes such as sseJ, sopD2, and pipB are a major concern in these Brazilian isolates, showing a higher pathogenic potential.
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Affiliation(s)
- Isabela Mancini Martins
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Amanda Aparecida Seribelli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo- USP, Ribeirão Preto, SP, Brazil
| | - Tamara R Machado Ribeiro
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Patrick da Silva
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Bruna Cardinali Lustri
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil
| | - Rodrigo T Hernandes
- Instituto de Biociências, Universidade Estadual Paulista- UNESP, Botucatu, SP, Brazil
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo- USP, Ribeirão Preto, SP, Brazil.
| | - Cristiano Gallina Moreira
- Faculdade de Ciências Farmacêuticas de Araraquara, Universidade Estadual Paulista- UNESP- Departamento de Ciências Biológicas, Araraquara, SP, Brazil; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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Khánh CM, Van Quyen D, Van TTH, Moore RJ. Heterologously expressed SacP23, a novel bacteriocin from Paenibacillus polymyxa #23, is active against methicillin resistant Staphylococcus aureus. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231119. [PMID: 38126065 PMCID: PMC10731318 DOI: 10.1098/rsos.231119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Antimicrobial peptides have the potential to be used in a range of applications, including as an alternative to conventional antibiotics for the treatment of bacterial infections of humans and animals. Therefore, there is interest in identifying novel bacteriocins which have desirable physico-chemical properties or antimicrobial activities. Paenibacillus polymyxa #23, isolated from a marine sponge, has wide spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. To explore the basis of this antimicrobial activity, the complete genome sequence of the strain was examined. Multiple genes predicted to encode antimicrobial peptides were identified. One gene was predicted to encode a novel sactipeptide bacteriocin, named SacP23. To confirm that SacP23 does have antimicrobial activity and to explore the antimicrobial spectrum of the peptide it was heterologously expressed in Bacillus subtilis. A cluster of eight genes, encoding a full complement of accessory genes as well as the structural gene expressed from the native promoter, was cloned into B. subtilis BS54A. The recombinant strain displayed antimicrobial activity against several Gram-positive bacteria, including multi-drug resistant Staphylococcus aureus. Heterologous expression of a whole gene cluster offers a powerful way to interrogate and resolve the various antimicrobial activities expressed by native strains that encode multiple compounds of interest.
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Affiliation(s)
- Châu Minh Khánh
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong, Loc Tho, Nha Trang, Khanh Hoa, Vietnam
| | - Dong Van Quyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Vietnam
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Robert J. Moore
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
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Yan S, Ma P, Zuo C, Zhu Y, Ma X, Zhang Z. Genetic Analysis Based on Mitochondrial nad2 Gene Reveals a Recent Population Expansion of the Invasive Mussel, Mytella strigata, in China. Genes (Basel) 2023; 14:2038. [PMID: 38002981 PMCID: PMC10671778 DOI: 10.3390/genes14112038] [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] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Mytella strigata is a highly adaptable invasive alien species that has been established in coastal China since 2014. Mitochondrial DNA (mtDNA) is an important tool for studying the evolution and population genetics of invasive species. In this study, the mitochondrial genome of M. strigata from China was sequenced by Illumina high-throughput sequencing and characterized with 13 protein-coding genes (PCGs). By assessing the selective pressure of 13 PCGs, the nad2 gene had the fastest evolutionary rate and was finally selected for population genetic analysis. A total of 285 nad2 sequences from seven M. strigata populations in China were analyzed and showed obviously T-rich and C-rich characteristics. According to population genetic diversity analysis, all the seven populations had haplotype (gene) diversity (Hd) ≥ 0.5 and nucleotide diversity (Pi) < 0.005. Haplotype networks showed a "star" distribution. Population historical dynamic analyses showed that Fu's Fs and Tajima's D values of all populations were negative except the Qukou (QK) and Beihai (BH) populations. The Zhangzhou (ZJ) and Xiamen (XM) populations were unimodal while the other populations were multimodal. These results suggested that the population of M. strigata in China may have passed the bottleneck period and is currently in a state of population expansion.
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Affiliation(s)
- Shaojing Yan
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
| | - Peizhen Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Chenxia Zuo
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- College of Life Sciences, Qingdao University, Qingdao 266000, China
| | - Yi Zhu
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojie Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Marcoux PÉ, Girard SB, Fournier KC, Tardif CA, Gosselin A, Charette SJ. Interaction of pAsa5 and pAsa8 Plasmids in Aeromonas salmonicida subsp. salmonicida. Microorganisms 2023; 11:2685. [PMID: 38004697 PMCID: PMC10673383 DOI: 10.3390/microorganisms11112685] [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: 10/08/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The plasmid known as pAsa5 is present in Aeromonas salmonicida subsp. salmonicida, a fish pathogen. The pAsa5 plasmid carries genes that are essential for the bacterium's virulence. Recombination events are known to occur in pAsa5, resulting in the loss of certain segments or the acquisition of additional genetic elements. For example, the transposon carried by the large pAsa8 plasmid was found to be inserted into the pAsa5 plasmid in the SHY16-3432 strain, enabling the addition of antibiotic resistance genes to this plasmid, which does not normally possess any. In this study, we present the isolation of additional strains carrying pAsa8. Further analyses of these strains revealed that a fusion between pAsa5 and the complete version of pAsa8 is possible. The pAsa8 transposon insertion in pAsa5 seen in the SHY16-3432 strain appears to be an aberrant event compared to the fusion of the two full-length plasmids. A 22-nucleotide sequence, present in both plasmids, serves as the site for the fusion of the two plasmids. Moreover, it is possible to introduce pAsa8 through conjugation into naive strains of A. salmonicida subsp. salmonicida and once the plasmid is within a new strain, the fusion with pAsa5 is detectable. This study reveals a previously unexplored aspect of pAsa5 plasmid biology, highlighting an additional risk for the spread of antibiotic resistance genes in A. salmonicida subsp. salmonicida.
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Affiliation(s)
- Pierre-Étienne Marcoux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Sarah B. Girard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Kim C. Fournier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Catherine A. Tardif
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Ariane Gosselin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
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Dahiya S, Katiyar A, Rai S, Sharma P, Punit Kaur, Kapil A. Ceftriaxone-resistant Salmonella Typhi isolated from paediatric patients in north India: Insights into genetic profiles and antibiotic resistance mechanisms. Indian J Med Microbiol 2023; 46:100448. [PMID: 37945130 DOI: 10.1016/j.ijmmb.2023.100448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE To investigate the antibiotic resistance and genetic profile of ceftriaxone-resistant Salmonella Typhi isolated from the blood culture of two paediatric cases of typhoid fever and one from the stool culture of their household contact, in North India. METHODS In this study, whole-genome sequencing was carried out with paired-end 2 × 150 bp reads on Illumina MiSeq (Illumina, USA) employing v2 and v3 chemistry. To check data quality, adapters and low-quality sequences were removed through Trimmomatic-v0.36. High quality reads were then assembled de novo using A5-miseq pipeline. For further refinement, reference-guided contig ordering and orienting were performed on the scaffold assemblies using ABACAS (http://abacas.sourceforge.net/). The assembled genome was annotated using Prokka v1.12 to identify and annotate the gene content. Plasmid replicons in bacterial isolates were identified by PlasmidFinder, whereas mobile genetic elements were predicted using Mobile Element Finder. Referenced-based SNP tree with maximum likelihood method was built with CSI phylogeny v1.4. RESULTS All three isolates exhibited resistance to ceftriaxone, cefixime, ciprofloxacin, ampicillin, and co-trimoxazole, while demonstrating sensitivity to azithromycin and chloramphenicol. The whole-genome sequencing of these strains revealed the presence of blaCTX-M-15 gene for cephalosporin resistance in addition to gyrA, qnr and IncY plasmid replicon. A 5 kb IS91 Sbo1 gene cassette (IncY plasmid) was identified which carried extended spectrum β-lactamase blaCTX-M-15, blaTEM-1D (resistance to ampicillin and cephalosporin), sul2, dfrA14 (resistant to trimethoprim-sulfamethoxazole) and qnrS (resistant to ciprofloxacin). These isolates belong to H58 lineage and grouped as sequence type 1 (ST1) on multilocus sequence typing (MLST) analysis. CONCLUSION In the present study we report the isolation of blaCTX-M-15 positive S. Typhi from two paediatric patients presenting with fever and one from stool culture of their contact from North India and highlight the need for further investigations to understand the different factors contributing to ceftriaxone resistance in Salmonella Typhi.
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Affiliation(s)
- Sushila Dahiya
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Sumit Rai
- Department of Clinical Microbiology and Infectious Diseases, Super Speciality Child Hospital and Post Graduate Teaching Institute, NOIDA, India.
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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Feng M, Kong H, Lin M, Zhang R, Gong W. The complete plastid genome provides insight into maternal plastid inheritance mode of the living fossil plant Ginkgo biloba. PLANT DIVERSITY 2023; 45:752-756. [PMID: 38197005 PMCID: PMC10772217 DOI: 10.1016/j.pld.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 01/11/2024]
Abstract
In the current research, we focus on uniparental inheritance of chloroplast genome of the living fossil plant, Ginkgo biloba L., one of the gymnosperms, using genomic data.•Our results provide strong genomic evidence to support plastid maternal inheritance mode of G. biloba, which is different from most other gymnosperms.•The combination of manually genetic crosses and genomic data is proved to be an efficient way to investigate the inheritance mode of chloroplasts genome in land plants.•The current research also provides a case study for further research of plastid inheritance in gymnosperms using genomic techniques, which will contribute to a better understanding of cytologically uniparental inheritance mode and evolutionary mechanism of plastids in both gymnosperms and angiosperms.
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Affiliation(s)
- Mengxue Feng
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Meixiu Lin
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
| | - Rongjing Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China
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Barra PJ, Duran P, Delgado M, Viscardi S, Claverol S, Larama G, Dumont M, Mora MDLL. Proteomic response to phosphorus deficiency and aluminum stress of three aluminum-tolerant phosphobacteria isolated from acidic soils. iScience 2023; 26:107910. [PMID: 37790272 PMCID: PMC10543181 DOI: 10.1016/j.isci.2023.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/27/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Aluminum (Al)-tolerant phosphobacteria enhance plant growth in acidic soils by improving Al complexing and phosphorus (P) availability. However, the impact of Al stress and P deficiency on bacterial biochemistry and physiology remains unclear. We investigated the single and mutual effects of Al stress (10 mM) and P deficiency (0.05 mM) on the proteome of three aluminum-tolerant phosphobacteria: Enterobacter sp. 198, Enterobacter sp. RJAL6, and Klebsiella sp. RCJ4. Cultivated under varying conditions, P deficiency upregulated P metabolism proteins while Al exposure downregulated iron-sulfur and heme-containing proteins and upregulated iron acquisition proteins. This demonstrated that Al influence on iron homeostasis and bacterial central metabolism. This study offers crucial insights into bacterial behavior in acidic soils, benefiting the development of bioinoculants for crops facing Al toxicity and P deficiency. This investigation marks the first proteomic study on the interaction between high Al and P deficiency in acid soils-adapted bacteria.
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Affiliation(s)
- Patricio Javier Barra
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Paola Duran
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
- Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 4811230, Chile
| | - Mabel Delgado
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sharon Viscardi
- Escuela de la Salud, Campus San Francisco, Universidad Católica de Temuco, Temuco 4811230, Chile
| | - Stéphane Claverol
- Plateforme Protéome, Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Giovanni Larama
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Marc Dumont
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - María de la Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
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Ma P, Liu Y, Wang J, Chen Y, Zhang Z, Zhang T, Wang H. Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications. Int J Biol Macromol 2023; 249:126081. [PMID: 37536404 DOI: 10.1016/j.ijbiomac.2023.126081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.
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Affiliation(s)
- Peizhen Ma
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yumeng Liu
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiahui Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ya Chen
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Haiyan Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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