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Hien VT, Lanh PT, Pham TTP, Tran KN, Duy ND, Hoa NT, Canh NX, Nguyen QH, Kim S, Quyen DV. Isolation and characterization of a novel lytic bacteriophage Pv27 with biocontrol potential against Vibrio parahaemolyticus infections in shrimp. PeerJ 2025; 13:e19421. [PMID: 40352283 PMCID: PMC12063606 DOI: 10.7717/peerj.19421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Accepted: 04/14/2025] [Indexed: 05/14/2025] Open
Abstract
Background Vibrio parahaemolyticus is a major disease-causing species of Vibrio that is pathogenic to both farmed shrimp and humans. With the increasing spread of antibiotic-resistant V. parahaemolyticus strains, bacteriophages (or phages) are considered potential agents for biocontrol as an alternative to antibiotics. In this study, a bacteriophage capable of lysing V. parahaemolyticus, named Pv27, was isolated, characterized, and evaluated for its potential to control Vibrio infections as a natural therapy. Methods Phage Pv27 was isolated using the double-layer agar technique and its morphology was characterized by transmission electron microscopy (TEM). We further assessed the host range specificity, optimal multiplicity of infection (MOI), one-step growth kinetics, and environmental stability of Pv27 under various pH and temperature conditions. The inhibitory activity of Pv27 against V. parahaemolyticus was evaluated in vitro. Finally, genomic analysis of Pv27 was conducted through whole-genome sequencing, followed by functional annotation of open reading frames (ORFs) and phylogenetic analysis. Results Phage Pv27 exhibited a Myovirus-like morphology, characterized by an icosahedral head (92.7 ± 2 nm) and a contractile tail (103 ± 11 nm), and belongs to the class Caudoviricetes. Pv27 demonstrated high lytic activity against its host cells, with a short latent period of approximately 25 minutes and a large burst size of 112 plaque-forming units (PFU) per infected cell. The phage displayed significant tolerance to a wide pH range (from 3 to 11) and remained heat-stable at temperatures up to 60 °C for 90 min. Genetically, Pv27 possesses a circular double-stranded DNA genome spanning 191,395 base pairs, with a G + C content of 35% and comprising 355 open reading frames (ORFs). Remarkably, up to 23 tRNA genes were identified in its genome, while no genes associated with antibiotic resistance, virulence, or lysogeny were detected, suggesting its potential as a valuable biocontrol agent. Results from the VIRIDIC, Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses revealed that Pv27 is closely related to the two known Vibrio phages, phiKT1024 and phiTY18. Several genes associated with enhanced environmental competitiveness were also identified in the Pv27 genome, including those encoding a PhoH-like phosphate starvation-inducible protein and endolysin. Phage Pv27 effectively lyses V. parahaemolyticus highlighting its potential as a biocontrol agent.
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Affiliation(s)
- Vu Thi Hien
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Lanh
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Khang Nam Tran
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Dinh Duy
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Thi Hoa
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Quang Huy Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Seil Kim
- University of Science & Technology (UST), Daejeon, Republic of South Korea
- Korea Research Institute of Standards and Science, Daejeon, Republic of South Korea
| | - Dong Van Quyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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Wang Y, Chen C, Zhou B, Zhang Y, Qin J, Huang J, Li X. Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China. JOURNAL OF HAZARDOUS MATERIALS 2025; 488:137435. [PMID: 39899931 DOI: 10.1016/j.jhazmat.2025.137435] [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: 11/19/2024] [Revised: 01/10/2025] [Accepted: 01/27/2025] [Indexed: 02/05/2025]
Abstract
Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.
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Affiliation(s)
- Yue Wang
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Chaoqi Chen
- School of Resource and Environmental Sciences, Wuhan University, Wuhan 430079, PR China.
| | - Bo Zhou
- Weiming Environmental Molecular Diagnostics (Changshu) Inc., Changshu, Jiangsu Province 215500, PR China
| | - Yu Zhang
- Weiming Environmental Molecular Diagnostics (Changshu) Inc., Changshu, Jiangsu Province 215500, PR China
| | - Jun Qin
- Weiming Environmental Molecular Diagnostics (Changshu) Inc., Changshu, Jiangsu Province 215500, PR China
| | - Jianwen Huang
- Weiming Environmental Molecular Diagnostics (Guangdong) Inc., Foshan, Guangdong Province 528300, PR China
| | - Xiqing Li
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China; Weiming Environmental Molecular Diagnostics (Guangdong) Inc., Foshan, Guangdong Province 528300, PR China.
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Gozashti L, Harringmeyer OS, Hoekstra HE. How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice. Cell Rep 2025; 44:115644. [PMID: 40327505 DOI: 10.1016/j.celrep.2025.115644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 01/08/2025] [Accepted: 04/11/2025] [Indexed: 05/08/2025] Open
Abstract
Large genomic rearrangements, such as chromosomal inversions, can play a key role in evolution, but the mechanisms by which these rearrangements arise remain poorly understood. To study the origins of inversions, we generated chromosome-level de novo genome assemblies for four subspecies of the deer mouse (Peromyscus maniculatus) with known inversion polymorphisms. We identified ∼8,000 inversions, including 47 megabase-scale inversions, that together affect ∼30% of the genome. Analysis of inversion breakpoints suggests that while most small (<1 Mb) inversions arose via ectopic recombination between retrotransposons, large (>1 Mb) inversions are primarily associated with segmental duplications (SDs). Large inversion breakpoints frequently occur near centromeres, which may be explained by an accumulation of retrotransposons in pericentromeric regions driving SDs. Additionally, multiple large inversions likely arose from ectopic recombination between near-identical centromeric satellite arrays located megabases apart, suggesting that centromeric repeats may also facilitate inversions. Together, our results illuminate how repeats give rise to massive shifts in chromosome architecture.
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Affiliation(s)
- Landen Gozashti
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Olivia S Harringmeyer
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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104
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Herbert J, Thompson S, Beckett AH, Robson SC. Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies. ENVIRONMENTAL MICROBIOME 2025; 20:47. [PMID: 40325409 PMCID: PMC12054170 DOI: 10.1186/s40793-025-00704-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 04/08/2025] [Indexed: 05/07/2025]
Abstract
INTRODUCTION Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes. AIM AND METHODS Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community. RESULTS Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits. CONCLUSION Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20 + sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT's adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.
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Affiliation(s)
- Josephine Herbert
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK
- Institute of Life Sciences and Healthcare, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK
| | - Stanley Thompson
- Institute of Life Sciences and Healthcare, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Angela H Beckett
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK
- Institute of Life Sciences and Healthcare, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK
| | - Samuel C Robson
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK.
- Institute of Life Sciences and Healthcare, University of Portsmouth, Portsmouth, Hampshire, PO1 2DT, UK.
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A J, Reddy B, Eapen SJ, Javed M, M A, A K. Pathogenomics Insights into Phytophthora capsici and Phytophthora tropicalis -Sibling Species Causing Black Pepper Foot Rot: Genomic Architecture, Metabolic Pathways, and Effector Diversity. Gene 2025; 947:149328. [PMID: 39952485 DOI: 10.1016/j.gene.2025.149328] [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: 12/26/2024] [Revised: 02/08/2025] [Accepted: 02/10/2025] [Indexed: 02/17/2025]
Abstract
Foot rot disease in black pepper, caused by Phytophthora species, is a major threat to cultivation. Along with the well-known Phytophthora capsici, a newly identified species, Phytophthora tropicalis, has also been implicated. Comparative genome analysis of P. capsici 05-06 from Kerala (80.51 Mb, 626 scaffolds) and P. tropicalis 98-93 from Karnataka (73.54 Mb, 302 scaffolds) revealed similar GC content (∼50.5%) and gene counts (19,639 and 17,716, respectively). Genomic ANI analysis clustered them with P. capsici LT1534-B, suggesting a species complex. Both species contain transposable elements (19.35% and 21.31%), indicating adaptive evolution. Pathway mapping highlights roles in carbohydrate metabolism, carbohydrate-active enzymes (CAZymes: 575 and 566), energy production, effector biosynthesis, and molecular signaling. The presence of unique protein families and shared orthologous genes underscores their pathogenic potential. These findings enhance understanding of their evolution and pathogenicity, aiding in the development of targeted management strategies for black pepper foot rot.
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Affiliation(s)
- Jeevalatha A
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India.
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
| | - Santhosh J Eapen
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Mohammed Javed
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
| | - Anandaraj M
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Kumar A
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India.
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Becchimanzi A, Zimowska B, Calandrelli MM, De Masi L, Nicoletti R. Genome Sequencing of a Fusarium Endophytic Isolate from Hazelnut: Phylogenetic and Metabolomic Implications. Int J Mol Sci 2025; 26:4377. [PMID: 40362614 PMCID: PMC12072968 DOI: 10.3390/ijms26094377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Revised: 04/27/2025] [Accepted: 05/03/2025] [Indexed: 05/15/2025] Open
Abstract
This study reports on the whole genome sequencing of the hazelnut endophytic Fusarium isolate Hzn5 from Poland. It was identified as a member of the Fusarium citricola species complex based on a phylogenetic analysis which also pointed out that other hazelnut isolates, previously identified as F. lateritium and F. tricinctum, actually belong to this species complex. Genome annotation allowed the mapping of 4491 different protein sequences to the genome assembly. A further in silico search for their potential biosynthetic activity showed that predicted genes are involved in 1110 metabolic pathways. Moreover, the analysis of the genome sequence carried out in comparison to another isolate, previously identified as an agent of hazelnut gray necrosis in Italy, revealed a homology to several regions containing biosynthetic gene clusters for bioactive secondary metabolites. The resulting indications for the biosynthetic aptitude concerning some emerging mycotoxins, such as the enniatins and culmorin, should be taken into consideration with reference to the possible contamination of hazelnuts and derived products.
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Affiliation(s)
- Andrea Becchimanzi
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Beata Zimowska
- Department of Plant Protection, University of Life Sciences, 20-069 Lublin, Poland;
| | - Marina Maura Calandrelli
- Research Institute on Terrestrial Ecosystems (IRET), National Research Council (CNR), 80131 Napoli, Italy;
| | - Luigi De Masi
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), 80055 Portici, Italy
| | - Rosario Nicoletti
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics, 81100 Caserta, Italy;
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107
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Rodríguez-Santiago J, Alvarado-Delgado A, Rodríguez-Medina N, Garza-González E, Tellez-Sosa J, Duarte-Zambrano L, Nava-Domínguez N, Sohlenkamp C, Vences-Guzmán MA, López-Jácome LE, Morfin-Otero R, Rodriguez-Noriega E, Hernández-Castro R, Mireles-Dávalos C, Becerril-Vargas E, Mena-Ramírez JP, Cruz-García E, Garza-Ramos U. Colistin-resistant Klebsiella pneumoniae species complex: The scenario in Mexico. J Glob Antimicrob Resist 2025:S2213-7165(25)00098-0. [PMID: 40334840 DOI: 10.1016/j.jgar.2025.04.024] [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: 01/29/2025] [Revised: 04/04/2025] [Accepted: 04/25/2025] [Indexed: 05/09/2025] Open
Abstract
OBJECTIVES Characterize the colistin-resistance mechanisms, determine the molecular epidemiology, and genomic traits of the colistin-resistant Klebsiella pneumoniae species complex (ColR-KpSC) clinical isolates in Mexico. METHODS In this study, 1,539 KpSC isolates were collected in Mexico from 2016 to 2021. We conducted a comprehensive analysis that included microbiological, genetic, molecular, and genomic approaches. RESULTS A total of 50 isolates (3.25%) were colistin-resistant; of which 49 (98%) corresponded to K. pneumoniae and 1 (2%) to Klebsiella quasipneumoniae. Whole genome sequencing of these resistant isolates revealed intra- and inter-hospital dissemination, and the mgrB inactivation was the main resistance mechanism. Some KpSC isolates carried plasmid-borne mcr-1 gene found in Escherichia coli from piglets in Mexico. The colistin-resistant isolates presented a high prevalence of ESBL- and NDM-1 genes, and one hypervirulent strain also produced ESBL CTX-M-15. CONCLUSION This study provides a comprehensive snapshot of the epidemiology of ColR-KpSC in Mexico, highlighting a high prevalence of NDM-1 carbapenemase among ColR-KpSC isolates; this is in line with previous reports identifying NDM-1 as the most prevalent carbapenemase in K. pneumoniae species complex. This problem is particularly concerning in Mexico because of the lack of therapeutic options.
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Affiliation(s)
- Jonathan Rodríguez-Santiago
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México; Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Resistencia Antimicrobiana, Cuernavaca, Morelos, México; Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Chiapas, Tuxtla Gutiérrez, Chiapas, México
| | - Alejandro Alvarado-Delgado
- Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Resistencia Antimicrobiana, Cuernavaca, Morelos, México
| | - Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Resistencia Antimicrobiana, Cuernavaca, Morelos, México
| | - Elvira Garza-González
- Facultad de Medicina, Universidad Autónoma de Nuevo León. Monterrey, Nuevo León, México
| | - Juan Tellez-Sosa
- Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Infeccciones Crónicas y Cancer, Cuernavaca, Morelos, México
| | - Luis Duarte-Zambrano
- Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Resistencia Antimicrobiana, Cuernavaca, Morelos, México
| | - Neli Nava-Domínguez
- Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Resistencia Antimicrobiana, Cuernavaca, Morelos, México
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Miguel A Vences-Guzmán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | | | | | | | | | | | | | - Juan Pablo Mena-Ramírez
- Hospital General de Zona No. 21 IMSS, Laboratorio de Microbiología, Tepatitlán de Morelos, Jalisco, Mexico
| | | | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública, Centro de Investigación sobre Enfermedades Infecciosas, Grupo de Investigación y Docencia en Resistencia Antimicrobiana, Cuernavaca, Morelos, México.
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108
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Quah FX, Almeida MV, Blumer M, Yuan CU, Fischer B, See K, Jackson B, Zatha R, Rusuwa B, Turner GF, Santos ME, Svardal H, Hemberg M, Durbin R, Miska E. Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements. Genome Res 2025; 35:1094-1107. [PMID: 40210437 PMCID: PMC12047535 DOI: 10.1101/gr.279674.124] [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: 06/16/2024] [Accepted: 02/06/2025] [Indexed: 04/12/2025]
Abstract
Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)-based studies have revealed little sequence difference, with 0.1%-0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference genome and ignored the contribution of larger-scale structural variants (SVs). We constructed a pangenome graph that integrates six new and two existing long-read genome assemblies of Lake Malawi haplochromine cichlids. This graph intuitively represents complex and nested variation between the genomes and reveals that the SV landscape is dominated by large insertions, many exclusive to individual assemblies. The graph incorporates a substantial amount of extra sequence across seven species, the total size of which is 33.1% longer than that of a single cichlid genome. Approximately 4.73% to 9.86% of the assembly lengths are estimated as interspecies structural variation between cichlids, suggesting substantial genomic diversity underappreciated in SNP studies. Although coding regions remain highly conserved, our analysis uncovers a significant proportion of SV sequences as transposable element (TE) insertions, especially DNA, LINE, and LTR TEs. These findings underscore that the cichlid genome is shaped both by small-nucleotide mutations and large, TE-derived sequence alterations, both of which merit study to understand their interplay in cichlid evolution.
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Affiliation(s)
- Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Moritz Blumer
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Kirsten See
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Ben Jackson
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Richard Zatha
- Department of Biological Sciences, University of Malawi, P.O. Box 280, Zomba, Malawi
| | - Bosco Rusuwa
- Department of Biological Sciences, University of Malawi, P.O. Box 280, Zomba, Malawi
| | - George F Turner
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2TH, United Kingdom
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Hannes Svardal
- Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Martin Hemberg
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Eric Miska
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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He S, Ding Q, Wu W, Zhang Y, Kang Y, Meng Y, Zhu S, Wu J. Unraveling the genetic traits and functional diversity of the pan-genome in Pantoea dispersa. BMC Genomics 2025; 26:435. [PMID: 40316932 PMCID: PMC12046954 DOI: 10.1186/s12864-025-11625-7] [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: 11/22/2024] [Accepted: 04/22/2025] [Indexed: 05/04/2025] Open
Abstract
BACKGROUND Medical devices are crucial in modern healthcare, but commonly used clinical tools such as cotton swabs can be easily contaminated by microorganisms (such as Pantoea), becoming vectors for pathogens and leading to patient infections or more severe outcomes. Despite the dual nature of the Pantoea that has garnered significant attention, research investigating Pantoea dispersa (P. dispersa) remains limited. This study conducted a pan-genome analysis of three isolates and 57 P. dispersa strains from NCBI to investigate their evolutionary relationships, population structure, and functional characteristics. RESULTS Whole-genome analysis revealed high genomic diversity among 60 strains of P. dispersa, identifying 6,791 orthologous gene clusters (OGs), with core genes accounting for 45.1% and accessory genes accounting for 54.9%. Additionally, 2,185 gene clusters were not annotated in the reference genome. Further analysis demonstrated that 782 gene clusters were annotated as 406 VFs that were unevenly distributed among different strains and primarily associated with nutritional or metabolic factors, motility, and immune modulation. This study also identified four VFs genes related to the type III secretion system (T3SS) and observed some VFs present only in specific genetic clusters. In the analysis of antibiotic resistance genes (ARGs), 12 ARGs were identified, with nine being highly conserved across all isolates, and resistance mechanisms primarily involved antibiotic efflux and antibiotic target alteration. Secondary metabolite analysis identified 289 gene clusters, with 23 matching known gene clusters, while the rest were new discoveries, including arylpolyene, NRPS, and terpene types. These results reveal the complex virulence factors (VFs) and secondary metabolite genes in P. dispersa, providing significant insights into its genetic diversity and biological significance. CONCLUSION This study provides the first pan-genome framework for P. dispersa, along with a map of its VFs, ARGs, and secondary metabolite gene clusters. This study provides a deep insight into the genetic diversity and potential biological significance of P. dispersa, offering valuable references for leveraging its unique strain characteristics and metabolic capabilities in industrial production and clinical therapy.
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Affiliation(s)
- Shiyao He
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Qi Ding
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Wenting Wu
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Yun Zhang
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Yan Kang
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Yang Meng
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Sirui Zhu
- Jiangxi Medical Device Testing Center, Nanchang, Jiangxi Province, 330029, PR China
| | - Jinyuan Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, PR China.
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Gravey F, Sévin C, Langlois B, Maillard K, Foucher N, Duquesne F, Léon A, Le Hello S, Petry S. Misidentification of Raoultella spp. (R. terrigena, R. planticola) and Klebsiella spp. (K. variicola, K. grimontii) as Klebsiella pneumoniae: Retrospective study of a necropsy-associated bacterial collection from horses. Vet Microbiol 2025; 304:110497. [PMID: 40156970 DOI: 10.1016/j.vetmic.2025.110497] [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: 10/09/2024] [Revised: 03/12/2025] [Accepted: 03/25/2025] [Indexed: 04/01/2025]
Abstract
Misidentifications as Klebsiella pneumoniae were observed during a French retrospective study of a necropsy-associated K. pneumoniae bacterial collection from horses. Accordingly, the present study aimed to further characterise the 12 Raoultella spp. and Klebsiella spp. strains involved in these misidentifications. The strains were identified and characterised using the Api 20E system, K. pneumoniae PCR detection, matrix-assisted laser desorption/ionisation time-of-flight mass spectroscopy and whole-genome sequencing. Antimicrobial susceptibilities were tested by the disc diffusion method with a panel of 40 antibiotics. Thus, misidentifications as K. pneumoniae mainly concerned Raoultella spp. (R. terrigena, R. planticola) rather than Klebsiella spp. (K. variicola, K. grimontii), with a dominance of R. terrigena. Among the 12 strains, only K. grimontii was multi-drug resistant and none were considered hypervirulent. MALDI-TOF was sufficient to avoid misidentification but commercial spectra databases should be expanded with K. grimontii and R. terrigena reference spectra to improve identification accuracy. This is probably (i) the first report of K. grimontii and R. planticola isolations from horses and (ii) the second report of R. terrigena and K. variicola isolations from horses.
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Affiliation(s)
- Francois Gravey
- Université de Caen Normandie, Université de Rouen Normandie, INSERM, DYNAMICURE UMR1311, CHU Caen, Department of Infectious Agents, Bacteriology, Caen 14000, France; CHU Caen, Department of Infectious Agents, Bacteriology, Caen 14000, France
| | - Corinne Sévin
- ANSES, Normandy Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Bénédicte Langlois
- Université de Caen Normandie, Université de Rouen Normandie, INSERM, DYNAMICURE UMR1311, CHU Caen, Department of Infectious Agents, Bacteriology, Caen 14000, France
| | | | - Nathalie Foucher
- ANSES, Normandy Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Fabien Duquesne
- ANSES, Normandy Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | | | - Simon Le Hello
- Université de Caen Normandie, Université de Rouen Normandie, INSERM, DYNAMICURE UMR1311, CHU Caen, Department of Infectious Agents, Bacteriology, Caen 14000, France; CHU Caen, Department of Infectious Agents, Bacteriology, Caen 14000, France
| | - Sandrine Petry
- ANSES, Normandy Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France.
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Slavinska A, Jauneikaite E, Meškytė U, Kirkliauskienė A, Misevič A, Petrutienė A, Kuisiene N. Genomic characterization of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021. Microb Genom 2025; 11. [PMID: 40392696 DOI: 10.1099/mgen.0.001410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025] Open
Abstract
Listeria monocytogenes is a saprophytic gram-positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania, and up to 20 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinical L. monocytogenes strains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasive L. monocytogenes and perform in-depth characterization of strains isolated from patients with neuroinfections through whole-genome sequencing. A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021 : 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, 5 (7.1%) from wounds, 1 (1.4%) from pleural fluid and 1 (1.4%) from a brain abscess. Two phylogenetic lineages were identified-I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)-along with three serogroups-IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2) and singletons for ST37, ST451 and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6-48 core SNPs from reference and 0, 4 or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly available L. monocytogenes genomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified. Our study highlights the complementary value of whole-genome sequencing in routine PCR-based surveillance in Lithuania. This is the first study to characterize and compare genomes for L. monocytogenes associated with neuroinfections in Lithuania using whole-genome sequencing. The retrospective detection of the ST155 clone underscores the need for a review and strengthening of epidemiological surveillance strategies in clinical and non-clinical settings in Lithuania.
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Affiliation(s)
- Anželika Slavinska
- Department of Microbiology and Biotechnology, Institute of Biosciences of Vilnius University Life Sciences Centre, 10257 Vilnius, Lithuania
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Ugnė Meškytė
- Department of Microbiology and Biotechnology, Institute of Biosciences of Vilnius University Life Sciences Centre, 10257 Vilnius, Lithuania
| | - Agnė Kirkliauskienė
- Faculty of Medicine, Institute of Biomedical science, Vilnius University, 03101 Vilnius, Lithuania
| | - Adam Misevič
- Faculty of Medicine, Institute of Biomedical science, Vilnius University, 03101 Vilnius, Lithuania
| | - Aurelija Petrutienė
- Department of Clinical Investigations of the National Public Health Surveillance Laboratory, 10210 Vilnius, Lithuania
| | - Nomeda Kuisiene
- Department of Microbiology and Biotechnology, Institute of Biosciences of Vilnius University Life Sciences Centre, 10257 Vilnius, Lithuania
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Parzygnat JL, Crespo R, Fosnaught M, Muyyarrikkandy M, Hull D, Harden L, Thakur S. Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States. Foodborne Pathog Dis 2025; 22:322-331. [PMID: 38635963 DOI: 10.1089/fpd.2023.0181] [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: 04/20/2024] Open
Abstract
Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.
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Affiliation(s)
- Jessica L Parzygnat
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Rocio Crespo
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary Fosnaught
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Muhammed Muyyarrikkandy
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brooking, South Dakota, USA
| | - Dawn Hull
- Bacterial Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lyndy Harden
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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113
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Calcagnile M, Quarta E, Sicuro A, Pecoraro L, Schiavone R, Tredici SM, Talà A, Corallo A, Verri T, Stabili L, Alifano P. Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota. MICROBIAL ECOLOGY 2025; 88:37. [PMID: 40310547 PMCID: PMC12045831 DOI: 10.1007/s00248-025-02531-2] [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: 04/07/2025] [Accepted: 04/08/2025] [Indexed: 05/02/2025]
Abstract
In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.
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Affiliation(s)
- Matteo Calcagnile
- Department of Experimental Medicine (DiMeS), University of Salento, Via Monteroni, 73100, Lecce, Italy
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Elisa Quarta
- Institute of Water Research (IRSA), Istituto Talassografico "A. Cerruti", National Research Council (CNR), Via Roma 3, 74123, Taranto, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Alessandro Sicuro
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Laura Pecoraro
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Roberta Schiavone
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | | | - Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Angelo Corallo
- Department of Experimental Medicine (DiMeS), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Loredana Stabili
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Monteroni, 73100, Lecce, Italy.
- Institute of Water Research (IRSA), Istituto Talassografico "A. Cerruti", National Research Council (CNR), Via Roma 3, 74123, Taranto, Italy.
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy.
| | - Pietro Alifano
- Department of Experimental Medicine (DiMeS), University of Salento, Via Monteroni, 73100, Lecce, Italy
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Ding J, Zhang M, Chang J, Hu Z, He P, Wang J, Feng L. Characterization of a multidrug-resistant hypovirulent ST1859-KL35 klebsiella quasipneumoniae subsp. similipneumoniae strain co-harboring tmexCD2-toprJ2 and bla KPC-2. J Glob Antimicrob Resist 2025; 42:253-261. [PMID: 40113085 DOI: 10.1016/j.jgar.2025.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 02/18/2025] [Accepted: 03/11/2025] [Indexed: 03/22/2025] Open
Abstract
OBJECTIVES The rise of multidrug-resistant (MDR) Klebsiella pneumoniae is a significant public health threat. Klebsiella quasipneumoniae is often misidentified as K. pneumoniae, and its genetic and virulence traits remain underexplored. This study characterizes the genomic and phenotypic features of a K. quasipneumoniae subsp. similipneumoniae strain (KP24). METHODS Antibiotic susceptibility was tested using microbroth dilution assay. Virulence was evaluated through serum killing assay and Galleria mellonella infection model. Whole genome sequencing (WGS) and bioinformatics analysis determined sequence typing, resistance profiles, and plasmid types. Conjugation assays assessed plasmid transferability, while phylogenetic analysis explored genetic relationships. RESULTS KP24 exhibited an MDR phenotype, including resistance to carbapenems, ceftazidime/avibactam, and tigecycline. KP24 showed significantly higher serum survival and G. mellonella lethality than ATCC700603, though it was less virulent than the hypervirulent strain NUTH-K2044. WGS identified KP24 as ST1859 and KL35, harboring the aerobactin virulence gene cluster (iucABCDiutA) and multiple resistance genes, including tmexCD2-toprJ2, blaKPC-2, blaOXA-10, blaIMP-4, and qnrS1. Notably, the tmexCD2-toprJ2 and blaKPC-2 genes were located on the same plasmid (pKP24-1), an uncommon co-existence. Conjugation assays confirmed the independent transferability of pKP24-1 to Escherichia coli J53. Phylogenetic analysis revealed that ST1859 forms a distinct monoclade with low genetic diversity, closely related to ST334, suggesting regional expansion and potential global dissemination. CONCLUSIONS KP24 represents a hypovirulent yet multidrug-resistant strain of K. quasipneumoniae subsp. similipneumoniae, with a concerning combination of virulence and resistance determinants. The co-location of tmexCD2-toprJ2 and blaKPC-2 on a transferable plasmid highlights the potential for horizontal gene transfer of critical resistance mechanisms.
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Affiliation(s)
- Jiawei Ding
- Department of Medical Laboratory, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China
| | - Mengying Zhang
- Department of Blood Transfusion, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China
| | - Jiyong Chang
- Department of Medical Laboratory, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China
| | - Zidan Hu
- Department of Medical Laboratory, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China
| | - Pei He
- Department of Medical Laboratory, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China
| | - Jia Wang
- Department of Medical Laboratory, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China
| | - Lei Feng
- Department of Medical Laboratory, Yan'an Hospital of Kunming city, Kunming City, Yunnan Province, People's Republic of China.
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115
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Sliti A, Kim RH, Lee D, Shin JH. Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules. Microb Pathog 2025; 202:107405. [PMID: 40024538 DOI: 10.1016/j.micpath.2025.107405] [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: 10/25/2024] [Revised: 02/13/2025] [Accepted: 02/20/2025] [Indexed: 03/04/2025]
Abstract
Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.
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Affiliation(s)
- Amani Sliti
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ryeong-Hui Kim
- NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dokyung Lee
- Department of Integrative Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea; Department of Livestock Microbial Ecology, University of Hohenheim, Emil-Wolff-Straße 8, 70599, Stuttgart, Germany
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea; NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea; Department of Integrative Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea.
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116
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Wang T, Ahmad S, Cruz-Lebrón A, Ernst SE, Olivos Caicedo KY, Jeong Y, Binion B, Mbuvi P, Dutta D, Fernandez-Materan FV, Breister AM, Tang E, Lee JW, Kang JD, Harris SC, Ikegawa S, Gaskins HR, Erdman JW, Yang G, Cann I, Daniel SL, Hylemon PB, Anantharaman K, Bernardi RC, Alves JMP, Sfanos KS, Irudayaraj J, Ridlon JM. An expanded metabolic pathway for androgen production by commensal bacteria. Nat Microbiol 2025; 10:1084-1098. [PMID: 40259019 DOI: 10.1038/s41564-025-01979-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 03/06/2025] [Indexed: 04/23/2025]
Abstract
Commensal bacteria have been implicated in the modulation of steroid hormones, including circulating androgen levels in the host. However, the microbial genetic pathways involved in androgen production have not been fully characterized. Here we identify a microbial gene encoding an enzyme that catalyses the conversion of androstenedione to epitestosterone in the gut microbiome member Clostridium scindens and named this gene desF. We demonstrate that epitestosterone impacts androgen receptor-dependent prostate cancer cell proliferation in vitro. We also demonstrate that stool desF levels are elevated in patients with prostate cancer who are unresponsive to abiraterone/prednisone therapy. Bacterial isolates from urine or prostatectomy tissue produced androgens, and 17β-hydroxysteroid dehydrogenase activity encoded by the desG gene was detected in strains of the urinary tract bacterium Propionimicrobium lymphophilum. Furthermore, we demonstrate that urinary androgen-producing bacterial strains can promote prostate cancer cell growth through metabolism of cortisol and prednisone. Abiraterone, which targets host desmolase (CYP17A1), a rate-limiting enzyme in adrenal steroidogenesis, does not inhibit bacterial desmolase (DesAB), whereas the conversion of prednisone to androgens by DesAB, DesF and DesG drives androgen-receptor-dependent prostate cancer cell line proliferation in vitro. Our results are a significant advance in steroid microbiology and highlight a potentially important role for gut and urinary tract bacteria in host endocrine function and drug metabolism.
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Affiliation(s)
- Taojun Wang
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
| | - Saeed Ahmad
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA
| | - Angélica Cruz-Lebrón
- Departments of Pathology, Oncology, and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E Ernst
- Departments of Pathology, Oncology, and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Yoon Jeong
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA
| | - Briawna Binion
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
| | - Pauline Mbuvi
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA
- Department of Urology, Carle Foundation Hospital, Urbana, IL, USA
| | - Debapriya Dutta
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA
- Department of Urology, Carle Foundation Hospital, Urbana, IL, USA
| | - Francelys V Fernandez-Materan
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
| | - Adam M Breister
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth Tang
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jae Won Lee
- Department of Biotechnology, Sungshin Women's University, Seoul, South Korea
| | - Jason D Kang
- Stravitz-Sanyal Institute for Liver Disease & Metabolic Health, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | - Spencer C Harris
- Stravitz-Sanyal Institute for Liver Disease & Metabolic Health, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | | | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John W Erdman
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Glen Yang
- Department of Urology, Carle Foundation Hospital, Urbana, IL, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven L Daniel
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Phillip B Hylemon
- Stravitz-Sanyal Institute for Liver Disease & Metabolic Health, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | | | | | - João M P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Karen S Sfanos
- Departments of Pathology, Oncology, and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Joseph Irudayaraj
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
- Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Song WL, Chen BZ, Feng L, Chen G, He SM, Hao B, Zhang GH, Dong Y, Yang SC. Telomere-to-telomere genome assembly and 3D chromatin architecture of Centella asiatica insight into evolution and genetic basis of triterpenoid saponin biosynthesis. HORTICULTURE RESEARCH 2025; 12:uhaf037. [PMID: 40236733 PMCID: PMC11997435 DOI: 10.1093/hr/uhaf037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 01/23/2025] [Indexed: 04/17/2025]
Abstract
Centella asiatica is renowned for its medicinal properties, particularly due to its triterpenoid saponins, such as asiaticoside and madecassoside, which are in excess demand for the cosmetic industry. However, comprehensive genomic resources for this species are lacking, which impedes the understanding of its biosynthetic pathways. Here, we report a telomere-to-telomere (T2T) C. asiatica genome. The genome size is 438.12 Mb with a contig N50 length of 54.12 Mb. The genome comprises 258.87 Mb of repetitive sequences and 25 200 protein-coding genes. Comparative genomic analyses revealed C. asiatica as an early-diverging genus within the Apiaceae family with a single whole-genome duplication (WGD, Apiaceae-ω) event following the ancient γ-triplication, contrasting with Apiaceae species that exhibit two WGD events (Apiaceae-α and Apiaceae-ω). We further constructed 3D chromatin structures, A/B compartments, and topologically associated domains (TADs) in C. asiatica leaves, elucidating the influence of chromatin organization on expression WGD-derived genes. Additionally, gene family and functional characterization analysis highlight the key role of CasiOSC03 in α-amyrin production while also revealing significant expansion and high expression of CYP716, CYP714, and UGT73 families involved in asiaticoside biosynthesis compared to other Apiaceae species. Notably, a unique and large UGT73 gene cluster, located within the same TAD, is potentially pivotal for enhancing triterpenoid saponin. Weighted gene coexpression network analysis (WGCNA) further highlighted the pathways modulated in response to methyl jasmonate (MeJA), offering insights into the regulatory networks governing saponin biosynthesis. This work not only provides a valuable genomic resource for C. asiatica but also sheds light on the molecular mechanisms driving the biosynthesis of pharmacologically important metabolites.
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Affiliation(s)
- Wan-ling Song
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
| | - Bao-zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
- State Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kumming 650201, China
| | - Lei Feng
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
| | - Geng Chen
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
| | - Si-mei He
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
| | - Bing Hao
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
| | - Guang-hui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
| | - Yang Dong
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Sheng-chao Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National-Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan 650106, China
- Honghe University, Mengzi, Yunnan 661199, China
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Al-Marzooq F, Ghazawi A, Allam M, Collyns T. Deciphering the genetic context of the emerging OXA-484-producing carbapenem-resistant Escherichia coli from ST167 high-risk clone in the United Arab Emirates. Eur J Clin Microbiol Infect Dis 2025; 44:1155-1166. [PMID: 40019666 DOI: 10.1007/s10096-025-05082-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2025] [Accepted: 02/21/2025] [Indexed: 03/01/2025]
Abstract
PURPOSE The evolution of new carbapenemase variants is alarming. We aimed to investigate the genetic context and molecular epidemiology of the emerging OXA-484 carbapenemase in the United Arab Emirates, to decipher its resistance mechanisms and evolutionary relationships. METHODS Antimicrobial susceptibility testing was performed for an E. coli isolate recovered from an intrauterine contraceptive device of a patient returning to the UAE after a trip to Pakistan. Whole genome sequencing was used to characterize the genetic environment of blaOXA-484, resistance and virulence determinants. Southern blotting was used to localize OXA-484 gene. Phylogenetic analysis established the sequence type (ST) and used to investigate relationships with global strains, and differences from other OXA-48-like types. RESULTS The strain demonstrated selective resistance against ertapenem while maintaining susceptibility to imipenem and meropenem. OXA-484 exhibited R214G substitution affecting the enzyme's activity and distinguishing it from closely related variants like OXA-181 (214R) and OXA-232 (214 S). blaOXA-484 was located on two non-conjugative plasmids (∼ 65 and 100 kb) within a genetic environment containing multiple insertion sequences. It belonged to the high-risk clone ST167, recognized for its enhanced capacity to acquire and maintain resistance determinants. The gene was mostly prevalent in the Western part of the world with limited distribution in the Middle East. CONCLUSION This study presents the first comprehensive characterization of OXA-484-producing E. coli ST167 in the UAE. The presence of blaOXA-484 in high-risk clone warrants concern on its dissemination potential and underscores the importance of genomic surveillance and targeted infection control to prevent the spread of emerging resistance determinants.
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Affiliation(s)
- Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box No. 15551, Al Ain, United Arab Emirates.
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box No. 15551, Al Ain, United Arab Emirates
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Garrido-Sanz D, Keel C. Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation. Nat Microbiol 2025; 10:1130-1144. [PMID: 40140705 PMCID: PMC12055584 DOI: 10.1038/s41564-025-01973-1] [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: 10/22/2024] [Accepted: 02/26/2025] [Indexed: 03/28/2025]
Abstract
Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.
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Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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Newstead L, Smith-Zaitlik T, Kelly C, Roberts E, Street S, Paterson G. Genomic characterization of Pseudomonas aeruginosa from canine otitis highlights the need for a One Health approach to this opportunistic pathogen. Microb Genom 2025; 11:001407. [PMID: 40310270 PMCID: PMC12046095 DOI: 10.1099/mgen.0.001407] [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: 10/10/2024] [Accepted: 04/03/2025] [Indexed: 05/02/2025] Open
Abstract
In humans, Pseudomonas aeruginosa is well known as a prominent opportunistic pathogen associated with antimicrobial resistance (AMR), which presents a major challenge to successful treatment. This is also the case in animals, particularly in companion dogs where P. aeruginosa is a common cause of otitis. Despite its clinical significance, little data are available on the genomics and epidemiology of P. aeruginosa in dogs. To address this, we have genome-sequenced 34 canine otitis P. aeruginosa isolates from a veterinary referral hospital and analysed these along with a further 62 publicly available genomes from canine isolates. Phylogenetic analysis revealed that all three P. aeruginosa phylogroups, A-C, are represented amongst a diverse bacterial population isolated from dogs. We identify examples of persistent or recurrent infection by the same strain of up to 309 days between sampling, demonstrating the difficulty of successfully eradicating infection. Isolates encoded a variety of AMR genes with genomic and phenotypic AMR correlating poorly for β-lactams but showing complete concordance between fluoroquinolone resistance and quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV. Pangenome-wide analysis between 80 canine otitis isolates (34 newly sequenced here and a further 46 publicly available) and a reference collection of 491 human isolates found no genes which were over-represented or specific to either host species, indicating similar strains infect both humans and dogs. This agrees with the sharing of multilocus sequence types between dogs and humans, including the isolation here of ST235 from three dogs, a lineage prominent among the multidrug resistant (MDR) and extensively drug-resistant (XDR) international high-risk clones of P. aeruginosa causing human infections. The presence of such 'high-risk' clones in companion dogs is concerning given their potential impact on animal health and the potential for zoonotic spread. These data provide new insight into this difficult-to-treat veterinary pathogen and promote the need for a One Health approach to tackling it.
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Affiliation(s)
- L. Newstead
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK
| | - T. Smith-Zaitlik
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK
| | - C. Kelly
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK
| | - E. Roberts
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK
| | - S. Street
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK
| | - G.K. Paterson
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK
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121
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Worden P, Webster A, Gandhi K, Gupta R, Deutscher AT, Hornitzky M, Bogema DR. Genomic diversity and tracing of Paenibacillus larvae in Australia: implications for American foulbrood outbreak surveillance in low-diversity populations. Microb Genom 2025; 11. [PMID: 40327033 DOI: 10.1099/mgen.0.001374] [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: 05/07/2025] Open
Abstract
Paenibacillus larvae is the causative agent of American foulbrood (AFB) in honeybees (Apis mellifera) and a devastating pathogen for honey and pollination industries worldwide. Despite this threat, a genomic survey of P. larvae has not been attempted within Australia. To examine the diversity of Australian populations, we sequenced 368 P. larvae genomes sourced primarily from south-eastern Australia. Multilocus sequencing typing analysis identified only 4 sequence types across all 368 samples, with 2 sequence types (ST18 and ST5) representing 96% of all isolates. In comparison to European-sourced P. larvae, sequences revealed much less genetic diversity in Australian isolates. However, Australian genotypes were very similar to those found in New Zealand populations. All Australian isolates were identified as enterobacterial repetitive intergenic consensus (ERIC) type I. To determine the feasibility of a genomic tracing system in a low-diversity genetic background, we investigated core-genome SNP (cgSNP) genotyping of isolates from a single beekeeper and from isolates across multiple apiaries and sample sites. We identified highly related cgSNP clusters, one with known epidemiological links, but another highly related cluster spanned several decades. Results strongly suggest that cgSNP analysis does have the discriminatory power to assist in the trace-forward and trace-back of AFB outbreaks, but importantly, the inclusion of background sequences and careful consideration of multiple analysis methods are required to avoid erroneous conclusions.
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Affiliation(s)
- Paul Worden
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, 17 Broadway, Ultimo, NSW, Australia
| | - Ashlea Webster
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Khushbu Gandhi
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Risha Gupta
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Ania T Deutscher
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Michael Hornitzky
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Daniel Ross Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, 17 Broadway, Ultimo, NSW, Australia
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Vasilchenko AS, Lukyanov DA, Dilbaryan DS, Usachev KS, Poshvina DV, Taldaev AK, Nikandrova AA, Imamutdinova AN, Garaeva NS, Bikmullin AG, Klochkova EA, Rusanov AL, Romashin DD, Luzgina NG, Osterman IA, Sergiev PV, Teslya AV. Macrolactin a is an inhibitor of protein biosynthesis in bacteria. Biochimie 2025; 232:25-34. [PMID: 39826886 DOI: 10.1016/j.biochi.2025.01.003] [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: 11/08/2024] [Revised: 01/10/2025] [Accepted: 01/14/2025] [Indexed: 01/22/2025]
Abstract
Macrolactin A (McA) is a secondary metabolite produced by Bacillus species. It has been known for its antimicrobial properties since the late 1980s, although the exact mechanism of its antibacterial activity remains unknown. In this study, we have found that McA is an inhibitor of protein synthesis in bacteria. Our conclusion is based on the results obtained by in vivo and in vitro bioreporter systems. We demonstrated that the inhibitory activity of McA is independent of bacterial species. However, the concentration of McA required to inhibit protein synthesis in the E. coli cell-free translational model was found to be 50 times lower than the concentration required in the S. aureus cell-free translational model. To investigate the mechanism of McA's inhibitory activity, we conducted a toe-printing assay, sequenced and annotated the genomes of McA-resistant Bacillus pumilus McAR and its parental strain. The results showed that McA inhibits the initial step of the elongation phase of protein synthesis. We identified single and multiple nucleotide polymorphisms in the gene encoding the translation elongation factor Tu (EF-Tu). Molecular modeling showed that the McA molecule can form non-covalent bonds with amino acids at the interface of domains 1 and 2 of EF-Tu. A cross-resistance assay was conducted using kirromycin on B. pumilus McAR. The results confirmed the assumption that McA has a mode of action similar to that of other elfamycin-like antibiotics (targeting EF-Tu). Overall, our study addresses a significant gap in our understanding of the mechanism of action of McA, a representative member of the macrolide antibiotics.
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Affiliation(s)
- Alexey S Vasilchenko
- Laboratory of Antimicrobial Resistance, Institute of Ecological and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia.
| | - Dmitry A Lukyanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, 121205, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Diana S Dilbaryan
- Laboratory of Antimicrobial Resistance, Institute of Ecological and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia
| | - Konstantin S Usachev
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center of Russian Academy of Sciences, 420111, Kazan, Russia
| | - Darya V Poshvina
- Laboratory of Antimicrobial Resistance, Institute of Ecological and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia
| | - Amir Kh Taldaev
- V.N. Orekhovich Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121, Moscow, Russia; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
| | - Arina A Nikandrova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, 121205, Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Arina N Imamutdinova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, 121205, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Natalia S Garaeva
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center of Russian Academy of Sciences, 420111, Kazan, Russia; Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Str., 420008, Kazan, Russia
| | - Aydar G Bikmullin
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Str., 420008, Kazan, Russia
| | - Evelina A Klochkova
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya Str., 420008, Kazan, Russia
| | - Alexander L Rusanov
- V.N. Orekhovich Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121, Moscow, Russia
| | - Daniil D Romashin
- V.N. Orekhovich Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121, Moscow, Russia
| | - Natalia G Luzgina
- V.N. Orekhovich Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121, Moscow, Russia
| | - Ilya A Osterman
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, 121205, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Petr V Sergiev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, 121205, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Anastasia V Teslya
- Laboratory of Antimicrobial Resistance, Institute of Ecological and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia
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Le NT, Hoang PH, Nguyen Q, Truong MNH, Van Dang C, Ho TH, Hoang PL, Truong DQ, Nguyen HTT, Van Le C, Phan TTP. Emergence of mcr-8.2-mediated colistin resistance in Klebsiella pneumoniae isolated from pediatric diarrhea cases in southern Vietnam. J Glob Antimicrob Resist 2025; 42:120-126. [PMID: 39988071 DOI: 10.1016/j.jgar.2025.02.007] [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: 12/05/2024] [Revised: 02/06/2025] [Accepted: 02/08/2025] [Indexed: 02/25/2025] Open
Abstract
BACKGROUND Colistin resistance poses a growing global challenge, particularly in low- and middle-income countries where antibiotic misuse is prevalent. This study investigates the prevalence of colistin resistance in Klebsiella spp. and characterizes the genetic features of resistant isolates, focusing on the mcr-8.2 gene identified in a Klebsiella pneumoniae isolate from pediatric diarrheal cases in southern Vietnam. METHODS Stool samples were collected from 500 pediatric patients (aged 0-5 years) hospitalized with diarrhea in two tertiary hospitals in Ho Chi Minh City between March and September 2022. Samples were cultured on Violet Red Bile Glucose Agar, then presumptive Klebsiella spp. colonies were selected, purified on nutrient agar, and identified using MALDI-TOF MS. Colistin resistance was determined via minimum inhibitory concentration testing, and the presence of mcr genes was confirmed through polymerase chain reaction. Whole-genome sequencing was performed on the Klebsiella pneumoniae strain harboring mcr-8.2 to elucidate resistance mechanisms. Strain characterization was performed using multi-locus sequence typing, while conjugation experiments assessed horizontal gene transfer potential. RESULTS Among 121 Klebsiella spp. isolates, 49 (40.5%) were resistant to colistin. The mcr-1 gene was detected in 31 isolates (25.6%), whereas the mcr-8 was identified in a single isolate (0.8%), with a colistin MIC of 16 µg/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple β-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance. CONCLUSIONS This study documents the emergence of mcr-8.2-mediated colistin resistance in K. pneumoniae from pediatric diarrhea in Vietnam and highlights a high prevalence of multidrug resistance in Klebsiella spp.. Continuous surveillance of mcr genes and novel therapeutic strategies are urgently needed.
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Affiliation(s)
- Nga Thi Le
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam; Vietnam National University, Ho Chi Minh City, Vietnam; Institute of Public Health, Ho Chi Minh City, Vietnam
| | | | - Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Minh Nhat Ha Truong
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam; Vietnam National University, Ho Chi Minh City, Vietnam
| | | | - Tinh Huu Ho
- Institute of Public Health, Ho Chi Minh City, Vietnam
| | | | | | | | - Chuong Van Le
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam; Vietnam National University, Ho Chi Minh City, Vietnam; Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam.
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Peeters C, Steyaert S, Shelomi M, Wieme AD, Depoorter E, De Canck E, Houf K, Vandamme P. Imbroritus primus gen. nov., sp. nov., a facultatively autotrophic bacterium from environmental water samples. Int J Syst Evol Microbiol 2025; 75. [PMID: 40359131 DOI: 10.1099/ijsem.0.006781] [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: 05/15/2025] Open
Abstract
A Gram-stain-negative coccobacillus, LMG 32992T, was isolated from water that had collected in a tyre in Pingtung, Donggang Township, Taiwan. Upon preliminary 16S rRNA gene sequence analysis, it was most closely related to members of the genus Ralstonia (16S rRNA gene sequence similarities of 96.7-97.5%). The present study aimed to elucidate its taxonomic position and to propose a formal classification. To this end, the complete genome sequence was determined, and taxonomic, phylogenomic, metabolic and physiological analyses were performed. Comparative genomic analyses demonstrated that strain LMG 32992T and another unclassified strain, Burkholderiaceae bacterium PBA, which was isolated earlier from textile wastewater in Malaysia, represented a single novel species within a novel genus of the family Burkholderiaceae. The G+C content of the LMG 32992T genomic DNA was 63.77 mol%. Genomic analyses and growth tests demonstrated that LMG 32992T had an asaccharolytic metabolism but that it was well-equipped to synthetize, if necessary autotrophically, and transform all required carbohydrates and that it used the Krebs and related cycles to generate reductive power for a heterotrophic energy metabolism. We propose the name Imbroritus primus gen. nov., sp. nov. with strain LMG 32992T (=CIP 112179T=BCRC 81361T=A30B1T) as the type strain, for this novel taxon.
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Affiliation(s)
- Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- National Reference Center for Burkholderia cepacia Complex, Jette, Belgium
| | - Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kurt Houf
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- National Reference Center for Burkholderia cepacia Complex, Jette, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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Boueroy P, Phetburom N, Duangjanchot R, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Hatrongjit R, Zheng H, Li J, Kerdsin A. Genomic characterization of Streptococcus suis serotype 31 isolated from one human and 17 clinically asymptomatic pigs in Thailand. Vet Microbiol 2025; 304:110482. [PMID: 40107014 DOI: 10.1016/j.vetmic.2025.110482] [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: 12/13/2024] [Revised: 03/09/2025] [Accepted: 03/12/2025] [Indexed: 03/22/2025]
Abstract
Streptococcus suis is a zoonotic pathogen capable of causing severe diseases in humans and pigs. Frequently, S. suis serotype 31 strains have been isolated from pigs. The first human case of S. suis was reported in Thailand in 2015. In total, 18 strains from one human and 17 clinically asymptomatic pigs in Thailand were analyzed to characterize S. suis serotype 31. In total, 11 different STs were identified, with the major ST being ST2767 (38.89 %; 7/18). The minimum core-genome (MCG) classification revealed that almost all of the serotype 31 strains belonged to MCG7 (94.44 %; 17/18). Genomic analysis revealed that the serotype 31 isolates were major clusters with the porcine-healthy strains from China, Viet Nam, and Thailand. The human serotype 31 ST221 isolate was closely related to S. suis serotype 5 and 24 strains (CC221/234) isolated from Thailand. All serotype 31 strains were multidrug resistant with resistance to azithromycin (100 %; 18/18) and tetracycline (100 %; 18/18). Notably, 10 (55.56 %) of the serotype 31 strains were resistant to penicillin, while 8 strains (44.44 %) showed intermediate resistance to this agent. High substitutions were observed in three penicillin-binding proteins (1 A, 2B, and 2X) of these serotype 31 strains. The most prevalent antimicrobial resistance genes were erm(B) (100 %; 18/18) and tet(O) (66.67 %; 12/18). Overall, 7 strains carried integrative conjugative elements (ICEs) that harbored antimicrobial resistance genes, such as erm(B), tet(O), and tet(W). This study contribute to understanding the genomic diversity and provide valuable information for public health awareness of multidrug-resistant S. suis serotype 31.
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Affiliation(s)
- Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand.
| | - Nattamol Phetburom
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rapeephan Duangjanchot
- Siriraj Long-read Laboratory, Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Siriraj Long-read Laboratory, Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Siriraj Long-read Laboratory, Division of Medical Bioinformatics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Han Zheng
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinquan Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, College of Food Science and Technology, Sakon Nakhon, Huazhong Agricultural University, Wuhan, China
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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Ortega-Sanz I, Rovira J, Megías G, Rivero-Pérez MD, Melero B. Genome-Wide association study to identify genetic markers associated with Campylobacter jejuni motility. Microb Pathog 2025; 205:107657. [PMID: 40318771 DOI: 10.1016/j.micpath.2025.107657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 04/18/2025] [Accepted: 04/30/2025] [Indexed: 05/07/2025]
Abstract
The ability of Campylobacter jejuni to survive and persist under harsh conditions is linked to the presence of flagella. This structure promotes the motility of the bacteria towards their optimum environment. The aim of this study was to examine the genetic basis for motility within 136 C. jejuni isolates through two different Genome-Wide Association Studies, gene presence/absence and Single Nucleotide Polymorphisms (SNPs). The motility phenotype was widely distributed across the phylogeny with large intra-lineage swarming performance variabilities. Accessory genes significantly associated with motility were found in four key genomic regions. One of these regions affected the Cj0727-Cj0733 operon, that encodes a putative ABC transporter system for phosphate uptake, while other influenced the capsule biosynthesis locus. Multiple SNPs mostly linked to increased motility were also discovered in clusters of genes, with special relevance to transport and membrane proteins. Therefore, the capsule and membrane composition might influence nutrient transfer, further impacting the protonmotive force that drives flagellar motor rotation in C. jejuni. The study provides novel genetic markers with a potential role in the motility phenotype of the pathogen.
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Affiliation(s)
- Irene Ortega-Sanz
- Department of Biotechnology and Food Science, University of Burgos, 9001 Burgos, Spain.
| | - Jordi Rovira
- Department of Biotechnology and Food Science, University of Burgos, 9001 Burgos, Spain.
| | - Gregoria Megías
- Microbiology Department of the University Hospital of Burgos (HUBU), Burgos, Spain.
| | | | - Beatriz Melero
- Department of Biotechnology and Food Science, University of Burgos, 9001 Burgos, Spain.
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Chan BK, Stanley GL, Kortright KE, Vill AC, Modak M, Ott IM, Sun Y, Würstle S, Grun CN, Kazmierczak BI, Rajagopalan G, Harris ZM, Britto CJ, Stewart J, Talwalkar JS, Appell CR, Chaudary N, Jagpal SK, Jain R, Kanu A, Quon BS, Reynolds JM, Teneback CC, Mai QA, Shabanova V, Turner PE, Koff JL. Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis. Nat Med 2025; 31:1494-1501. [PMID: 40301561 PMCID: PMC12092284 DOI: 10.1038/s41591-025-03678-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/27/2025] [Indexed: 05/01/2025]
Abstract
Bacteriophage (phage) therapy, which uses lytic viruses as antimicrobials, is a potential strategy to address the antimicrobial resistance crisis. Cystic fibrosis, a disease complicated by recurrent Pseudomonas aeruginosa pulmonary infections, is an example of the clinical impact of antimicrobial resistance. Here, using a personalized phage therapy strategy that selects phages for a predicted evolutionary trade-off, nine adults with cystic fibrosis (eight women and one man) of median age 32 (range 22-46) years were treated with phages on a compassionate basis because their clinical course was complicated by multidrug-resistant or pan-drug-resistant Pseudomonas that was refractory to prior courses of standard antibiotics. The individuals received a nebulized cocktail or single-phage therapy without adverse events. Five to 18 days after phage therapy, sputum Pseudomonas decreased by a median of 104 CFU ml-1, or a mean difference of 102 CFU ml-1 (P = 0.006, two-way analysis of variance with Dunnett's multiple-comparisons test), without altering sputum microbiome, and an analysis of sputum Pseudomonas showed evidence of trade-offs that decreased antibiotic resistance or bacterial virulence. In addition, an improvement of 6% (median) and 8% (mean) predicted FEV1 was observed 21-35 days after phage therapy (P = 0.004, Wilcoxon signed-rank t-test), which may reflect the combined effects of decreased bacterial sputum density and phage-driven trade-offs. These results show that a personalized, nebulized phage therapy trade-off strategy may affect clinical and microbiologic endpoints, which must be evaluated in larger clinical trials.
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Gail L Stanley
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Kaitlyn E Kortright
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Albert C Vill
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Mrinalini Modak
- Department of Medicine, Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Isabel M Ott
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Ying Sun
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Silvia Würstle
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Infectious Diseases, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Casey N Grun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Barbara I Kazmierczak
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Govindarajan Rajagopalan
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Zachary M Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Clemente J Britto
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jill Stewart
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jaideep S Talwalkar
- Department of Internal Medicine, Section General Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Casey R Appell
- Department of Kinesiology & Sports Management, Texas Tech University, Lubbock, TX, USA
| | - Nauman Chaudary
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Sugeet K Jagpal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Raksha Jain
- Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adaobi Kanu
- Department of Pediatrics, Texas Tech University Health Sciences Center School of Medicine, Lubbock, TX, USA
| | - Bradley S Quon
- Faculty of Medicine, Centre for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada
| | - John M Reynolds
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Charlotte C Teneback
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Quynh-Anh Mai
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
| | - Veronika Shabanova
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan L Koff
- Center for Phage Biology and Therapy, Yale University, New Haven, CT, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
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Songo A, Jacquier H, Danjean M, Compain F, Dorchène D, Edoo Z, Woerther PL, Arthur M, Lebeaux D. Analysis of two Nocardia brasiliensis class A β-lactamases (BRA-1 and BRS-1) and related resistance to β-lactam antibiotics. J Glob Antimicrob Resist 2025; 42:135-141. [PMID: 39947613 DOI: 10.1016/j.jgar.2025.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 01/21/2025] [Accepted: 01/31/2025] [Indexed: 03/24/2025] Open
Abstract
OBJECTIVE Molecular determinants of β-lactam resistance are poorly explored for most Nocardia species, such as Nocardia brasiliensis. In this study, we characterised resistance mediated by two β-lactamases in the reference strain N. brasiliensis HUJEG-1 and extended our analysis to nine N. brasiliensis clinical strains. METHODS The susceptibility of N. brasiliensis HUJEG-1 was determined by measuring the MIC via microdilution for five β-lactam antibiotics that were or were not associated with β-lactamase inhibitors (clavulanate and avibactam, 4 µg/mL). Two putative class A β-lactamase-encoding genes (blaBRA-1 and blaBRS-1) were identified in the HUJEG-1 genome. The kinetic parameters of purified BRA-1 and BRS-1 were determined by spectrophotometry. Measurement of β-lactam resistance was then extended to nine clinical strains. These phenotypic data were compared with the genomic diversity of whole genomes (next-generation sequencing). RESULTS N. brasiliensis HUJEG-1 was resistant to amoxicillin, cefuroxime, and cefotaxime, but susceptible to their combination with clavulanate or avibactam. This strain was resistant to imipenem (with or without inhibitors) and susceptible to meropenem. BRA-1 showed high catalytic efficiencies against penams (penicillin, ampicillin) and cephems (cephaloridine, cephalothin, and cefamandole), but not against penems (imipenem, meropenem), suggesting that imipenem resistance was mediated by another mechanism. The hydrolytic activity of BRS-1 was 100-1000-fold lower than that of BRA-1 for all β-lactams tested, suggesting that BRS-1 has a minor contribution to β-lactam resistance. Analysis of the nine clinical strains showed variations in susceptibility to cefotaxime, as well as diversity in genetic backgrounds and BRA-1 sequences. CONCLUSIONS N. brasiliensis HUJEG-1 resistance to penams and cephems is mainly due to the class A β-lactamase BRA-1.
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Affiliation(s)
- Aimee Songo
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, U1138, LRMA, Equipe 12, Paris, France
| | - Hervé Jacquier
- EA DYNAMYC 7380, Faculté de Santé, Université Paris-Est Créteil, Créteil, France; Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Henri Mondor, Créteil, France
| | - Maxime Danjean
- EA DYNAMYC 7380, Faculté de Santé, Université Paris-Est Créteil, Créteil, France; Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Henri Mondor, Créteil, France
| | - Fabrice Compain
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, U1138, LRMA, Equipe 12, Paris, France
| | - Delphine Dorchène
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, U1138, LRMA, Equipe 12, Paris, France
| | - Zainab Edoo
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, U1138, LRMA, Equipe 12, Paris, France
| | - Paul-Louis Woerther
- EA DYNAMYC 7380, Faculté de Santé, Université Paris-Est Créteil, Créteil, France; Unité de Bactériologie, Département de Prévention, Diagnostic et Traitement des Infections, APHP, GHU Henri Mondor, Créteil, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, U1138, LRMA, Equipe 12, Paris, France
| | - David Lebeaux
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, U1138, LRMA, Equipe 12, Paris, France; Université Paris Cité, Paris, France; Service de Microbiologie, Unité Mobile d'Infectiologie, APHP, Hôpital Européen Georges Pompidou, Paris, France.
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Fang Y, Li X, Wu Z, Fang Y, Wang Y, Li X, Bu L, Chen K, Shen K, Ma Y, Wu M. Emergence of an XDR Klebsiella pneumoniae ST5491 strain co-harboring NDM-5, MCR-1.1, tmexCD1-toprJ1, and a novel plasmid carrying CTX-M-15. Front Microbiol 2025; 16:1581851. [PMID: 40371110 PMCID: PMC12075367 DOI: 10.3389/fmicb.2025.1581851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2025] [Accepted: 04/14/2025] [Indexed: 05/16/2025] Open
Abstract
Objective The rapid emergence of antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a significant global health threat. The study aimed to analyze and describe the genomic architecture and resistance mechanisms of an extensively drug-resistant (XDR) K. pneumoniae isolate, KP09, by focusing on plasmids that harbor multiple resistance genes, including tmexCD1-toprJ1, blaCTX-M-15 , blaNDM-5 , and mcr-1.1. Methods The KP09 strain, isolated from a clinical sample, was subjected to antimicrobial susceptibility testing and conjugation experiments. Whole-genome sequencing with both long- and short-read methods facilitated hybrid assembly for complete genome reconstruction. Bioinformatics analyses identified resistance genes, plasmid structures, and sequence types (STs), whereas comparative genomic analysis elucidated the context and dissemination mechanisms of resistance determinants. Results KP09 exhibited broad-spectrum resistance to carbapenems, colistin, eravacycline, and tigecycline, and only remained susceptible to cefiderocol. The conjugation experiments successfully produced four transconjugants, each carrying specific plasmids: JKP09-1 harbored the tmexCD1-toprJ1 gene, JKP09-2 harbored tmexCD1-toprJ1 and mcr-1.1 genes, JKP09-3 harbored the mcr-1.1 gene, and JKP09-4 harbored blaNDM-5 and mcr-1.1 genes. Genomic analysis revealed a novel IncFIA/IncFII/IncQ1 hybrid plasmid carrying bla CTX-M-15, along with a large conjugative plasmid encoding the tmexCD1-toprJ1 efflux pump. The bla NDM-5 and mcr-1.1 genes were located in separate IncX-type plasmids, suggesting independent dissemination pathways. Furthermore, KP09 was identified as a new sequence type, ST5491, closely related to the endemic ST15 clone. The comparative analysis highlighted the role of mobile genetic elements, such as IS26 and ISEcp1, in facilitating the spread of resistance genes. Conclusion This study provides critical information on the genetic mechanisms that drive AMR in K. pneumoniae, including the identification of a novel bla CTX-M-15 encoding IncFIA/IncFII/IncQ1 hybrid plasmid and the emergence of the ST5491 strain. Understanding the genetic basis of resistance is essential to inform public health interventions and mitigate the impact of AMR.
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Affiliation(s)
- Yinfei Fang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiangchen Li
- Jiaxing Key Laboratory of Clinical Laboratory Diagnostics and Translational Research, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Zhaoxia Wu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yongjin Fang
- Department of Otolaryngology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yeping Wang
- Department of Pediatrics, Jinhua Women’s and Children’s Hospital, Jinhua, China
| | - Xiaobing Li
- Department of Pediatrics, Jinhua Women’s and Children’s Hospital, Jinhua, China
| | - Lihong Bu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Keqiang Chen
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Kai Shen
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mingjuan Wu
- Department of Health Management, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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Shave CD, Haider MJA, Onyishi CU, McDonald MC, Stones L, Jagielski T, May RC. Phylogenetic analysis of pathogenic algae reveals lineage-dependent patterns of phagocytosis. mBio 2025:e0049825. [PMID: 40304495 DOI: 10.1128/mbio.00498-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Accepted: 04/07/2025] [Indexed: 05/02/2025] Open
Abstract
Prototheca is an unusual genus of algae that lack chlorophyll and are obligate heterotrophs. To date, six paraphyletic pathogenic species have been identified in the context of vertebrates, principally in cattle-associated and human-associated infections. Together with the genus Auxenochlorella and Helicosporidium, rDNA sequence analysis currently favors grouping Prototheca under a clade known as the Auxenochlorella, Helicosporidium and Prototheca (AHP) lineage. Most studies so far have focused only on Prototheca bovis and Prototheca ciferrii as cattle-associated species and on Prototheca wickerhamii as a human-associated species. However, such studies remain limited in scope as they focus on only three species of Prototheca, which is not representative of the total number of species within the AHP lineage. In this study, we employ a phylogenetics approach based on five new organelle-encoded genes to delineate higher-level relationships within the AHP lineage. We use the resultant data to then guide a live-cell imaging-based investigation of aspects of the mammalian innate immune response to 11 Prototheca species and four Auxenochlorella species. Our data reveal varying patterns of phagocytosis dynamics that are both host cell type- and algal species-dependent. Together, these findings reveal the interaction between pathogen phylogeny and host immune response, revealing ways to identify new therapeutic targets in the future. IMPORTANCE Protothecosis is a rare algal infection caused by members of the genus Prototheca, which is comprised of unusual non-photosynthetic algae. Six pathogenic species have been identified so far that can cause infection in vertebrates, primarily cattle and humans. The phylogeny of this genus remains obscure and has been revised multiple times recently. However, this phylogeny has largely been based on only three species of Prototheca. To resolve this phylogenetic conundrum, here, we employ a phylogenetics approach based on five new organelle-encoded genes. We then use these data to perform live-cell imaging of a selected range of Prototheca species co-cultured with mammalian immune cells. Visualizing these phagocytic interactions in this context helps delineate both host cell-type- and species-dependent differences in phagocytic uptake, thereby providing novel insight into lineage-based differences.
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Affiliation(s)
- Christopher D Shave
- Institute of Microbiology and Infection and School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Mohammed J A Haider
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sabah Al-Salem University City, Kuwait City, Kuwait
| | - Chinaemerem U Onyishi
- Institute of Microbiology and Infection and School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- Molecular Mycology and Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, Maryland, USA
| | - Megan C McDonald
- Institute of Microbiology and Infection and School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Leanne Stones
- College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warszawa, Poland
| | - Robin C May
- Institute of Microbiology and Infection and School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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Howlader AA, Nahiduzzaman F, Annan RI, Saha A, Ariful Islam M, Minara Khatun M. Draft whole-genome sequence of multidrug-resistant Enterococcus faecium strain MKL_BAU_Fe01 isolated from chicken meat. Microbiol Resour Announc 2025:e0004325. [PMID: 40304481 DOI: 10.1128/mra.00043-25] [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: 01/17/2025] [Accepted: 03/31/2025] [Indexed: 05/02/2025] Open
Abstract
We report the draft genome sequence of Enterococcus faecium MKL_BAU_Fe01 from chicken meat in Bangladesh. The 2,953,746 bp genome, with 37.99% GC content across 264 contigs, contains 3,117 genes, including 3,007 Coding Sequences (CDSs), 17 rRNAs, and 89 tRNAs, along with several antibiotic resistance and pathogenic genes.
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Affiliation(s)
- Al Amin Howlader
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Fnu Nahiduzzaman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Raihan Islam Annan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Arnob Saha
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Ariful Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mst Minara Khatun
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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132
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Sonawala U, Busidan A, Haak D, Pilot G. Characterization and whole genome sequencing of Saccharomyces cerevisiae strains lacking several amino acid transporters: Tools for studying amino acid transport. PLoS One 2025; 20:e0315789. [PMID: 40305508 PMCID: PMC12043151 DOI: 10.1371/journal.pone.0315789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Accepted: 03/17/2025] [Indexed: 05/02/2025] Open
Abstract
Saccharomyces cerevisiae mutants have been used since the early 1980s as a tool for characterizing genes from other organisms by functional complementation. This approach has been extremely successful in cloning and studying transporters; for instance, plant amino acid, sugar, urea, ammonium, peptide, sodium, and potassium transporters were characterized using yeast mutants lacking these functions. Over the years, new strains lacking even more endogenous transporters have been developed, enabling the characterization of transport properties of heterologous proteins in a more precise way. Furthermore, these strains provide the added possibility of characterizing a transporter belonging to a family of proteins in isolation, and thus can be used to study the relative contribution of redundant transporters to the whole function. We focused on amino acid transport, starting with the yeast strain 22 ∆ 8AA, which was developed to clone plant amino acid transporters in the early 2000s. We recently deleted two additional amino acid permeases, Gnp1 and Agp1, creating 22 ∆ 10α. In the present work, five additional permeases (Bap3, Tat1, Tat2, Agp3, Bap2) were deleted from 22 ∆ 10α genome, in a combination of up to three at a time. Unexpectedly, the amino acid transport properties of the new strains were not very different from the parent, suggesting that these amino acid permeases play a minor role in amino acid uptake, at least in our conditions. Furthermore, the inability to utilize certain amino acids as sole nitrogen source did not correlate with reduced uptake activity, questioning the well-accepted relationship between lack of growth and loss of transport properties. Finally, in order to verify the mutations and the integrity of 22 ∆ 10α genome, we performed whole-genome sequencing of 22 ∆ 10α using long-read PacBio sequencing technology. We successfully assembled 22 ∆ 10α's genome de novo, identified all expected mutations and precisely characterized the nature of the deletions of the ten amino acid transporters. The sequencing data and genome will serve as a valuable resource to researchers interested in using these strains as a tool for amino acid transport study.
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Affiliation(s)
- Unnati Sonawala
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Aymeric Busidan
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - David Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Guillaume Pilot
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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Kaufmann H, Salvador C, Salazar VW, Cruz N, Dias GM, Tschoeke D, Campos L, Sawabe T, Miyazaki M, Maruyama F, Thompson F, Thompson C. Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments. MICROBIAL ECOLOGY 2025; 88:36. [PMID: 40301151 PMCID: PMC12041005 DOI: 10.1007/s00248-025-02533-0] [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: 12/02/2024] [Accepted: 04/10/2025] [Indexed: 05/01/2025]
Abstract
The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.
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Affiliation(s)
- Hannah Kaufmann
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil
| | - Carolina Salvador
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil
| | - Vinicius W Salazar
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil
- Faculty of Medicine, Dentistry, and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - Natália Cruz
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil
| | - Graciela Maria Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo Tschoeke
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil
- Instituto Alberto Luiz Coimbra de Pós-Graduação E Pesquisa de Engenharia (COPPE), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lucia Campos
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Laboratory of Microbiology, Fisheries Sciences School, Hokkaido University, Hakodate, Japan
| | - Masayuki Miyazaki
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Yokosuka, Japan
- Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Fumito Maruyama
- Microbial Genomics and Ecology Laboratory, Hiroshima University, Hiroshima, Japan
| | - Fabiano Thompson
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil.
| | - Cristiane Thompson
- Laboratory of Microbiology, Institute of Biology, UFRJ, Rio de Janeiro, Brazil.
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Bespalova AV, Kulikova DA, Zelentsova ES, Rezvykh AP, Guseva IO, Dorador AP, Evgen’ev MB, Funikov SY. Paramutation-Like Behavior of Genic piRNA-Producing Loci in Drosophila virilis. Int J Mol Sci 2025; 26:4243. [PMID: 40362480 PMCID: PMC12072073 DOI: 10.3390/ijms26094243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Revised: 04/24/2025] [Accepted: 04/28/2025] [Indexed: 05/15/2025] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of a paramutation-like process. However, the variability in piRNA clusters' capacity to induce such conversions remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the subtelomeric RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Importantly, the maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. The present findings suggest that the paramutation-like behavior of piRNA clusters may be influenced not only by piRNAs but also by structural features and the chromatin environment in the proximity to telomeres, providing new insights into the epigenetic regulation of the Drosophila genome.
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Affiliation(s)
- Alina V. Bespalova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dina A. Kulikova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Elena S. Zelentsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander P. Rezvykh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Iuliia O. Guseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Center for Advanced Studies, Kulakova Str. 20, 123592 Moscow, Russia
| | - Ana P. Dorador
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mikhail B. Evgen’ev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergei Y. Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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135
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Rubio-Mora E, Amoroto-Bengoetxea M, Rico Nieto A, Díez-Vidal A, Mingorance J, Quiles-Melero I. Complete genome sequence of a Neisseria meningitidis isolate from an ankle joint with septic arthritis. Microbiol Resour Announc 2025:e0011125. [PMID: 40298420 DOI: 10.1128/mra.00111-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 04/11/2025] [Indexed: 04/30/2025] Open
Abstract
Neisseria meningitidis has been identified as the causative agent of a wide variety of infections. We report the complete genome sequence of an N. meningitidis isolate from a joint fluid sample collected from a patient with primary meningococcal septic arthritis. This strain belongs to the sequence type 17488 of the ST-11 clonal complex, and its assembled genome consists of 2,242,622 base pairs with 51.75% GC content.
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Affiliation(s)
- Eduardo Rubio-Mora
- Servicio de Microbiología y Parasitología. Hospital Universitario La Paz, Madrid, Spain
| | | | - Alicia Rico Nieto
- Servicio de Microbiología y Parasitología. Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
- Unidad de Enfermedades Infecciosas, Hospital Universitario La Paz, Madrid, Spain
| | - Alejandro Díez-Vidal
- Unidad de Enfermedades Infecciosas, Hospital Universitario La Paz, Madrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología y Parasitología. Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Quiles-Melero
- Servicio de Microbiología y Parasitología. Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
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136
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Zeng Y, Cai Y, Zhou X, Wang S, Li L, Yao Y, Yu J, Liu X, Yang H, Wei T, Dong S, Liu Y. Chromosome-level genomes of Arctic and Antarctic mosses: Aulacomnium turgidum and Polytrichastrum alpinum. Sci Data 2025; 12:705. [PMID: 40301385 PMCID: PMC12041281 DOI: 10.1038/s41597-025-04960-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 04/07/2025] [Indexed: 05/01/2025] Open
Abstract
Bryophytes play a crucial role in the ecosystems of polar regions. These simple plants are among the predominant vegetation types in both Arctic and Antarctic landscapes, where they contribute significantly to biodiversity and ecological stability. Here, we report the chromosome-level genomes of two polar moss species, the Arctic Aulacomnium turgidum and Antarctic Polytrichastrum alpinum. Utilizing a combination of Illumina short reads, Nanopore long reads, and Hi-C data, we assembled genomes of 277.84 Mb for A. turgidum and 498.33 Mb for P. alpinum, respectively. These assemblies were anchored to 11 chromosomes for A. turgidum and 8 chromosomes for P. alpinum. Both species exhibited a sex chromosome with distinct genomic characteristics. Gene annotations revealed 25,999 protein-coding genes in A. turgidum and 28,070 in P. alpinum. The high completeness of the gene space was validated via BUSCO, achieving impressive scores of 98.2% and 98.0%. These high-quality genomes provide critical resources for studying the adaptive evolution and stress tolerance mechanisms of mosses in extreme polar environments.
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Affiliation(s)
- Yuying Zeng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Yuqing Cai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Xuping Zhou
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Sibo Wang
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Linzhou Li
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Yifeng Yao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jin Yu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Xin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Huanming Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Tong Wei
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yang Liu
- BGI Research, Wuhan, 430074, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China.
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137
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Radhamanalan G, Mickymaray S, Alothaim AS, Alsowayeh N, Dharumadurai D. Whole-genome analysis of Streptococcus mutans GDP01 isolate of dental caries tooth. Microbiol Resour Announc 2025:e0105724. [PMID: 40298426 DOI: 10.1128/mra.01057-24] [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: 09/27/2024] [Accepted: 04/09/2025] [Indexed: 04/30/2025] Open
Abstract
Dental caries is a multifactorial infectious disease primarily driven by Streptococcus mutans. Here, we present the whole-genome sequence of Streptococcus mutans GDP01, which was isolated from the dental caries-infected children from Madurai, Tamil Nadu, India.
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Affiliation(s)
- Guhanraj Radhamanalan
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Suresh Mickymaray
- Department of Biology, College of Science, Al-Zulfi, Majmaah University, Al Majmaah, Riyadh Province, Saudi Arabia
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science, Al-Zulfi, Majmaah University, Al Majmaah, Riyadh Province, Saudi Arabia
| | - Noorah Alsowayeh
- Department of Biology, College of Science, Al-Zulfi, Majmaah University, Al Majmaah, Riyadh Province, Saudi Arabia
| | - Dhanasekaran Dharumadurai
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- National Repository for Microalgae and Cyanobacteria, Freshwater (NRMC-F) (Sponsored by the DBT, Govt. of India), Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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138
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Ben Romdhane W, Ben Saad R, Guiderdoni E, Ali AAM, Tarroum M, Al-Doss A, Hassairi A. De novo, high-quality assembly and annotation of the halophyte grass Aeluropus littoralis draft genome and identification of A20/AN1 zinc finger protein family. BMC PLANT BIOLOGY 2025; 25:556. [PMID: 40295936 PMCID: PMC12039208 DOI: 10.1186/s12870-025-06610-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Accepted: 04/24/2025] [Indexed: 04/30/2025]
Abstract
BACKGROUND Aeluropus littoralis is considered a valuable natural forage plant for ruminant livestock and is highly tolerant to extreme abiotic stresses, especially salinity, drought, and heat. It is a monocotyledonous halophyte, has salt glands, performs C4-type photosynthesis and has a close genetic relationship with cereal crops. Moreover, previous studies have shown its huge potential as a reservoir of genes and promoters to understand and improve abiotic stress tolerance in crops. RESULTS The sequencing and hybrid assembly of the A. littoralis genome (2n = 2X = 20) using short and long reads from the BGISeq-500 and PacBio high-fidelity (HiFi) sequencing platforms, respectively. Using the k-mer analysis method, the haploid genome size of A. littoralis was estimated to be 360 Mb (with a heterozygosity rate of 1.88%). The hybrid assembled genome included 4,078 contigs with a GC content of 44% and covered 348 Mb. The longest contig and the N50 values were 5.1 Mb and 133.77 kb, respectively. The Benchmarking Universal Single Copy Ortholog (BUSCO) value was 91.1%, indicating good integrity of the assembled genome. The discovered repetitive elements accounted for 90.6 Mb, representing 26.03% of the total genome, and included a significant component of transposable elements (11.48%, ~40 Mb). Using a homology-based approach, 35,147 genes were predicted from the genome assembly. We next focused our analysis on the zinc-finger A20/AN1 gene family, a member of which (AlSAP) was previously shown to confer increased tolerance to osmotic and salt stresses when it was over-expressed in tobacco, wheat, and rice. Here, we identified the complete set of members of this family in the Aeluropus littoralis genome, thereby laying the foundation for their future functional analysis in cereal crops. In addition, the expression patterns of four novel genes from this family were analyzed by qPCR. CONCLUSION This resource and our findings will contribute to improve the current understanding of salinity tolerance in halophytes while providing useful genes and allelic variation to improve salinity and drought tolerance in cereals through genetic engineering and gene editing, respectively.
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Affiliation(s)
- Walid Ben Romdhane
- King Saud University, College of Food and Agricultural Sciences, Plant Production Department, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
| | - Rania Ben Saad
- Centre of Biotechnology of Sfax, Biotechnology and Plant Improvement Laboratory, University of Sfax, B.P 1177, Sfax, 3018, Tunisia
| | - Emmanuel Guiderdoni
- University of, -Institut Agro-University of Montpellier, Montpellier, CIRAD-INRAE, Montpellier, France
| | - Ahmed Abdelrahim Mohamed Ali
- King Saud University, College of Food and Agricultural Sciences, Plant Production Department, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Mohamed Tarroum
- King Saud University, College of Food and Agricultural Sciences, Plant Production Department, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdullah Al-Doss
- King Saud University, College of Food and Agricultural Sciences, Plant Production Department, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Afif Hassairi
- King Saud University, College of Food and Agricultural Sciences, Plant Production Department, P.O. Box 2460, Riyadh, 11451, Saudi Arabia.
- Centre of Biotechnology of Sfax, Biotechnology and Plant Improvement Laboratory, University of Sfax, B.P 1177, Sfax, 3018, Tunisia.
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139
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Choudoir MJ, Narayanan A, Rodriguez-Ramos D, Simoes R, Efroni A, Sondrini A, DeAngelis KM. Pangenomes suggest ecological-evolutionary responses to experimental soil warming. mSphere 2025; 10:e0005925. [PMID: 40105318 PMCID: PMC12039271 DOI: 10.1128/msphere.00059-25] [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: 01/27/2025] [Accepted: 02/04/2025] [Indexed: 03/20/2025] Open
Abstract
Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change.IMPORTANCEAnthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.
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Affiliation(s)
- Mallory J. Choudoir
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Achala Narayanan
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Damayanti Rodriguez-Ramos
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin, USA
| | - Rachel Simoes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Alon Efroni
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Abigail Sondrini
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Aguilar-Ancori EG, Marin-Carrasco M, Campo-Pfuyo LI, Muñiz-Duran JG, Espinoza-Culupú A. Identification of pandemic ST147, ESBL-type β-lactamases, carbapenemases, and virulence factors in Klebsiella pneumoniae isolated from southern Peru. Sci Rep 2025; 15:14870. [PMID: 40295561 PMCID: PMC12037762 DOI: 10.1038/s41598-025-97464-8] [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: 10/02/2024] [Accepted: 04/04/2025] [Indexed: 04/30/2025] Open
Abstract
Multidrug-resistant Klebsiella pneumoniae (MDR K. pneumoniae) is a significant pathogen associated with nosocomial infections, often leading to high morbidity and mortality. This resistance is largely due to the efficient horizontal transfer of mobile genetic elements such as plasmids, which carry resistance genes and virulence factors. These elements contribute to the production of extended-spectrum β-lactamases (ESBL) and carbapenemases, which further complicates treatment. Despite the high prevalence of MDR K. pneumoniae in Peruvian hospitals, the genomic characterization of these strains remains limited. This study investigated the phenotypic and molecular identification of extended-spectrum β-lactamases (ESBLs), carbapenemases, and virulence factors in 91 MDR K. pneumoniae strains collected from three hospitals between 2022 and 2023. Phenotypic detection of ESBLs was performed using the Jarlier method, while carbapenemases were identified via double-disk synergy testing with boronic acid, EDTA, and Carba NP test. The positive isolates were further analyzed for resistance genes (blaCTX-M, blaTEM, blaSHV, blaKPC, blaNDM, blaIMP, and blaVIM). Four isolates were subjected to whole-genome sequencing (WGS) for further characterization. All multidrug-resistant K. pneumoniae strains (100%) were ESBL-positive, with 14.3% producing carbapenemases, primarily KPC-type and metallo-β-lactamases (MBLs). The virulence factor analyses revealed that only 7.7% exhibited hypermucoviscosity. Protease activity was detected in 19.8% of the strains, and lipase activity in 1.1%. Regarding biofilm formation, 85.7% of the strains showed moderate adherence. Molecular analysis identified ESBL (blaCTX-M, 78%; blaTEM, 71.4%; blaSHV, 82.4%) and carbapenemase genes (blaKPC 7.7%, blaNDM 4.4%). Genomic analysis revealed various antimicrobial resistance mechanisms, including porin-coding gene mutations, aminoglycoside resistance linked to fluoroquinolone resistance, and multidrug efflux pump regulators. Sequence typing has identified high-risk clones (ST147, ST629, and ST37) associated with hospital outbreaks globally. These findings underscore the considerable concern of MDR and hypervirulent K. pneumoniae in Peruvian hospitals. These findings emphasize the pressing need for sustained genomic surveillance, enhanced infection control measures, and strategies to address the expanding problem of MDR K. pneumoniae.
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Affiliation(s)
- Elsa Gladys Aguilar-Ancori
- Faculty of Biological Sciences, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru.
- University Institute of Tropical Diseases and Biomedicine of Cusco, UNSAAC, Cusco, Peru.
| | - Marishani Marin-Carrasco
- Faculty of Biological Sciences, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru
- University Institute of Tropical Diseases and Biomedicine of Cusco, UNSAAC, Cusco, Peru
| | | | | | - Abraham Espinoza-Culupú
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima, Peru
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141
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Záhonová K, Füssy Z, Albanaz ATS, Butenko A, Kachale A, Kraeva N, Galan A, Zakharova A, Stojanova B, Votýpka J, Kostygov AY, Spodareva VV, Malysheva MN, Frolov AO, Rogozin IB, Paris Z, Valášek LS, Yurchenko V, Lukeš J. Comparative genomic analysis of trypanosomatid protists illuminates an extensive change in the nuclear genetic code. mBio 2025:e0088525. [PMID: 40293238 DOI: 10.1128/mbio.00885-25] [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: 03/19/2025] [Accepted: 03/31/2025] [Indexed: 04/30/2025] Open
Abstract
Trypanosomatids are among the most extensively studied protists due to their parasitic interactions with insects, vertebrates, and plants. Recently, Blastocrithidia nonstop was found to depart from the canonical genetic code, with all three stop codons reassigned to encode amino acids (UAR for glutamate and UGA for tryptophan), and UAA having dual meaning also as a termination signal (glutamate and stop). To explore features linked to this phenomenon, we analyzed the genomes of four Blastocrithidia and four Obscuromonas species, the latter representing a sister group employing the canonical genetic code. We found that all Blastocrithidia species encode cognate tRNAs for UAR codons, possess a distinct 4 bp anticodon stem tRNATrpCCA decoding UGA, and utilize UAA as the only stop codon. The distribution of in-frame reassigned codons is consistently non-random, suggesting a translational burden avoided in highly expressed genes. Frame-specific enrichment of UAA codons immediately following the genuine UAA stop codon, not observed in Obscuromonas, points to a specific mode of termination. All Blastocrithidia species possess specific mutations in eukaryotic release factor 1 and a unique acidic region following the prion-like N-terminus of eukaryotic release factor 3 that may be associated with stop codon readthrough. We infer that the common ancestor of the genus Blastocrithidia already exhibited a GC-poor genome with the non-canonical genetic code. Our comparative analysis highlights features associated with this extensive stop codon reassignment. This cascade of mutually dependent adaptations, driven by increasing AU-richness in transcripts and frequent emergence of in-frame stops, underscores the dynamic interplay between genome composition and genetic code plasticity to maintain vital functionality. IMPORTANCE The genetic code, assigning amino acids to codons, is almost universal, yet an increasing number of its alterations keep emerging, mostly in organelles and unicellular eukaryotes. One such case is the trypanosomatid genus Blastocrithidia, where all three stop codons were reassigned to amino acids, with UAA also serving as a sole termination signal. We conducted a comparative analysis of four Blastocrithidia species, all with the same non-canonical genetic code, and their close relatives of the genus Obscuromonas, which retain the canonical code. This across-genome comparison allowed the identification of key traits associated with genetic code reassignment in Blastocrithidia. This work provides insight into the evolutionary steps, facilitating an extensive departure from the canonical genetic code that occurred independently in several eukaryotic lineages.
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Affiliation(s)
- Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Zoltán Füssy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czechia
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czechia
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czechia
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Arnau Galan
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Bojana Stojanova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Viktoria V Spodareva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Marina N Malysheva
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexander O Frolov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Igor B Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czechia
| | | | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czechia
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142
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Mixão V, Pinto M, Brendebach H, Sobral D, Dourado Santos J, Radomski N, Majgaard Uldall AS, Bomba A, Pietsch M, Bucciacchio A, de Ruvo A, Castelli P, Iwan E, Simon S, Coipan CE, Linde J, Petrovska L, Kaas RS, Grimstrup Joensen K, Holtsmark Nielsen S, Kiil K, Lagesen K, Di Pasquale A, Gomes JP, Deneke C, Tausch SH, Borges V. Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens. Nat Commun 2025; 16:3961. [PMID: 40295532 PMCID: PMC12038046 DOI: 10.1038/s41467-025-59246-8] [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: 08/14/2024] [Accepted: 04/15/2025] [Indexed: 04/30/2025] Open
Abstract
Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-pipeline clustering congruence across all resolution levels and perform an in-depth comparative analysis of cluster composition at outbreak level for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni. We found a general concordance between allele-based pipelines for all species, except for C. jejuni, where the different resolution power of allele-based schemas led to marked discrepancies. Still, we identified non-negligible differences in outbreak detection and demonstrated how a threshold flexibilization favors the detection of similar outbreak signals by different laboratories. These results, together with the observation that different traditional typing groups (e.g., serotypes) exhibit a remarkably different genetic diversity, represent valuable information for future outbreak case-definitions and WGS-based nomenclature design. This study reinforces the need, while demonstrating the feasibility, of conducting continuous pipeline comparability assessments, and opens good perspectives for a smoother international and intersectoral cooperation towards an efficient One Health FWD surveillance.
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Affiliation(s)
- Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Holger Brendebach
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Nicolas Radomski
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Teramo, Italy
| | | | - Arkadiusz Bomba
- Department of Omics Analyses, National Veterinary Research Institute (PIWet), Puławy, Poland
| | - Michael Pietsch
- Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI), Wernigerode, Germany
| | - Andrea Bucciacchio
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Teramo, Italy
| | - Andrea de Ruvo
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Teramo, Italy
- Computer Science, Gran Sasso Science Institute, L'Aquila, Italy
| | - Pierluigi Castelli
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Teramo, Italy
| | - Ewelina Iwan
- Department of Omics Analyses, National Veterinary Research Institute (PIWet), Puławy, Poland
| | - Sandra Simon
- Unit of Enteropathogenic Bacteria and Legionella, Robert Koch Institute (RKI), Wernigerode, Germany
| | - Claudia E Coipan
- Department for Infectious Diseases, Epidemiology and Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute (FLI), Jena, Germany
| | | | - Rolf Sommer Kaas
- National Food Institute, Technical University of Denmark (DTU), Lyngby, Denmark
| | | | - Sofie Holtsmark Nielsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Karin Lagesen
- Section for Epidemiology, Norwegian Veterinary Institute (NVI), Ås, Norway
| | - Adriano Di Pasquale
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZSAM), Teramo, Italy
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Center (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Carlus Deneke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Simon H Tausch
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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143
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Leung V, Ritchie G, Stefanovic A, Lee C, Chorlton S, Matic N, Romney MG, Hayden A, Lowe CF. An Outbreak of Multidrug-Resistant Shigella flexneri Serotype 2a Among People Experiencing Homelessness in Vancouver. Trop Med Infect Dis 2025; 10:120. [PMID: 40423350 DOI: 10.3390/tropicalmed10050120] [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: 03/15/2025] [Revised: 04/14/2025] [Accepted: 04/23/2025] [Indexed: 05/28/2025] Open
Abstract
Background: We describe a community-based outbreak of multidrug-resistant Shigella flexneri serotype 2a among people experiencing homelessness (PEH) in Vancouver's Downtown Eastside during the COVID-19 pandemic. Methods: In this observational cohort study, we followed the Outbreak Reports and Intervention Studies of Nosocomial Infection (ORION) reporting guidelines. We identified cases by laboratory surveillance and collected demographic and clinical data from the medical charts or patient interviews. We implemented enhanced surveillance and disseminated testing and management guidelines. Shigella flexneri isolates were serotyped, and whole-genome sequencing was performed. Results: We identified 101 confirmed cases of Shigella flexneri 2a (80% male; median age 43) between 31 January and 16 December 2021. All the affected individuals experienced homelessness, and substance use disorder was the most common comorbidity (88%). Five patients required ICU hospitalization, and one death occurred within 30 days. Core-genome multilocus sequence typing analysis confirmed a clonal outbreak. All S. flexneri isolates were phenotypically and genotypically multidrug-resistant. Conclusions: COVID-19 exacerbated longstanding public health concerns around the dearth of hygiene and sanitation resources available to PEH. Preventing similar outbreaks will require addressing these risks and finding solutions to the crisis of homelessness in Canada.
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Affiliation(s)
- Victor Leung
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Division of Infectious Diseases, Department of Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Colin Lee
- Lower Mainland Pharmacy Services, Providence Health Care, Vancouver, BC V5Z 3N9, Canada
| | - Sam Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Nancy Matic
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Marc G Romney
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Althea Hayden
- Public Health, Vancouver Coastal Health, Vancouver, BC V5S 1M9, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology, Department of Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
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144
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Liang H, Zou Y, Wang M, Hu T, Wang H, He W, Ju Y, Guo R, Chen J, Guo F, Zeng T, Dong Y, Zhang Y, Wang B, Liu C, Jin X, Zhang W, Xu X, Xiao L. Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies. GIGABYTE 2025; 2025:gigabyte154. [PMID: 40329937 PMCID: PMC12051259 DOI: 10.46471/gigabyte.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 04/22/2025] [Indexed: 05/08/2025] Open
Abstract
Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, which are cost-effective and accurate but often produce fragmented draft genomes. Here, we used CycloneSEQ for long-read sequencing of ATCC BAA-835, producing long-reads with an average length of 11.6 kbp and an average quality score of 14.4. Hybrid assembly with short-reads data resulted in an error rate of only 0.04 mismatches and 0.08 indels per 100 kbp compared to the reference genome. This method, validated across nine species, successfully assembled complete circular genomes. Hybrid assembly significantly enhances genome completeness by using long-reads to fill gaps and accurately assembling multi-copy rRNA genes, unlike short-reads alone. Data subsampling showed that combining over 500 Mbp of short-read data with 100 Mbp of long-read data yields high-quality circular assemblies. CycloneSEQ long-reads improves the assembly of circular complete genomes from mixed microbial communities; however, its base quality needs improving. Integrating DNBSEQ short-reads improved accuracy, resulting in complete and accurate assemblies.
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Affiliation(s)
- Hewei Liang
- BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen 518083, China
| | - Yuanqiang Zou
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen 518083, China
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China
| | - Mengmeng Wang
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongyuan Hu
- BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Haoyu Wang
- BGI Research, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxin He
- BGI Research, Shenzhen 518083, China
| | | | | | - Junyi Chen
- BGI Research, Shenzhen 518083, China
- BGI Hangzhou CycloneSEQ Technology Co., Ltd, Hangzhou 310030, China
| | - Fei Guo
- BGI Research, Shenzhen 518083, China
- BGI Hangzhou CycloneSEQ Technology Co., Ltd, Hangzhou 310030, China
| | - Tao Zeng
- BGI Research, Shenzhen 518083, China
- BGI Hangzhou CycloneSEQ Technology Co., Ltd, Hangzhou 310030, China
| | - Yuliang Dong
- BGI Research, Shenzhen 518083, China
- BGI Hangzhou CycloneSEQ Technology Co., Ltd, Hangzhou 310030, China
| | - Yuning Zhang
- BGI Research, Shenzhen 518083, China
- BGI Hangzhou CycloneSEQ Technology Co., Ltd, Hangzhou 310030, China
| | - Bo Wang
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China
- China National GeneBank, BGI Research, Shenzhen 518120, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Research, Shenzhen 518083, China
| | | | - Xin Jin
- BGI Research, Shenzhen 518083, China
| | | | - Xun Xu
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China
| | - Liang Xiao
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen 518083, China
- State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China
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145
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Revilla J, Rodríguez-Rodríguez S, Solórzano R, Reyes G, Barja JL. First draft genome sequence of Vibrio rotiferianus isolated from diseased larvae of the spiny rock-scallop Spondylus limbatus during hatchery outbreaks. Microb Pathog 2025; 205:107617. [PMID: 40288427 DOI: 10.1016/j.micpath.2025.107617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 03/06/2025] [Accepted: 04/17/2025] [Indexed: 04/29/2025]
Abstract
Scallop aquaculture is of economic importance along the east coast of the tropical Pacific. However, scallop diseases have been observed and there is limited knowledge about bacterial pathogens, especially in hatcheries. The objective of this study was to identify and characterize one of the predominant bacteria in outbreaks of vibriosis that occurred in a scallop hatchery in south-central Ecuador. The strain SA-10GR was isolated from moribund veliger larvae of the scallop Spondylus limbatus. SA-10GR was identified as Vibrio rotiferianus by phenotypic characterization and whole genome sequence analysis. SA-10GR is a strain with lytic activity, susceptible to many antibiotics except amoxicillin (25 μg), capable of producing siderophores and extracellular products with alkaline phosphatase, esterase, lipase esterase, leucine arylamidase, acid phosphatase, among others. The genome of V. rotiferianus consists of 5,579,217 bp; 5160 genes; 5086 protein-coding sequences (CDSs); 74 RNA genes (57 tRNA, 13 rRNA, and 4 ncRNA), and 40 pseudogenes. A total of six resistance genes vanT, adeF, E. coli parE, txR, CRP, and PBP3 were identified, and 110 virulence factors were detected. Functional characterization of SA-10GR shows extracellular products that cause damage to the fish model cell line (Epithelioma Papulosum Cyprini) and pathogenicity against larvae of the scallop Spondylus crassisquama and the oyster Magallana gigas (≥86 % mortality at a concentration of 104 CFU mL-1 at 24 h post-challenge). Both species of larvae infected with the SA-10GR strain showed clinical signs of vibriosis. This study represents the first documentation of a Vibrio rotiferianus strain as a potential pathogen of two important cultured bivalve species along the Pacific coast, expanding the susceptible host range and geographic distribution for this Vibrio species.
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Affiliation(s)
- Jormil Revilla
- Laboratorio de Fisiología y Genética Marina (FIGEMA), Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Republic of Chile; Programa Doctorado en Acuicultura, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Republic of Chile
| | - Sergio Rodríguez-Rodríguez
- Departamento de Microbiología y Parasitología, Centro de Investigaciones Biológicas (CIBUS)/Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Kingdom of Spain
| | - Ramiro Solórzano
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Republic of Ecuador
| | - Guillermo Reyes
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Republic of Ecuador.
| | - Juan L Barja
- Departamento de Microbiología y Parasitología, Centro de Investigaciones Biológicas (CIBUS)/Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Kingdom of Spain.
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146
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Yang YQ, Li X, Wang ZF, Deng YL, Wang ZZ, Fang XY, Zhang MD, Sun W, Zhao XQ, Liu ZQ, Zhang FL. Whole Genome Sequencing of Kodamaea ohmeri SSK and Its Characterization for Degradation of Inhibitors from Lignocellulosic Biomass. BIOLOGY 2025; 14:458. [PMID: 40427648 PMCID: PMC12109290 DOI: 10.3390/biology14050458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Revised: 04/11/2025] [Accepted: 04/18/2025] [Indexed: 05/29/2025]
Abstract
Lignocellulosic biomass is widely recognized as a renewable resource for bioconversion. However, the presence of inhibitors such as furfural, 5-HMF, and acetic acid can inhibit cell growth, thereby affecting the overall efficiency of the bioconversion process. The studies on the degradation of lignocellulosic hydrolysate inhibitors by Saccharomyces cerevisiae have been limited. In this research, a yeast strain Kodamaea ohmeri can degrade inhibitors furfural, 5-HMF, and acetic acid, and the genome sequence of the strain was analyzed. Furthermore, the molecular detoxification mechanism of K. ohmeri SSK against lignocellulosic hydrolysate inhibitors was predicted using whole genome sequencing. Annotation based on the COG/KEGG databases identified 57 key detoxification genes, including the alcohol dehydrogenase (ADH) gene, aldo-keto/aldehyde reductase (AKR/ARI) gene, and aldehyde dehydrogenase (ALDH) gene. Stress tolerance experiments revealed that the maximum tolerance concentration for the strain was 5.2 g/L of furfural, 2.5 g/L of 5-HMF, and 5.9 g/L of acetic acid, respectively. A NAD(P)+-dependent bifunctional enzyme with possible ADH and ARI activities was found by conserved domain analysis. Phylogenetic analysis indicated that this enzyme shared 99% homology with the detoxification enzyme from S. cerevisiae S288C (GenBank: Q04894.1). This study represents the first comprehensive analysis of the inhibitor detoxification network in K. ohmeri SSK from a genome perspective, providing theoretical targets and design strategies for developing highly efficient biorefinery strains.
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Affiliation(s)
- Yong-Qiang Yang
- School of Life and Health Sciences, Hainan University, Haikou 570228, China;
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Xu Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Zhi-Fei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Yu-Long Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Zhen-Zhi Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Xing-Yu Fang
- School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Mao-Dong Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Wei Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
| | - Zhi-Qiang Liu
- School of Life and Health Sciences, Hainan University, Haikou 570228, China;
| | - Feng-Li Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (X.L.); (Z.-F.W.); (Y.-L.D.); (Z.-Z.W.); (M.-D.Z.); (W.S.); (X.-Q.Z.)
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147
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Hakimi M, Ye F, Saxena A, Hu X, Shen H, Elankumaran P, Stinman CC, Macedo N, Sahin O, Burrough ER, Li G. Genomic insights into the population structure, antimicrobial resistance, and virulence of Brachyspira hyodysenteriae from diverse geographical regions. Microbiol Spectr 2025:e0338624. [PMID: 40272172 DOI: 10.1128/spectrum.03386-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Accepted: 04/04/2025] [Indexed: 04/25/2025] Open
Abstract
Swine dysentery, caused by the anaerobic spirochete Brachyspira hyodysenteriae, leads to mucohemorrhagic diarrhea in grower-finisher pigs, impacting swine production. Knowledge regarding its genomic epidemiology is limited. We performed a whole-genome sequence analysis for 251 B. hyodysenteriae genomes from 10 countries, including 117 isolates sequenced in this study. Phylogenomic analysis based on core-genome single nucleotide polymorphisms (SNPs) revealed nine lineages, with L7 (72 isolates, 28.69%), L9 (67 isolates, 26.69%), and L2 (53 isolates, 21.12%) predominating. Geographical clustering was observed with distinct lineage distributions. Multilocus sequence typing identified 69 sequence types (STs), including 20 novel STs across 251 genomes. Association between specific lineages, STs, and geographical regions was evident, highlighting evolutionary and regional patterns. The pan-genome analysis identified 5,231 genes, categorized into core (1,648), accessory (2,619), and unique (964) components. Functional annotation linked core genes to essential cellular processes, while accessory and unique genes were enriched in genetic variability, defense mechanisms, and secondary metabolism. The pan-genome exhibited a high proportion of hypothetical genes, necessitating further functional characterization. Antimicrobial resistance (AMR) screening detected the tva(A) and lnu(C) genes associated with tiamulin and lincomycin resistance, respectively, in specific lineages and STs. Virulence factor analysis identified genes linked to hemolysin production, iron uptake, and survival in host environments in most isolates, with a subset of genes demonstrating lineage-specific associations that are further linked to pathogenic potential. This comprehensive genomic epidemiological analysis elucidates the genetic diversity, antimicrobial resistance, and virulence of B. hyodysenteriae globally, enhancing understanding of its epidemiology and guiding interventions to mitigate swine dysentery. IMPORTANCE Brachyspira hyodysenteriae, the primary causative agent of swine dysentery, remains a less-studied pathogen than other bacterial species that impact animal health. This study uses whole-genome sequencing and advanced phylogenomic approaches to reveal the genetic diversity and geographical distribution of B. hyodysenteriae isolates, focusing on U.S. populations. The identification of nine distinct phylogenetic lineages and associated sublineages highlights the pathogen's complex population structure and regional variation. Importantly, the study detects AMR genes, including tva(A) and lnu(C), linked to tiamulin and lincomycin resistance, that may pose significant challenges to disease management. The analysis also identifies virulence-associated genes, shedding light on molecular mechanisms underlying pathogenicity. By combining core-genome SNP phylogenies with multilocus sequence typing and accessory genome insights, this work provides a robust framework for a better understanding of B. hyodysenteriae evolution. Overall, these findings underscore the importance of genomic surveillance in informing control strategies and improving swine health worldwide.
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Affiliation(s)
- Maria Hakimi
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, USA
| | - Fangshu Ye
- Department of Statistics, Iowa State University, Ames, Iowa, USA
| | - Anugrah Saxena
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
| | - Xiao Hu
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
| | - Huigang Shen
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
| | - Paarthiphan Elankumaran
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Chloe C Stinman
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
| | - Nubia Macedo
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Orhan Sahin
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Eric R Burrough
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, Iowa, USA
| | - Ganwu Li
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, Iowa, USA
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, Iowa, USA
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148
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Ayoub H, Kumar MS, Mehta R, Sethuraj SE, Thomas P, Dhanze H, Dubey M, Salih HM, Chandrashekaraiah GB, Cull CA, Veeranna RP, Amachawadi RG. Genomic insights into Brucella melitensis in India: stability of ST8 and the role of virulence genes in regional adaptations. Microbiol Spectr 2025:e0264724. [PMID: 40272150 DOI: 10.1128/spectrum.02647-24] [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: 10/20/2024] [Accepted: 03/23/2025] [Indexed: 04/25/2025] Open
Abstract
Brucella melitensis is a highly infectious zoonotic pathogen responsible for brucellosis, which significantly affects both human and livestock health worldwide. This study employed whole-genome sequencing (WGS) to analyze the genetic diversity of 24 B. melitensis isolates from India. Pangenome analysis revealed a highly conserved nature with the involved strains having very limited accessory genes. Multilocus Sequence Typing (MLST) identified sequence type ST8 as predominant among Indian strains. Analysis of virulence genes revealed a total of 43 virulence-related genes in all strains, emphasizing their critical role in the pathogenicity of B. melitensis. Unique gene profiles and distinct phylogenetic clusters suggest regional adaptations and evolutionary pressures. The comprehensive genomic insights from this study help to elucidate the geographic distribution and interspecies transmission of Indian strains, highlighting the importance of targeted brucellosis control measures in India. Additionally, the identification of conserved virulence genes involved in immune evasion and intracellular survival highlights their importance in the bacterium's pathogenicity. This research contributes to the global understanding of B. melitensis genomic diversity, providing valuable insights for broader epidemiological studies and brucellosis management strategies worldwide.IMPORTANCEB. melitensis is a significant cause of illness in both humans and animals, particularly in India, where the disease remains a major concern. This study highlights that only a few genetic types of the bacteria are circulating in the region, which means control efforts can be better focused on these specific types. By understanding the unique characteristics of Indian strains, and how these strains spread and adapt, this research offers valuable guidance for improving brucellosis prevention strategies. These insights can help in developing more effective diagnostic tools, enhancing vaccination efforts, and strengthening disease control programs to reduce the impact of brucellosis on public health and livestock industries.
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Affiliation(s)
- Haris Ayoub
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - M Suman Kumar
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Rishabh Mehta
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Sanjumon E Sethuraj
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Himani Dhanze
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Muskan Dubey
- Xavier University School of Medicine, Xavier University School of Veterinary Medicine, Oranjestad, Aruba
| | - Harith M Salih
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Charley A Cull
- Midwest Veterinary Services, Inc, Oakland, New Jersey, USA
| | - Ravindra P Veeranna
- Xavier University School of Medicine, Xavier University School of Veterinary Medicine, Oranjestad, Aruba
| | - Raghavendra G Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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149
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Sun Y, Cai Q, Li T, Chen J, Fang Y. Genome assembly of Klebsiella michiganensis based on metagenomic next-generation sequencing reveals its genomic characteristics in population genetics and molecular epidemiology. Front Microbiol 2025; 16:1546594. [PMID: 40342595 PMCID: PMC12058774 DOI: 10.3389/fmicb.2025.1546594] [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: 12/17/2024] [Accepted: 04/02/2025] [Indexed: 05/11/2025] Open
Abstract
Introduction Klebsiella michiganensis, a significant member of the Klebsiella oxytoca complex, has emerged as a potential pathogen in clinical settings. Despite extensive research on the Klebsiella pneumoniae complex, the pathogenicity and drug resistance of the K. oxytoca complex remain understudied, particularly regarding the reconstruction of whole genomes from metagenomic next-generation sequencing (mNGS) data. Methods In this study, bronchoalveolar lavage fluid (BALF) from a 55-year-old woman with a suspected right lung infection in Anhui Province, China, was analyzed using mNGS. Results Three distinct assembly strategies were employed to reconstruct the genome of K. michiganensis, leading to the identification of a novel ST452 strain, KMLRT2206. Comprehensive genomic analysis of this strain and 206 clinical isolates (genomes downloaded from public databases) revealed the population structure, distribution of drug resistance genes, and virulence factors of K. michiganensis. The results demonstrated significant genetic diversity, with the species divided into three major clades, each exhibiting distinct patterns of drug resistance and virulence genes. Notably, 38.6% of the strains harbored the bla OXY-1-1 gene, highlighting a potential threat of drug resistance. While virulence gene distribution was not correlated with sequence type (ST), significant differences were observed among clades. Conclusion This study underscores the value of mNGS combined with optimized assembly strategies for accurate species identification within the K. oxytoca complex, providing critical insights for clinical pathogen detection and epidemiological surveillance.
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Affiliation(s)
- Yong Sun
- Department of Respiratory and Critical Care Medicine, Anqing Medical Center of Anhui Medical University, Anqing Municipal Hospital, Anqing, China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Tianyu Li
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Jingbo Chen
- Faculty of Naval Medicine, Navy Medical University, Shanghai, China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc., Shanghai, China
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150
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Alnaimat SM, Abushattal S, Dmour SM, Al-Awaida WJ, Ayyash AM, Goh KW. Genomic insights into the taxonomic status and bioactive gene cluster profiling of Bacillus velezensis RVMD2 isolated from desert rock varnish in Ma'an, Jordan. PLoS One 2025; 20:e0319345. [PMID: 40273114 PMCID: PMC12021177 DOI: 10.1371/journal.pone.0319345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 01/30/2025] [Indexed: 04/26/2025] Open
Abstract
Extreme environments like arid and semi-arid deserts harbor unique microbial diversity, offering rich sources of specialized microbial metabolites. This study explores Bacillus velezensis RVMD2, a strain isolated from rock varnish in the Ma'an Desert, Jordan. The genome was sequenced using the Illumina NextSeq 2000 platform, resulting in a 4,212,579 bp assembly with a GC content of 45.94%. The assembled genome comprises 112 contigs and encodes 4,250 proteins, 77 tRNA genes, and 4 rRNA genes. Phylogenetic analysis of the 16S rRNA gene indicated a 99.84% similarity to previously identified B. velezensis strains. Whole-genome phylogeny using EzBiome, MiGA, and TYGS confirmed its classification as B. velezensis. Functional annotation identified genes involved in carbohydrate metabolism, including 324 carbohydrate-active enzyme (CAZyme) genes, stress response, and secondary metabolite biosynthesis. The genome also contains 50 genes associated with heavy metal resistance and plant growth promotion. Analysis using AntiSMASH identified 12 biosynthetic gene clusters involved in the production of secondary metabolites, including fengycin, surfactin, polyketides, terpenes, and bacteriocins. Notably, several clusters did not match any known sequences, suggesting the presence of potentially novel antimicrobial compounds. The genomic features of RVMD2 highlight its adaptability to extreme environments and its potential for biotechnological applications, including bioremediation and the discovery of novel bioactive metabolites.
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Affiliation(s)
- Sulaiman M. Alnaimat
- Department of Medical Analysis, Princess Aisha Bint Al-Hussein College of Nursing and Health Sciences, Al-Hussein Bin Talal University, Ma’an, Jordan
| | - Saqr Abushattal
- Department of Medical Analysis, Princess Aisha Bint Al-Hussein College of Nursing and Health Sciences, Al-Hussein Bin Talal University, Ma’an, Jordan
| | - Saif M. Dmour
- Department of Medical Analysis, Princess Aisha Bint Al-Hussein College of Nursing and Health Sciences, Al-Hussein Bin Talal University, Ma’an, Jordan
| | - Wajdy J. Al-Awaida
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba, Jordan
| | - Amani M. Ayyash
- Department of Pharmacy, Faculty of Health Sciences, American University of Madaba, Madaba, Jordan
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai, Malaysia
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