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Dong X, Xiang Y, Li L, Zhang Y, Wu T. Genomic insights into the rapid rise of Pseudomonas aeruginosa ST463: A high-risk lineage's adaptive strategy in China. Virulence 2025; 16:2497901. [PMID: 40320374 PMCID: PMC12051580 DOI: 10.1080/21505594.2025.2497901] [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: 10/01/2024] [Revised: 12/19/2024] [Accepted: 04/17/2025] [Indexed: 05/08/2025] Open
Abstract
High-risk lineages of Pseudomonas aeruginosa pose a serious threat to public health, causing severe infections with high mortality rates and limited treatment options. The emergence and rapid spread of the high-risk lineage ST463 in China have further exacerbated this issue. However, the basis of its success in China remains unidentified. In this study, we analyzed a comprehensive dataset of ST463 strains from 2000 to 2023 using whole genome sequencing to unravel the epidemiological characteristics, evolutionary trajectory, and antibiotic resistance profiles. Our findings suggest that ST463 likely originated from a single introduction from North America in 2007, followed by widespread domestic dissemination. Since its introduction, the lineage has undergone significant genomic changes, including the acquisition of three unique regions that enhanced its metabolism and adaptability. Frequent recombination events, along with the burden of bacteriophages, antibiotic resistance genes, and the spread of c1-type (blaKPC-2) plasmid-carrying strains, have played crucial roles in its expansion in China. Mutation analysis reveals adaptive responses to antibiotics and selective pressures on key virulence factors, indicating that ST463 is evolving toward a more pathogenic lifestyle.
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Affiliation(s)
- Xu Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanghui Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Tiantian Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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2
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Serna C, Calderón Bernal JM, Torre-Fuentes L, García Muñoz Á, Díez Guerrier A, Hernández M, Fernández-Garayzábal JF, Vela AI, Cid D, Alvarez J. Integrative and conjugative elements associated with antimicrobial resistance in multidrug resistant Pasteurella multocida isolates from bovine respiratory disease (BRD)-affected animals in Spanish feedlots. Vet Q 2025; 45:1-15. [PMID: 40055923 PMCID: PMC11892046 DOI: 10.1080/01652176.2025.2474220] [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: 09/24/2024] [Revised: 12/16/2024] [Accepted: 02/24/2025] [Indexed: 05/13/2025] Open
Abstract
The emergence of multidrug-resistance (MDR) in Pasteurella multocida, a major contributor to bovine respiratory disease (BRD) is being increasingly reported, often linked to the carriage of antimicrobial resistance genes (ARGs) on integrative and conjugative elements (ICEs). The resistance phenotype for 19 antimicrobials was determined using broth microdilution in 75 Pasteurella multocida isolates from healthy and BRD-affected cattle from five feedlots. The genomes of 32 isolates were sequenced to identify ARG) and mobile genetic elements (MGEs) and assess their genetic diversity. MDR isolates (with phenotypic resistance to aminoglycosides, macrolides, fluoroquinolones and/or tetracyclines) were primarily found among BRD-affected compared to healthy animals. Non-susceptible isolates, belonging to ST79 and ST13, harbored point mutations and four to nine ARGs, including rarely reported mechanisms in Europe (mph(E), msr(E) and aadA31 ARGs and newly described mutations in the gyrA/parC genes). All ARGs were linked to the presence of MGEs including two ICEs, Tn7407 and the novel Tn7809, a prophage and a putative composite transposon. Clonally related isolates were found in different batches from the same feedlot, suggesting maintenance of MDR strains. Our findings demonstrate the diverse genetic basis of AMR in P. multocida from BRD-affected cattle in Spain, emphasizing the role of MGEs in the ARG dissemination.
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Affiliation(s)
- Carlos Serna
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | | | - Laura Torre-Fuentes
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Ángel García Muñoz
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Alberto Díez Guerrier
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | - José Francisco Fernández-Garayzábal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Ana Isabel Vela
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
| | - Dolores Cid
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Julio Alvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET,), Universidad Complutense, Madrid, Spain
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3
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Valentin C, Brito Rodrigues P, Verce M, Delbauve S, La Palombara L, Demaret F, Allard J, Salmon I, Cani PD, Köhler A, Everard A, Flamand V. Maternal probiotic exposure enhances CD8 T cell protective neonatal immunity and modulates offspring metabolome to control influenza virus infection. Gut Microbes 2025; 17:2442526. [PMID: 39710590 DOI: 10.1080/19490976.2024.2442526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 12/04/2024] [Accepted: 12/09/2024] [Indexed: 12/24/2024] Open
Abstract
Maternal gut microbiota composition contributes to the status of the neonatal immune system and could influence the early life higher susceptibility to viral respiratory infections. Using a novel protocol of murine maternal probiotic supplementation, we report that perinatal exposure to Lacticaseibacillus rhamnosus (L.rh) or Bifidobacterium animalis subsp. lactis (B.lac) increases the influenza A/PR8 virus (IAV) clearance in neonates. Following either supplementation, type 1 conventional dendritic cells (cDC1) were amplified in the lymph nodes leading to an enhanced IAV antigen-experienced IFN-γ producing effector CD8 T cells in neonates and IAV-specific resident memory CD8 T cells in adulthood. This was compatible with a higher protection of the offspring upon a secondary infection. Interestingly, only mice born to L.rh supplemented mothers further displayed an increased activation of IFN-γ producing virtual memory CD8 T cells and a production of IL-10 by CD4 and CD8 T cells that could explain a better control of the lung damages upon infection. In the offspring and the mothers, no disturbance of the gut microbiota was observed but, as analyzed through an untargeted metabolomic approach, both exposures modified neonatal plasma metabolites. Among them, we further demonstrated that genistein and 3-(3-hydroxyphenyl)propionic acid recapitulate viral clearance or cDC1 activation in neonates exposed to IAV. We conclude that maternal L.rh or B.lac supplementation confers the neonates specific metabolomic modulations with a better CD8 T cell-mediated immune protection against IAV infection.
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Affiliation(s)
- Clara Valentin
- Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Patricia Brito Rodrigues
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
| | - Marko Verce
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
| | - Sandrine Delbauve
- Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Léa La Palombara
- Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Florine Demaret
- Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Justine Allard
- DIAPath, Center for Microscopy and Molecular Imaging, Université Libre de Bruxelles, Gosselies, Belgium
| | - Isabelle Salmon
- DIAPath, Center for Microscopy and Molecular Imaging, Université Libre de Bruxelles, Gosselies, Belgium
| | - Patrice D Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
- Institute of Experimental and Clinical Research (IREC), UCLouvain, Université Catholique de Louvain, Brussels, Belgium
| | - Arnaud Köhler
- Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Amandine Everard
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, UCLouvain, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
| | - Véronique Flamand
- Institute for Medical Immunology, Université Libre de Bruxelles, Gosselies, Belgium
- ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
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Mukhopadhya I, Martin JC, Shaw S, Gutierrez-Torrejon M, Boteva N, McKinley AJ, Gratz SW, Scott KP. Novel insights into carbohydrate utilisation, antimicrobial resistance, and sporulation potential in Roseburia intestinalis isolates across diverse geographical locations. Gut Microbes 2025; 17:2473516. [PMID: 40089923 PMCID: PMC11913394 DOI: 10.1080/19490976.2025.2473516] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 02/11/2025] [Accepted: 02/21/2025] [Indexed: 03/17/2025] Open
Abstract
Roseburia intestinalis is one of the most abundant and important butyrate-producing human gut anaerobic bacteria that plays an important role in maintaining health and is a potential next-generation probiotic. We investigated the pangenome of 16 distinct strains, isolated over several decades, identifying local and time-specific adaptations. More than 50% of the genes in each individual strain were assigned to the core genome, and 77% of the cloud genes were unique to individual strains, revealing the high level of genome conservation. Co-carriage of the same enzymes involved in carbohydrate binding and degradation in all strains highlighted major pathways in carbohydrate utilization and reveal the importance of xylan, starch and mannose as key growth substrates. A single strain had adapted to use rhamnose as a sole growth substrate, the first time this has been reported. The ubiquitous presence of motility and sporulation gene clusters demonstrates the importance of these phenotypes for gut survival and acquisition of this bacterium. More than half the strains contained functional, potentially transferable, tetracycline resistance genes. This study advances our understanding of the importance of R. intestinalis within the gut ecosystem by elucidating conserved metabolic characteristics among different strains, isolated from different locations. This information will help to devise dietary strategies to increase the abundance of this species providing health benefits.
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Affiliation(s)
- Indrani Mukhopadhya
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
- Microbiology and Immunity, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jennifer C. Martin
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, UK
- All Wales Medical Genomics Service, Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, UK
| | | | - Nikoleta Boteva
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Aileen J. McKinley
- Department of Surgery, Aberdeen Royal Infirmary Foresterhill, Aberdeen, UK
| | - Silvia W. Gratz
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Karen P. Scott
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
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Samarra A, Renwick S, Arzamasov AA, Rodionov DA, Spann K, Cabrera-Rubio R, Acuna-Gonzalez A, Martínez-Costa C, Hall L, Segata N, Osterman AL, Bode L, Collado MC. Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome. Gut Microbes 2025; 17:2501192. [PMID: 40340669 PMCID: PMC12068340 DOI: 10.1080/19490976.2025.2501192] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 03/22/2025] [Accepted: 04/28/2025] [Indexed: 05/10/2025] Open
Abstract
Breast milk, rich in human milk oligosaccharides (HMOs), supports the early-life colonization of beneficial bacteria such as bifidobacteria and lactobacilli, potentially reducing early-life antibiotic resistance. However, antibiotic treatment may interfere with the beneficial functions of HMO-degrading bacteria. This study investigated the metabolism of HMOs by bifidobacteria and lactobacilli isolated from human milk and mother-infant paired fecal samples, along with their antibiotic resistance profiles. Understanding these species- and sample-type-specific interactions will provide valuable insights into how bioactive components in human milk may shape the infant resistome during early life. A total of 39 Bifidobacterium and 14 Lactobacillaceae strains were isolated from paired mother-infant fecal and breast milk samples. Whole genome sequencing (WGS) allowed functional predictions on the HMO metabolism abilities and the resistance genotype of each strain. In vitro HMO utilization was assessed using growth kinetics assays combined with HMO glycoprofiling in culture supernatant. The minimum inhibitory concentration (MIC) was also determined for each strain. HMO metabolism by the bifidobacteria was species-specific. Bifidobacterium bifidum (B. bifidum) and Bifidobacterium longum subsp. infantis (B. infantis) exhibited the highest capacity for HMO degradation, consistent with genomic predictions. In contrast, lactobacilli were unable to degrade HMOs in vitro but were predicted to metabolize the by-products of HMO degradation. Phenotypic analysis revealed that B. bifidum strains had the lowest levels of antibiotic resistance, while Bifidobacterium animalis subsp. lactis (B. lactis) strains were resistant to most tested antibiotics. Overall, B. bifidum demonstrated the strongest HMO-degrading ability while remaining the most antibiotic-susceptible species. Early-life colonizing bifidobacterial species possess the essential machinery required to degrade HMOs and are highly susceptible to antibiotics. A better understanding of these dynamics could inform clinical strategies to protect and restore the infant gut microbiome, particularly in neonates exposed to antibiotics.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Valencia, Spain
| | - Simone Renwick
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, CA, USA
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Kennedy Spann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Valencia, Spain
| | - Antia Acuna-Gonzalez
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, Valencia, Spain
| | - Lindsay Hall
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Department of Microbes, Infection and Microbiomes, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham, Birmingham, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lars Bode
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, CA, USA
- Human Milk Institute, University of California San Diego, La Jolla, CA, USA
| | - MCarmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Valencia, Spain
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6
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Grote A, Hendin N, Amit S, Adani B, Rahav G, Adler A, Livny J, Gal-Mor O, Earl AM. Genetic diversity of Salmonella enterica during acute human infections. Gut Microbes 2025; 17:2491666. [PMID: 40260673 PMCID: PMC12026202 DOI: 10.1080/19490976.2025.2491666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 03/27/2025] [Accepted: 04/05/2025] [Indexed: 04/24/2025] Open
Abstract
The ubiquitous bacterial pathogen Salmonella enterica is the causative agent of both enteric fever and gastroenteritis. Despite its significant global health burden, we lack an understanding of its genetic diversity during acute infection, with ramifications for treatment and prevention. Here, we investigated within-host infection diversity of acute salmonellosis using whole-genome sequencing of blood or stool isolates obtained from 23 different patients. We found that intestinal infections exhibited greater genetic variation than blood infections, including in their plasmid content. While same-patient isolates were separated by 10 single nucleotide polymorphisms or less, they often differed in the carriage of genes or alleles, including those associated with antibiotic resistance or virulence. Given the longstanding emphasis on single colony isolation in clinical and laboratory microbiology, these findings have implications for how we both study evolution and transmission and how we treat salmonellosis in an age of increasing antibiotic resistance.
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Affiliation(s)
- Alexandra Grote
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Natav Hendin
- The Infectious Diseases unit, Sheba Medical Center, Tel-Hashomer, Israel
| | - Sharon Amit
- Microbiology Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Boaz Adani
- The Infectious Diseases unit, Sheba Medical Center, Tel-Hashomer, Israel
| | - Galia Rahav
- The Infectious Diseases unit, Sheba Medical Center, Tel-Hashomer, Israel
| | - Amos Adler
- Clinical Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Tel-Aviv University, Tel-Aviv, Israel
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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7
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Chen Y, Liu Q, Xu XW. Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions. MARINE POLLUTION BULLETIN 2025; 217:118121. [PMID: 40344797 DOI: 10.1016/j.marpolbul.2025.118121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Revised: 04/22/2025] [Accepted: 05/05/2025] [Indexed: 05/11/2025]
Abstract
Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3-]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.
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Affiliation(s)
- Yuhao Chen
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200000, PR China; Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310000, PR China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310000, PR China; Ocean College, Zhejiang University, Hangzhou, Zhejiang 310000, PR China.
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200000, PR China; Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang 310000, PR China; Ocean College, Zhejiang University, Hangzhou, Zhejiang 310000, PR China; National Deep Sea Center, Ministry of Natural Resources, Qingdao, Shandong 266237, PR China.
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8
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Jiang S, Matuszewska M, Chen M, Hong Y, Chen Y, Wang Z, Zhuang H, Sun L, Zhu F, Wang H, Wu X, Ji S, Holmes MA, Ba X, Chen Y, Yu Y. Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance. Microbiol Res 2025; 297:128196. [PMID: 40311457 DOI: 10.1016/j.micres.2025.128196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 04/23/2025] [Accepted: 04/24/2025] [Indexed: 05/03/2025]
Abstract
The globally disseminated Staphylococcus aureus ST5 clone poses a major public health threat due to its multidrug resistance and virulence. Here, we identified an agr-dysfunctional (agrA-I238K) ST5 MRSA clone that has spread across East and Southeast Asia, with recent increases in China since its emergence in the 1970s. Comparative genomic analyses identified distinct single-nucleotide polymorphisms and mobile genetic elements linked to enhanced resistance and virulence. This clone exhibits resistance to seven antimicrobial classes, including third-generation tetracyclines and fusidic acid, and shares phenotypic and genetic similarities with the vancomycin-intermediate S. aureus Mu50 strain, including reduced susceptibility to vancomycin, teicoplanin, and daptomycin. The agrA-I238K mutation attenuates hemolytic activity, increases biofilm formation, and reduces daptomycin susceptibility, suggesting a key role in the clone's success. Our results demonstrate the important role of agrA-I238K mutation in the widespread distribution of agr-dysfunctional MRSA and highlight the importance of genomic surveillance in tracking the spread of agr-dysfunctional ST5 MRSA.
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Affiliation(s)
- Shengnan Jiang
- Centre of Laboratory Medicine, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China; Zhejiang University School of Medicine, Hangzhou, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, University of Cambridge, Cambridge, UK
| | - Mengzhen Chen
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Yueqin Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiyi Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengan Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hemu Zhuang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Sun
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiteng Zhu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiping Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueqing Wu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shujuan Ji
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Yan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Yunsong Yu
- Centre of Laboratory Medicine, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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9
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Li G, Srinivasan V, Tooker NB, Wang D, Onnis-Hayden A, Bott C, Dombrowski P, Pinto A, Gu AZ. Metagenomic analysis revealed community-level metabolic differences between full-scale EBPR and S2EBPR systems. WATER RESEARCH 2025; 280:123509. [PMID: 40138860 DOI: 10.1016/j.watres.2025.123509] [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: 08/30/2024] [Revised: 03/11/2025] [Accepted: 03/15/2025] [Indexed: 03/29/2025]
Abstract
Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) has emerged as a promising technology addressing certain challenges of conventional Enhanced Biological Phosphorus Removal (EBPR), notably stability in phosphorus removal, yet the underlying mechanisms are not fully understood. Metagenomic analysis presents a powerful approach to elucidate community-level metabolic differences between EBPR and S2EBPR configurations. In this study, we compared three EBPR and three S2EBPR activated sludge communities using metagenomic analysis at taxonomy, key functional pathways/genes, and polyphosphate-metabolism marker genes. Our analysis revealed larger genus-level diversity variance in S2EBPR communities, indicating distinct microbial community compositions influenced by different operational configurations. A higher diversity index in the S2EBPR than the EBPR was observed, and a higher Ca. Accumulibacter abundance was detected in EBPRs, whereas the fermentative candidate PAOs genera, including Ca. Phosphoribacter and Ca. Promineifilum, were more abundant in S2EBPR systems. EBPR and S2EBPR groups displayed similar gene and pathway abundance patterns related to core metabolisms essential for carbon and nitrogen metabolism. PolyP-metabolism marker gene phylogeny analysis suggested that exopolyphosphatase gene (ppx) showed better distinctions between EBPR and S2EBPR communities than polyphosphate kinase gene (ppk). This also highlighted the needs in fine-cale microdiversity analysis and finding novel Ca. Accumulibacter clades and species as resolved using the ppk gene. These findings provide valuable insights into AS community dynamics and metabolic functionalities, paving the way for further research into optimizing phosphorus removal processes in wastewater treatment systems.
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Affiliation(s)
- Guangyu Li
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Varun Srinivasan
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States; Brown and Caldwell, One Tech Drive, Andover, MA 01810, United States
| | - Nicholas B Tooker
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Dongqi Wang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States; Department of Municipal and Environmental Engineering, School of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Annalisa Onnis-Hayden
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Charles Bott
- Hampton Roads Sanitation District, Virginia Beach, VA, United States
| | | | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States; Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30318, United States
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States.
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10
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Han Q, Wang Y, Shi C, Qian Y, Wang X, Wang S, Sun X, Yu Q, Li H. Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138101. [PMID: 40174457 DOI: 10.1016/j.jhazmat.2025.138101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Revised: 03/19/2025] [Accepted: 03/28/2025] [Indexed: 04/04/2025]
Abstract
The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.
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Affiliation(s)
- Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yu Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Chenwei Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yuan Qian
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaofang Sun
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China.
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11
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Karthik M, Panchal NK, T M, Bakthavatchalam YD, Neeravi A, Abirami B, Walia K, Veeraraghavan B. Evolutionary insights into NDM variants: Identification and functional analysis of novel NDM-58 in Pseudomonas aeruginosa. Microb Pathog 2025; 204:107574. [PMID: 40228751 DOI: 10.1016/j.micpath.2025.107574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 03/27/2025] [Accepted: 04/09/2025] [Indexed: 04/16/2025]
Abstract
The emergence of New Delhi Metallo-β-lactamase (NDM) variants in P. aeruginosa has significantly contributed to carbapenem resistance, posing a global threat to antimicrobial therapy. The catalytic activity of NDM, dependent on Zn (II), is enhanced by specific mutations. In this study, we report the identification and characterization of a novel NDM-58 variant (GenBank: OR081828.1) in P. aeruginosa BA24848, which exhibited resistance to multiple β-lactams, including cephalosporins, carbapenems, and BL/BLI combinations. WGS revealed that NDM-58 harbors a unique P185S substitution. This strain is associated with other ARGs (blaPAO, PME-1, fosA, blaOXA-396, blaOXA-494, blaOXA-50, sul1, dfrA1, qacE, aph(3')-VI, qnrVC1, and cat7), indicating a XDR phenotype. Comparative genomic analysis revealed the presence of MGEs (ISpre2, ISPa6, ISPa2, ISPsy29, IS26, Tn4661, ISPa37, and ISUnCu4) associated with NDM-58, which may facilitate the horizontal transfer of resistance determinants. Structural modeling and molecular dynamics simulations demonstrated that NDM-58 exhibits altered stability and compactness compared to NDM-1, likely influencing its enzymatic activity and resistance profile. Residual conservation analysis revealed that Pro185 is highly conserved, and its substitution to serine may impact protein stability and function. The molecular dynamics analysis indicated that NDM-58 has lower residual fluctuations and increased flexibility, which may enhance its adaptability under varying physiological conditions. Our findings provide novel insights into the evolutionary dynamics of NDM enzymes and the role of genetic environments in their dissemination. Understanding these mechanisms is crucial for developing effective surveillance and mitigation strategies against emerging carbapenem-resistant P. aeruginosa.
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Affiliation(s)
- Maruthan Karthik
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Nagesh Kishan Panchal
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Monisha T
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Baby Abirami
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
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12
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Li X, Shao Q, Li L, Xie L, Ruan Z, Fang Q. Cryo-EM Reveals Structural Diversity in Prolate-headed Mycobacteriophage Mycofy1. J Mol Biol 2025; 437:169126. [PMID: 40187685 DOI: 10.1016/j.jmb.2025.169126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/07/2025]
Abstract
Mycobacteriophages show promise in treating antibiotic-resistant mycobacterial infections. Here, we isolated Mycofy1, a mycobacteriophage, using M. smegmatis as a host. Cryo-EM analysis revealed that Mycofy1 possesses a prolate head and a long non-contractile tail. We determined structures of its head, head-to-tail interface, terminator, and tail tube to resolutions of ∼3.5 Å. Unexpectedly, we identified two distinct types of prolate head structures, exhibiting a 36° relative rotation in the top cap region. Additionally, the head-to-tail interface demonstrated flexibility. Our structures provide high-resolution cryo-EM data of a mycobacteriophage with a prolate head, as well as detailed structural information of the head-to-tail interface and head-proximal tail region in this phage group. These findings advance our understanding of assembly mechanisms in tailed bacteriophages.
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Affiliation(s)
- Xiangyun Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Qianqian Shao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Lin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Linlin Xie
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Zhiyang Ruan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China
| | - Qianglin Fang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China; Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China.
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13
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Huang Y, Li XT, Jiang Z, Liang ZL, Liu W, Liu ZH, Li LZ, Yang ZN, Zhang GQ, Yin HQ, Liang JL, Zhou N, Liu SJ, Jiang CY. Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage. WATER RESEARCH 2025; 278:123367. [PMID: 40020468 DOI: 10.1016/j.watres.2025.123367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 02/16/2025] [Accepted: 02/21/2025] [Indexed: 03/03/2025]
Abstract
Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Jiangxi Institute of Respiratory Disease, Jiangxi Clinical Research Center for Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zong-Ling Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wan Liu
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, PR China
| | - Zheng-Hua Liu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410006, PR China
| | - Liang-Zhi Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410006, PR China
| | - Zhen-Ni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Guo-Qing Zhang
- University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, PR China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410006, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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14
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Abelouah MR, Idbella M, Nouj N, Ben-Haddad M, Hajji S, Ouheddou M, Ourouh J, Iacomino G, El Haouti R, Barra I, Oualid JA, Bonanomi G, Banni M, Alla AA. Marine plastic exposure triggers rapid recruitment of plastic-degrading bacteria and accelerates polymer-specific transformations. JOURNAL OF HAZARDOUS MATERIALS 2025; 490:137724. [PMID: 40037197 DOI: 10.1016/j.jhazmat.2025.137724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 02/15/2025] [Accepted: 02/22/2025] [Indexed: 03/06/2025]
Abstract
Plastic pollution in marine ecosystems is a growing concern, yet the degradation behavior of different plastic types and their interactions with microbial communities remain poorly understood. This study investigated the degradation kinetics and microbial colonization of four widely used plastic materials, surgical masks (most made of PP), PET bottles, PS foam, and PP cups, over 40 days of seawater exposure in the Central Atlantic of Morocco. Mass loss measurement revealed distinct degradation patterns, with PS foam showing the highest mass loss (13 %), followed by PET bottles (5 %), likely due to environmental stressors that promote mechanical fragmentation. Surgical masks and PP cups exhibited minimal degradation, retaining nearly all their original mass, as well as limited extent of biodegradation. Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Diffraction (XRD) analyses showed the formation of oxidative functional groups on PP cups and significant structural changes in PS foam and PET, particularly in their crystalline structures, correlating with their higher mass reduction rates. SEM/EDX biofilm imaging confirmed extensive microbial colonization, particularly on PS and PET surfaces. Using 16S rRNA metabarcoding, we identified a striking enrichment of Exiguobacterium, followed by Pseudomonas, Acinetobacter and Bacillus genera, containing reported plastic degrading strains, which were strongly correlated with the accelerated breakdown of plastics. However, its role in accelerating plastic breakdown in this study remains unclear and may warrant further investigation. Co-occurrence network analysis revealed a progressive shift in microbial community structure, evolving from highly interconnected networks at day 0 to more specialized, modular clusters by day 40, dominated by Proteobacteria and Firmicutes. Atomic Absorption Spectrometry (AAS) demonstrated significant heavy metal accumulation on plastic surfaces, potentially influencing microbial colonization and activity. While the observed fragmentation of PS foam and PET highlights the susceptibility of certain plastics to environmental stressors, this study also positions microbial colonization as a potential contributor to plastic surface changes, providing novel insights into the interplay between microbial communities and plastic degradation in marine environments.
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Affiliation(s)
- Mohamed Rida Abelouah
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco; Laboratory of Agrobio diversity and Ecotoxicology LR20AGR02, ISA, University of Sousse, Tunisia; Higher Institute of Biotechnology, ISBM, University of Monastir, Tunisia.
| | - Mohamed Idbella
- College of Agriculture and Environmental Sciences, AgroBioSciences (AgBS) program, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
| | - Nisrine Nouj
- Institut National Thématique de Recherche Scientifique-Eau (INTR-Eau), Ibn Zohr University, Agadir 80000, Morocco; Laboratory of Materials and Environment (LME), Faculty of Sciences, Ibn Zohr University, Agadir 80000, Morocco
| | - Mohamed Ben-Haddad
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Sara Hajji
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Maryam Ouheddou
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Jamila Ourouh
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Giuseppina Iacomino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, NA 80055, Italy
| | - Rachid El Haouti
- Laboratory of Materials and Environment (LME), Faculty of Sciences, Ibn Zohr University, Agadir 80000, Morocco
| | - Issam Barra
- Mohammed VI Polytechnic University (UM6P), Center of Excellence in Soil and Fertilizer Research in Africa (CESFRA), AgroBioSciences (AgBS), Benguerir 43150, Morocco
| | - Jaouad Abou Oualid
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples Federico II, Portici, NA 80055, Italy
| | - Mohamed Banni
- Laboratory of Agrobio diversity and Ecotoxicology LR20AGR02, ISA, University of Sousse, Tunisia; Higher Institute of Biotechnology, ISBM, University of Monastir, Tunisia
| | - Aicha Ait Alla
- Laboratory of Aquatic Systems: Marine and Continental Environments (AQUAMAR), Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
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15
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Chen P, Yu Q, Wang C, Montoya L, West PT, Xu L, Varoquaux N, Cole B, Hixson KK, Kim YM, Liu L, Zhang B, Zhang J, Li B, Purdom E, Vogel J, Jansson C, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, Taylor JW, Gao C. Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen. THE NEW PHYTOLOGIST 2025; 246:2702-2717. [PMID: 40247824 DOI: 10.1111/nph.70155] [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: 12/04/2024] [Accepted: 03/30/2025] [Indexed: 04/19/2025]
Abstract
Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.
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Affiliation(s)
- Peilin Chen
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyi Yu
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cong Wang
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Patrick T West
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100049, China
| | - Nelle Varoquaux
- Department of Statistics, University of California, Berkeley, CA, 94720, USA
| | - Benjamin Cole
- Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kim K Hixson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ling Liu
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baodan Zhang
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Zhang
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baiyang Li
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, 94720, USA
| | - John Vogel
- Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Christer Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Robert B Hutmacher
- UC Davis Department of Plant Sciences, University of California West Side Research & Extension Center, Five Points, CA, 93624, USA
| | - Jeffery A Dahlberg
- University of California Kearney Agricultural Research & Extension Center, Parlier, CA, 93648, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA, 94710, USA
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Cheng Gao
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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16
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Yuan J, Yang J, Sun Y, Meng Y, He Z, Zhang W, Dang L, Song Y, Xu K, Lv N, Zhang Z, Guo P, Yin H, Shi W. An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP). SCIENCE CHINA. LIFE SCIENCES 2025; 68:1541-1554. [PMID: 40178790 DOI: 10.1007/s11427-024-2894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Accepted: 02/28/2025] [Indexed: 04/05/2025]
Abstract
China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.
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Affiliation(s)
- Junxia Yuan
- Shenzhou Space Biotechnology Group, Beijing, 100086, China
| | - Jinlu Yang
- Beijing Institute of Spacecraft System Engineering, Beijing, 100094, China
| | - Yue Sun
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yaqi Meng
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ziwei He
- Shenzhou Space Biotechnology Group, Beijing, 100086, China
| | - Wende Zhang
- Shenzhou Space Biotechnology Group, Beijing, 100086, China
| | - Lei Dang
- Shenzhou Space Biotechnology Group, Beijing, 100086, China
| | - Yan Song
- Beijing Institute of Spacecraft System Engineering, Beijing, 100094, China
| | - Kanyan Xu
- Beijing Institute of Spacecraft System Engineering, Beijing, 100094, China
| | - Na Lv
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ziding Zhang
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Pei Guo
- Beijing Institute of Spacecraft System Engineering, Beijing, 100094, China
| | - Hong Yin
- Shenzhou Space Biotechnology Group, Beijing, 100086, China.
| | - Wenyu Shi
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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17
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van Westerhoven A, Fokkens L, Wissink K, Kema GJ, Rep M, Seidl M. Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen. NAR Genom Bioinform 2025; 7:lqaf034. [PMID: 40176926 PMCID: PMC11963757 DOI: 10.1093/nargab/lqaf034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 02/19/2025] [Accepted: 03/14/2025] [Indexed: 04/05/2025] Open
Abstract
Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when these chromosomes are missing in the reference genome. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for 73 diverse Fusarium oxysporum genomes, a major fungal plant pathogen with a compartmentalized genome that includes conserved core as well as variable accessory chromosomes. To obtain insights into accessory chromosome dynamics, we first constructed a chromosome similarity network using all-vs-all similarity mapping. We identified eleven core chromosomes conserved across all strains and a substantial number of highly variable accessory chromosomes. Some of these accessory chromosomes are host-specific and likely play a role in determining host range. Using a k-mer based approach, we further identified the presence of these accessory chromosomes in all available (581) F. oxysporum assemblies and corroborated the occurrence of host-specific accessory chromosomes. To further analyze the evolution of chromosomes in F. oxysporum, we constructed a pangenome variation graph per group of homologous chromosomes. This reveals that accessory chromosomes are composed of different stretches of accessory regions, and possibly rearrangements between accessory regions gave rise to these mosaic accessory chromosomes. Furthermore, we show that accessory chromosomes are likely horizontally transferred in natural populations. Our findings demonstrate that a pangenome variation graph is a powerful approach to elucidate the evolutionary dynamics of accessory chromosomes in F. oxysporum, which is not only a useful resource for Fusarium but also provides a framework for similar analyses in other species containing accessory chromosomes.
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Affiliation(s)
- Anouk C van Westerhoven
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3583CH, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Like Fokkens
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Kyran Wissink
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3583CH, Utrecht, the Netherlands
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute of Life Sciences, University of Amsterdam,1090GE, Amsterdam, the Netherlands
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3583CH, Utrecht, the Netherlands
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18
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Molina-López J, Simon-Olea B, Espinoza-Mellado MDR, Hernández-Chiñas U, Eslava-Campos CA, Balcázar JL, González-Villalobos E. Characterization of a new lytic bacteriophage (vB_KpnM_KP1) targeting Klebsiella pneumoniae strains associated with nosocomial infections. Virology 2025; 607:110526. [PMID: 40203466 DOI: 10.1016/j.virol.2025.110526] [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: 11/14/2024] [Revised: 04/01/2025] [Accepted: 04/03/2025] [Indexed: 04/11/2025]
Abstract
A new bacteriophage, vB_KpnM_KP1, was identified and characterized, exhibiting a strong lytic effect on Klebsiella pneumoniae. Host range analysis revealed its effectiveness against 77.4% of clinical strains, achieving complete lysis of those associated with urinary tract infections (UTIs). Phage stability tests demonstrated that vB_KpnM_KP1 remained stable at neutral pH and across all tested temperatures. However, inactivation was observed at high ethanol concentrations and extreme pH levels. Transmission electron microscopy (TEM) analysis identified vB_KpnM_KP1 as a Myo-type phage with an icosahedral head and a contractile tail. Moreover, genome annotation of vB_KpnM_KP1 revealed a linear DNA genome of 174,802 bp, containing 307 open reading frames. Functional predictions suggest the presence of genes involved in DNA replication, transcription, morphogenesis, and cell lysis. Phylogenetic analysis classified vB_KpnM_KP1 within the Slopekvirus genus of the Straboviridae family, showing high sequence identity with phages that infect Enterobacter, Escherichia and Klebsiella species. These findings highlight the potential of phage vB_KpnM_KP1 as an alternative treatment for multidrug-resistant K. pneumoniae infections, particularly in UTIs, while offering valuable insights into its stability and genetic composition.
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Affiliation(s)
- José Molina-López
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas, Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510, Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación, Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720, Mexico City, Mexico.
| | - Berenice Simon-Olea
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas, Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510, Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación, Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720, Mexico City, Mexico; Central de Instrumentación de Microscopía, Depto. Investigación, Instituto Politécnico Nacional-Escuela Nacional de Ciencias Biológicas (IPN-ENCB), Prolongación de Carpio y Plan de Ayala, Mexico City, 11340, Mexico; Laboratorio de Biología Molecular División de Investigación, Departamento de Salud Pública, Facultad de Medicina UNAM, C.P. 04510, Mexico City, Mexico
| | - María Del Rosario Espinoza-Mellado
- Central de Instrumentación de Microscopía, Depto. Investigación, Instituto Politécnico Nacional-Escuela Nacional de Ciencias Biológicas (IPN-ENCB), Prolongación de Carpio y Plan de Ayala, Mexico City, 11340, Mexico
| | - Ulises Hernández-Chiñas
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas, Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510, Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación, Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720, Mexico City, Mexico
| | - Carlos Alberto Eslava-Campos
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas, Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510, Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación, Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720, Mexico City, Mexico
| | | | - Edgar González-Villalobos
- Laboratorio de Biología Molecular División de Investigación, Departamento de Salud Pública, Facultad de Medicina UNAM, C.P. 04510, Mexico City, Mexico.
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19
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Biguenet A, Valot B, El Garch F, Bertrand X, Hocquet D, the ComPath Study Group. Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from companion animals and human infections in Europe. One Health 2025; 20:100971. [PMID: 39898316 PMCID: PMC11787529 DOI: 10.1016/j.onehlt.2025.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 11/26/2024] [Accepted: 01/07/2025] [Indexed: 02/04/2025] Open
Abstract
In high-income countries, dogs and cats are often considered members of the family. Because of this proximity, it has been suggested that pets and humans might exchange bacterial species from their gut microbiota, with multidrug resistant bacteria being of particular concern. The aim of this study was to compare the genomes of third-generation cephalosporin-resistant (3GC-R) Escherichia coli responsible for human and pet infections in Europe. Whole-genome sequencing data from 3GC-R E. coli isolated from clinical samples of humans, dogs and cats, and published in eight European studies were re-analyzed using bioinformatics tools. The acquired genes responsible for 3GC-R were identified. The sequence type (ST) of all genomes were assessed by multilocus sequence typing. Alpha and beta diversities were measured within and between the two populations. We included genomes of 1327 3GC-R E. coli isolated from humans and animals with 109 (8.2 %) being responsible for infections in dogs and cat, and 1218 (91.8 %) responsible for human infections. Alpha diversity analysis suggested greater diversity within ST and 3GC-R genes in the animal population. Beta diversity analysis by principal coordinate analysis separated animal and human strains. ST131 was more abundant in human strains (43.4 %) than in animal strains (14.7 %) (p < 0.001). Six STs, including ST372, were identified almost exclusively in 3GC-R E. coli from animal origin. The bla CTX-M-15 gene was more frequent in humans (49.24 %) than in companion animals (17.9 %) (p < 0.001). The resistance genes bla CMY-2 (30.8 %) and bla CTX-M-1 (15.4 %) were more frequent in E. coli isolated from pets (p < 0.001). We found that populations of 3GC-R E. coli responsible for human and pet infections in Europe do not overlap. Although it cannot rule out occasional transmission of bacteria between pets and humans within a household, it suggests that dogs and cats are not a major source of human infection with this antibiotic-resistant pathogen.
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Affiliation(s)
- Adrien Biguenet
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, F-25000 Besançon, France
- CHU de Besançon, Hygiène Hospitalière, F-25000 Besançon, France
| | - Benoit Valot
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, F-25000 Besançon, France
- Université de Franche-Comté, UFR Santé, CHU de Besançon, Bioinformatique et Big Data Au Service de La Santé, F-25000 Besançon, France
| | - Farid El Garch
- ComPath Study Group, Bruxelles, Belgium
- Vétoquinol SA, Scientific Division, Lure, France
| | - Xavier Bertrand
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, F-25000 Besançon, France
- CHU de Besançon, Hygiène Hospitalière, F-25000 Besançon, France
| | - Didier Hocquet
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, F-25000 Besançon, France
- CHU de Besançon, Hygiène Hospitalière, F-25000 Besançon, France
- Université de Franche-Comté, UFR Santé, CHU de Besançon, Bioinformatique et Big Data Au Service de La Santé, F-25000 Besançon, France
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20
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Ly T, de Melo Teixeira M, Jofre GI, Blanchet D, MacDonald S, Alvarado P, Marques da Silva SH, Sepúlveda VE, Zeb Q, Vreden S, Adenis A, Yegres F, Demar M, Buitrago MJS, Barker BM, Nacher M, Matute DR. High Genetic Diversity of Histoplasma in the Amazon Basin, 2006-2017. Emerg Infect Dis 2025; 31:1169-1177. [PMID: 40439432 PMCID: PMC12123918 DOI: 10.3201/eid3106.241386] [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: 06/02/2025] Open
Abstract
Histoplasmosis is one of the most common pulmonary mycosis diseases in the world. Genome sequencing has revealed that Histoplasma, the cause of histoplasmosis, is composed of several phylogenetic species. The genetic diversity of the pathogen remains largely unknown, especially in the tropics. We sequenced the genomes of 91 Histoplasma isolates from the Amazon basin of South America and used phylogenomics and population genetic evidence to measure the genetic variation of the genus in South America. We report a previously unidentified clade of Histoplasma endemic to the Amazon basin. The lineage is widespread across the continent and contains 5 lineages that are sufficiently differentiated to be considered phylogenetic species. We found the geographic range of those lineages is largely but not completely overlapping. Finally, we found that the patient median age and sex ratio differs among species, suggesting differences in the epidemiology of histoplasmosis caused by each Histoplasma lineage.
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21
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Torres MC, Nemitz LC, da Silva MERJ, Martins AF, Barth AL, Siqueira FM. Genomic and phenotypic characterization of Chryseomicrobium imtechense from canine pyometra. Braz J Microbiol 2025; 56:1421-1427. [PMID: 39934528 PMCID: PMC12095752 DOI: 10.1007/s42770-025-01635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 02/03/2025] [Indexed: 02/13/2025] Open
Abstract
Chryseomicrobium imtechense is a bacterium primarily isolated in environment samples. Here we demonstrated the virulent and antimicrobial resistant profile of the C. imtechense LBV029/19 strain, which was isolated in a pyometra infection in canines, being related as causal agent of that disease. The bacterium was recovered from purulent content of a uterus with pyometra and the identity was confirmed by both, biochemical tests followed MALDI-TOF MS and 16S-rDNA gene sequencing. Antimicrobial susceptibility test, biofilm formation assessment, genomic sequencing with Illumina MiSeq platform followed by the genome characterization and phylogenetic relationships were conducted with C. imtechense LBV029/19 strain. The phylogenetic analysis revealed a close evolutionary relationship between the C. imtechense LBV029/19 and the others publicly available 16S-rDNA genes of C. imtechense. The in vitro assays shown that C. imtechense LBV029/19 has a strong ability for biofilm formation. Additionally, the antimicrobial susceptibility tests revealed a smaller inhibition zone for novobiocin, cefuroxime, and erythromycin. To the best of our knowledge the C. imtechense LBV029/19 genome is the first genome sequenced and available of C. imtechense. Regarding the genotypic profile, resistance genes to tetracyclines, fluoroquinolones, beta-lactams, and multidrug resistance were present in this genome. Additionally, genes encoded to virulence factors, including biofilm formation, motility, and sporulation were identified. The phenotypic profile associated with the genotypic description indicates the potential of C. imtechense LBV029/19 as a primary agent of animal infectious diseases. The genomic description will contribute to the understanding of the biology of the bacterium and the pathogenesis process involved in the disease.
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Affiliation(s)
- Mariana Costa Torres
- Veterinary Bacteriology Laboratory (LaBacVet), Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9090, Prédio 42704, Bairro Agronomia, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil
- Postgraduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Laura Cadó Nemitz
- Veterinary Bacteriology Laboratory (LaBacVet), Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9090, Prédio 42704, Bairro Agronomia, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil
| | - Maria Eduarda Rocha Jacques da Silva
- Veterinary Bacteriology Laboratory (LaBacVet), Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9090, Prédio 42704, Bairro Agronomia, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil
- Postgraduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Andreza Francisco Martins
- Bacterial Resistance Research Laboratory (LABRESIS), Hospital de Clinicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-903, Brazil
- Postgraduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, 90610-000, Brazil
| | - Afonso Luis Barth
- Bacterial Resistance Research Laboratory (LABRESIS), Hospital de Clinicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-903, Brazil
- Postgraduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, 90610-000, Brazil
| | - Franciele Maboni Siqueira
- Veterinary Bacteriology Laboratory (LaBacVet), Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9090, Prédio 42704, Bairro Agronomia, Porto Alegre, Rio Grande do Sul, 91540-000, Brazil.
- Postgraduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil.
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Boby F, Bhuiyan DMNH, Khan DMS, Parvez MM. Draft genome sequence data on Bacillus safensis FB03 isolated from the rhizosphere soil of leguminous plant in Bangladesh. Data Brief 2025; 60:111527. [PMID: 40248511 PMCID: PMC12005218 DOI: 10.1016/j.dib.2025.111527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 03/10/2025] [Accepted: 03/24/2025] [Indexed: 04/19/2025] Open
Abstract
With the aim of investigating the biotechnological potential of Bacillus safensis' FB03, isolated from the rhizosphere soil of Bahrind region of Bangladesh, the current work focused on its complete genomic analysis and phenotypic description. The size of the genome of the isolate was 3.6 Mb with 41.59 % GC content. Genome annotation revealed the presence of many genes related to siderophore production, enzyme degradation, UV and stress tolerance. Six biosynthesis gene clusters for bacillibacin, bacilysin, bottromycin, Schizokinen, fengycin, and lychensin were identified through genome mining. Significantly, FB03 was found to contain only two acquired antimicrobial resistance genes and was anticipated to be non-pathogenic to humans. The openness of the Bacillus safensis pan-genome was demonstrated by the pan-genome analysis. According to this research, Bacillus safensis FB03 may be a good fit for a variety of biotechnological applications.
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Affiliation(s)
- Farhana Boby
- BCSIR Laboratories, Dhaka, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Dr. Md Nurul Huda Bhuiyan
- BCSIR Laboratories, Dhaka, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Dr. Md. Salim Khan
- BCSIR Rajshahi Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Rajshahi 6206, Bangladesh
| | - Md. Mashud Parvez
- BCSIR Laboratories, Dhaka, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
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23
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Choi H, Yu OH, Eyun SI. Evolutionary insights into adaptation of hemocyanins from deep-sea hydrothermal vent shrimps. MARINE POLLUTION BULLETIN 2025; 215:117872. [PMID: 40199006 DOI: 10.1016/j.marpolbul.2025.117872] [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: 03/12/2024] [Revised: 03/22/2025] [Accepted: 03/22/2025] [Indexed: 04/10/2025]
Abstract
Deep-sea hydrothermal vent shrimps inhabit environments with low oxygen levels and may even be exposed to hypoxic conditions. In response, their respiratory pigment, hemocyanin (Hc) may undergo molecular adaptations to enable them to survive in such extreme ecosystems. Therefore, we sampled four Alvinocarididae species from hydrothermal vents in the northern Central Indian Ridge and two types of Hc genes (α and γ) were observed. Employing the branch model, we detected positive selection for the deep-sea hydrothermal vent lineage, including 11 Decapoda species. Furthermore, using the branch-site model, we identified a putative mutant residue (Leu226, Ser377, and Ile390) close to the active site of Hc. Moreover, our results suggested potential molecular docking between two α-type Hc proteins. Thus, this study provides valuable and novel perspectives on the functional significance of the Hc gene in deep-sea hydrothermal vent shrimps, laying the foundation for future investigations in this intriguing area of research.
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Affiliation(s)
- Hyeongwoo Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; Research Center for Marine-Integrated Biomedical Technology, Pukyong National University, Busan 47122, Korea.
| | - Ok-Hwan Yu
- Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Korea.
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea.
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24
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Fernández L, Duarte AC, Jurado A, Bueres L, Rodríguez A, García P. Multipronged impact of environmental temperature on Staphylococcus aureus infection by phage Kayvirus rodi: Implications for biofilm control. Biofilm 2025; 9:100248. [PMID: 39845530 PMCID: PMC11751508 DOI: 10.1016/j.bioflm.2024.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 12/11/2024] [Accepted: 12/27/2024] [Indexed: 01/24/2025] Open
Abstract
Environmental cues sometimes have a direct impact on phage particle stability, as well as bacterial physiology and metabolism, having a profound effect on phage infection outcome. Here, we explore the impact of temperature on the interplay between phage Kayvirus rodi (phiIPLA-RODI) and its host, Staphylococcus aureus. Our results show that phiIPLA-RODI is a more effective predator at room (25 °C) compared to body temperature (37 °C) against planktonic cultures of several strains with varying degrees of phage susceptibility. This result differs from most known examples of temperature-dependent phage infection, in which optimum infection is correlated with the host growth rate. Further characterization of this phenomenon was carried out with strains IPLA15 and IPLA16, whose respective MICs were 7 log units and a 1-log unit higher at 37 °C than at 25 °C. Our results demonstrated that the phage also had a greater impact at room temperature during biofilm development and for the treatment of preformed biofilms. There was no difference in phage adsorption between the two temperatures for strain IPLA16. Conversely, adsorption of phiIPLA-RODI to IPLA15 was reduced at 37 °C compared to 25 °C. Moreover, confocal microscopy analysis indicated that the biofilm matrix of both strains has a greater content of PIA/PNAG at 37 °C than at 25 °C. Regarding infection parameters, we observed longer duration of the lytic cycle at 25 °C for both strains, and infection of IPLA15 by phiIPLA-RODI resulted in a smaller burst size at 37 °C than at 25 °C. Finally, we also found that the rate of phage resistant mutant selection was higher at 37 °C for both strains. Altogether, this information highlights the impact that bacterial responses to environmental factors have on phage-host interactions. Moreover, phage phiIPLA-RODI appears to be a highly effective candidate for biofilm disinfection at room temperature, while its efficacy in biofilm-related infections will require combination with other antimicrobials.
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Affiliation(s)
- Lucía Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC)C/ Francisco Pintado Fe 26, 33011, Oviedo, Asturias, Spain
- DairySafe GroupInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ana Catarina Duarte
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC)C/ Francisco Pintado Fe 26, 33011, Oviedo, Asturias, Spain
- DairySafe GroupInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Andrea Jurado
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC)C/ Francisco Pintado Fe 26, 33011, Oviedo, Asturias, Spain
- DairySafe GroupInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Laura Bueres
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC)C/ Francisco Pintado Fe 26, 33011, Oviedo, Asturias, Spain
- DairySafe GroupInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC)C/ Francisco Pintado Fe 26, 33011, Oviedo, Asturias, Spain
- DairySafe GroupInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pilar García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC)C/ Francisco Pintado Fe 26, 33011, Oviedo, Asturias, Spain
- DairySafe GroupInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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25
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Pagnossin D, Smith A, Weir W, McDonald E, Coelho J, Ure R, Oravcová K. Epidemiological and genomic characterisation of an outbreak of Streptococcus pyogenes emm5.23. J Infect 2025; 90:106498. [PMID: 40319945 DOI: 10.1016/j.jinf.2025.106498] [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: 11/06/2024] [Revised: 04/15/2025] [Accepted: 04/25/2025] [Indexed: 05/07/2025]
Abstract
OBJECTIVES This retrospective cross-sectional study examined the epidemiology, clinical presentations, and genomics of Streptococcus pyogenes genotype emm5.23, linked to severe outcomes in Scotland. METHODS Between 2014 and 2022, 58 cases of invasive Group A Streptococcus (iGAS) disease associated with emm5.23 were reported in Scotland. Surveillance data from 45 cases were analysed for clinical characteristics and risk factors. Whole-genome sequencing (WGS) included all available emm5.23 strains from Scotland (n=58), a subset from England (n=29), and emm5 strains of non-5.23 subtypes from Scotland (n=10), England (n=2), and Canada (n=1). RESULTS Nearly all cases (96%, 43/45) were hospitalised, of whom 33% (15/45) required intensive care and 20% (9/45) died with iGAS. The most common presentations were bacteraemia (51%, 23/45) and pneumonia (24%, 11/45). WGS identified an emerging emm5.23 clade in Scotland, encompassing most isolates, which shared highly similar genomes and three non-synonymous polymorphisms. CONCLUSIONS Although genomic traits known to increase GAS virulence potential were not found, polymorphisms that may affect the emm5.23 phenotype were detected. This suggests this emm5.23 genotype was transiently successful rather than hypervirulent, with low population-level immunity contributing to its spread. This study emphasises the need for integration of real-time genomic data in public health surveillance to enhance source attribution and guide interventions.
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Affiliation(s)
| | - Andrew Smith
- University of Glasgow, Glasgow, Scotland, UK; Scottish Microbiology Reference Laboratories, Glasgow, Scotland, UK
| | | | | | | | - Roisin Ure
- Scottish Microbiology Reference Laboratories, Glasgow, Scotland, UK
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26
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Patra SD, Ghosh S, Panda RK, Sahu BR, Misra N, Kushwaha GS, Suar M. Whole genome sequence analysis of multidrug-resistant Salmonella enterica Typhimurium ms203 provides insights into virulence and antibiotic resistance. Curr Genet 2025; 71:12. [PMID: 40448711 DOI: 10.1007/s00294-025-01318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2025] [Revised: 05/21/2025] [Accepted: 05/22/2025] [Indexed: 06/02/2025]
Abstract
Salmonella enterica subspecies enterica serovar Typhimurium, is a leading cause of gastroenteritis food-borne illness that leads to hospitalizations worldwide. These infections are further complicated because of the rapid development of antibiotic resistance and the spread of infections by the resistant strains. Thus, the overall aim of this study is to identify a multidrug-resistant strain of Salmonella Typhimurium, whole genome sequencing, and computational analysis of genome sequence. This study presents a comprehensive analysis of Salmonella Typhimurium ms203, isolated from a gastroenteritis patient in Odisha, India. The strain was characterized by microbiological and biochemical assays using a set of standard tests. An antibiotic-susceptibility test of the strain was carried out using VITEK system. Whole genome sequencing facilitated an in-depth examination of genomic architecture, distribution of pathogenic island regions, and antibiotic-resistant sequences. Utilizing diverse computational tools and bioinformatics analysis, including Prokka annotations, protein-protein interaction analysis, genomic island identification, plasmid and phage characterization, antibiotic resistance gene profiling, and average nucleotide identity (AAI) determination, this study elucidates key insights into the genetic makeup and pathogenic potential of S. Typhimurium ms203. These findings may provide valuable contributions to understanding the epidemiology, pathogenesis, and antibiotic resistance mechanisms of this Salmonella strain, with implications for public health interventions and surveillance strategies.
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Affiliation(s)
- Saumya Darshana Patra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT- DU), Bhubaneswar, 751024, India
| | - Soujanya Ghosh
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT- DU), Bhubaneswar, 751024, India
| | | | - Bikash Ranjan Sahu
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT- DU), Bhubaneswar, 751024, India
- Department of Zoology, Centurion University of Technology and Management, Bhubaneswar, 752050, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT- DU), Bhubaneswar, 751024, India
| | - Gajraj Singh Kushwaha
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT- DU), Bhubaneswar, 751024, India.
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT- DU), Bhubaneswar, 751024, India.
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27
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Larini I, Ferrara M, Troiano E, Gatto V, Mulè G, Vitulo N, Capozzi V, Salvetti E, Felis GE, Torriani S. Unlocking the potential of Metschnikowia pulcherrima: a dive into the genomic and safety characterization of four plant-associated strains. Appl Microbiol Biotechnol 2025; 109:128. [PMID: 40439729 PMCID: PMC12122572 DOI: 10.1007/s00253-025-13515-0] [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: 02/21/2025] [Revised: 05/06/2025] [Accepted: 05/09/2025] [Indexed: 06/02/2025]
Abstract
Metschnikowia pulcherrima includes strains of applied agro-food interest, particularly due to the antimicrobial activity against plant pathogens, contribution to the aroma of fermented beverages, and preliminary evidence related to probiotic activity. This biotechnological relevance sheds new light of interest on the biology of this yeast. To better understand and expand its biotechnological potential and applicability, the genomes of M. pulcherrima NRRL Y-7111 T, NRRL Y-48695, CBS 10357, and NRRL Y-48712 were sequenced, and de-novo assembled. Between 10,671 and 14,548 genes were predicted and the cooperative genomic analyses were integrated with experimental assessments relating to traits relevant for biotechnological application and safety. In silico and in vitro safety assessment revealed intermediate sensitivity for itraconazole; furthermore, variants of the genes related to pulcherrimin production and transport were found in all the genomes. Moreover, an arsenal of carbohydrate-active enzymes (CAZymes) was unravelled, and their predicted localization was investigated. This study expands the body of knowledge on M. pulcherrima, including traits relevant for defining its safety as a bioresource, which is a pivotal aspect for its possible inclusion in the European Food Safety Authority (EFSA) Qualified Presumption of Safety (QPS) list and its application in REgulated food/feed PROducts (REPRO) both in the European Union & aligned European countries. KEY POINTS: • A pipeline for genomic characterisation and safety assessment of unconventional yeasts, using M. pulcherrima as a model species was developed. • M. pulcherrima strains can be considered safe and safety data can be used to develop a body of knowledge to include M. pulcherrima in EFSA QPS list. • Analysis of the predicted localization of CAZymes allowed the detection of compounds as potential biological control agents.
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Affiliation(s)
- Ilaria Larini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
| | - Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Eleonora Troiano
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
| | - Veronica Gatto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
| | - Giuseppina Mulè
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
| | - Vittorio Capozzi
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Michele Protano, 71121, Foggia, Italy.
| | - Elisa Salvetti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy.
- Department of Biotechnology, VUCC-DBT, Verona University Culture Collection, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy.
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
- Department of Biotechnology, VUCC-DBT, Verona University Culture Collection, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Ca' Vignal 2, 37134, Verona, VR, Italy
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28
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Yang LL, Xin YH, Liu Q. Flavobacterium algoriphilum sp. nov., Flavobacterium arabinosi sp. nov., Flavobacterium cryoconiti sp. nov., Flavobacterium galactosi sp. nov., Flavobacterium melibiosi sp. nov., and Flavobacterium algoris sp. nov., six novel cold-adapted bacteria isolated from glaciers. BMC Microbiol 2025; 25:336. [PMID: 40437367 PMCID: PMC12117939 DOI: 10.1186/s12866-025-04067-4] [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: 02/25/2025] [Accepted: 05/21/2025] [Indexed: 06/01/2025] Open
Abstract
BACKGROUND Six novel cold-adapted bacteria, LB3P122T, LT1R49T, ZT3R17T, ZT3R25T, XS2P12T, and GB2R13T, were isolated from glaciers on the Tibetan Plateau. This study aimed to characterize their taxonomic status and elucidate their molecular adaptations to cold environments using a polyphasic approach. RESULTS All strains were Gram-stain-negative, rod-shaped, and psychrophilic, growing at 0 °C with an optimum at 14-20 °C and at pH values of 6.0-8.0 (optimum pH 7.0). Analysis of the 16S rRNA gene sequences placed their taxonomic positions within the genus Flavobacterium, with similarities ranging from 97.2 to 98.4% to species with validly published names. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the six strains formed distinct clades with Flavobacterium gawalongense GSP16T. Phylogenomic analysis showed that these strains clustered with Flavobacterium gawalongense GSP16T and exhibited a close relationship with Flavobacterium urumqiense CGMCC 1.9230T and Flavobacterium xinjiangense CGMCC 1.2749T. Average nucleotide identity (ANI) values ranging from 82.5 to 93.6% and digital DNA-DNA hybridization (dDDH) values ranging from 26.1 to 51.5% between these strains and their closest relatives were well below the bacterial species delineation thresholds (95-96% ANI, 70% dDDH). The predominant fatty acids were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Genomic analysis identified genes associated with cryoprotection, oxidative stress response, cold-shock response, and osmoprotection in these strains, underscoring their adaptations to glacial environments. CONCLUSIONS Based on polyphasic taxonomic evidence, the strains represent six novel species within the genus Flavobacterium, with the proposed names Flavobacterium algoriphilum sp. nov. (LB3P122T = CGMCC 1.11443 T = NBRC 114820T), Flavobacterium arabinosi sp. nov. (LT1R49T = CGMCC 1.11617T = NBRC 114822T), Flavobacterium cryoconiti sp. nov. (ZT3R17T = CGMCC 1.11707T = NBRC 114824T), Flavobacterium galactosi sp. nov. (ZT3R25T = CGMCC 1.11711T = NBRC 114825T), Flavobacterium melibiosi sp. nov. (XS2P12T = CGMCC 1.23198T = NBRC 114826T), and Flavobacterium algoris sp. nov. (GB2R13T = CGMCC 1.24741T = NBRC 114830T). These findings enhance our understanding of Flavobacterium diversity and cold adaptation in cryospheric ecosystems.
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Affiliation(s)
- Lei-Lei Yang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Beijing Key Laboratory of Genetic Element Biosourcing & Intelligent Design for Biomanufacturing, Beijing, 100101, China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- Beijing Key Laboratory of Genetic Element Biosourcing & Intelligent Design for Biomanufacturing, Beijing, 100101, China.
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- Beijing Key Laboratory of Genetic Element Biosourcing & Intelligent Design for Biomanufacturing, Beijing, 100101, China.
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29
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Putumbaka S, Barrow CE, Poole FL, Adams MWW. Genome sequence of Cetobacterium somerae ATCC BAA-474 isolated from human feces. Microbiol Resour Announc 2025:e0119624. [PMID: 40434121 DOI: 10.1128/mra.01196-24] [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: 11/12/2024] [Accepted: 05/02/2025] [Indexed: 05/29/2025] Open
Abstract
Cetobacterium somerae ATCC BAA-474 was first isolated from human feces and is emerging as an important species for animal and human health. Here, we report the complete genome sequence of this strain of C. somerae to improve the currently available genome sequence.
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Affiliation(s)
- Saisuki Putumbaka
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Claire E Barrow
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Farris L Poole
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Michael W W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
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30
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Lee JY, Lee Y, Park J, Kang HY, Heo YU, Lee JM, Nguyen TL, Kim DH. Complete genome sequence of Bacillus safensis strain BS22LVI isolated from the intestine of whiteleg shrimp, Litopenaeus vannamei. Microbiol Resour Announc 2025:e0011925. [PMID: 40422972 DOI: 10.1128/mra.00119-25] [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: 02/16/2025] [Accepted: 04/17/2025] [Indexed: 05/28/2025] Open
Abstract
We report the complete genome sequence of Bacillus safensis strain BS22LVI, isolated from the mid-hindgut of whiteleg shrimp (Litopenaeus vannamei) in Korea. The 3,824,412 bp circular genome has a G + C content of 41.65% and encodes 3,828 predicted coding sequences, including genes associated with antimicrobial activity and quorum quenching.
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Affiliation(s)
- Ju-Yeop Lee
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - Jiyeon Park
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - Hyo-Young Kang
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - Young-Ung Heo
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - Jung Min Lee
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - Thanh Luan Nguyen
- Department of Science, Technology and International Affairs, HUTECH University, Ho Chi Minh City, Vietnam
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, South Korea
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31
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Li W, Cai J, Chen G, Liu Y, Wu X, Bai Y, Wu Y, Wang T. Microbial community succession mediated by planting patterns in the Loess Plateau, China: Implications for ecological restoration. PLoS One 2025; 20:e0324786. [PMID: 40424445 PMCID: PMC12112373 DOI: 10.1371/journal.pone.0324786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/01/2025] [Indexed: 05/29/2025] Open
Abstract
Microbial community succession plays a key role in restoring fragile ecosystems and mitigating ecological degradation. However, the mechanisms by which vegetation restoration promotes ecological restoration and microbial community reconstruction in degraded soils remain unclear. This study utilized metagenomic high-throughput sequencing technology to analyze microbial community dynamics in soil samples collected from eight different planting patterns in the ecologically degraded areas of the Chinese Loess Plateau. The results indicated significant effects of terrain location and restorative cropping patterns on soil microbial abundance and function. In particular, soil C and N nutrient abundance was highest in mixed forest soils, and the total number of microorganisms was highest and more diverse. Therefore, through vegetation restoration, mixed forests significantly enhanced regional ecological functions. Notably, creating mixed forests with both trees and shrubs resulted in optimal ecological functions, providing a valuable direction for vegetation construction and structural optimization in the region.
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Affiliation(s)
- Weiqian Li
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Jinjun Cai
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Gang Chen
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Yitong Liu
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Xia Wu
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Yangyang Bai
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Yan Wu
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
| | - Tianning Wang
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, P.R. China
- The Key Laboratory of Soil and Plant Nutrition of Ningxia, Yinchuan, P.R. China.
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32
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Yang Z, Zhang S, Li X. Complete genome sequence of Cupriavidus sp. Agwp_2, isolated from soil in an iron mining area. Microbiol Resour Announc 2025:e0088424. [PMID: 40422977 DOI: 10.1128/mra.00884-24] [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: 08/11/2024] [Accepted: 11/20/2024] [Indexed: 05/28/2025] Open
Abstract
Cupriavidus spp. is a Gram-negative bacterium belonging to the Burkholderia family. Here, we report the complete genome sequence of Cupriavidus sp. Agwp_2, whose genome consists of two chromosomes of 3,823,900 bp and 2,784,676 bp, respectively, and one plasmid of 847,469 bp with an average GC content of 66.17%.
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Affiliation(s)
- Zilin Yang
- School of Sciences, Kaili University, Kaili, China
- School of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Shiping Zhang
- School of Life and Health Science, Bacterial Genome Data Mining & Bioinformatic Analysis Center, Kaili University, Kaili, China
| | - Xiangyang Li
- School of Life and Health Science, Bacterial Genome Data Mining & Bioinformatic Analysis Center, Kaili University, Kaili, China
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Thapa S, Shrestha B, Joshi DR, Tuladhar R, Getino M, Shrestha M, Pokhrel Y, Jauneikaite E. Draft genome sequence of carbapenem-resistant Klebsiella pneumoniae ST6260 isolated from the catheter tip of a female patient in Nepal. Microbiol Resour Announc 2025:e0014525. [PMID: 40422976 DOI: 10.1128/mra.00145-25] [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: 02/11/2025] [Accepted: 05/06/2025] [Indexed: 05/28/2025] Open
Abstract
Klebsiella pneumoniae is an opportunistic human pathogen, particularly associated with nosocomial infections and multidrug resistance. Here, we present a draft genome sequence of a carbapenem-resistant K. pneumoniae ST6260 isolated from the catheter tip of a female patient in a referral case received at Kathmandu Model Hospital, Kathmandu, Nepal.
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Affiliation(s)
- Suchitra Thapa
- Department of Microbiology, Tribhuvan University, Kirtipur, Central Development Region, Nepal
| | - Basudha Shrestha
- Department of Microbiology, Kathmandu Model Hospital, Kathmandu, Nepal
| | - Dev Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal
| | - Reshma Tuladhar
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Manisha Shrestha
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal
| | - Yojana Pokhrel
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Nepal
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
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Shi L, Ng JKW, Xiong Q, Ao KFK, Shin SK, Law CTY, Mu W, Liu GM, Rao S, Tsui SKW. Comparative genomic analysis of immune-related genes and chemosensory receptors provides insights into the evolution and adaptation of four major domesticated Asian carps. BMC Genomics 2025; 26:529. [PMID: 40419972 PMCID: PMC12105343 DOI: 10.1186/s12864-025-11719-2] [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: 10/14/2024] [Accepted: 05/15/2025] [Indexed: 05/28/2025] Open
Abstract
BACKGROUND Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited. METHODS The complete genomes of Ctenopharyngodon idella, Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus Hypophthalmichthys nobilis, and Hypophthalmichthys molitrix, a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species. RESULTS High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus. CONCLUSION This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis. The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction.
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Affiliation(s)
- Ling Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
- Department of Applied Science, School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | - Judy Kin-Wing Ng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Qing Xiong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Kelvin Fu-Kiu Ao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Soo-Kyung Shin
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Cherie Tsz-Yiu Law
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Weixue Mu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
| | - Guang-Ming Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, 361021, China
| | - Shitao Rao
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, 350122, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
- Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong, China.
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Kirdat K, Patwekar U, Jain K, Mubarak M, Choudhary P, Thakkar L, Thorat V, Madamwar D, Lodha T, Yadav A. Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance. Antonie Van Leeuwenhoek 2025; 118:82. [PMID: 40418388 DOI: 10.1007/s10482-025-02093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Accepted: 05/03/2025] [Indexed: 05/27/2025]
Abstract
A novel Gram-stain-negative, aerobic rod-shaped bacterial strain, which was catalase- and oxidase-positive, designated as DMV24BSW_DT, was isolated from the estuarine waters of the Bhavnagar (India) coast of the Arabian Sea. Its 16S rRNA gene exhibited 99.52% similarity with Neopusillimonas maritima 17-4AT, followed by 97.95% similarity with the Pusillimonas caeni strain EBR-8-1 and 97.4% similarity with the P. noertemannii strain BN9T. Phylogenomic analysis using BPGA (14,332 aa) and UBCG (90,261 bp) tools revealed a unique phylogenetic position within the genus Neopusillimonas. The genome exhibited a G + C content of 53.25%. In comparison with N. maritima 17-4AT, the strain demonstrated an average nucleotide identity (ANIb) of 94.47% and a digital DNA-DNA hybridization (dDDH) value of 60.1%, indicating distinct genomic divergence. The genome of DMV24BSW_DT contains several unique metabolic genes that facilitate efficient electron transfer during aerobic respiration. Additionally, it harbours one intact prophage and four defective prophages, indicating ongoing viral interactions. The genome encodes a complete pathway for ectoine biosynthesis and transportation. Strain DMV24BSW_DT tested positive for gelatin hydrolysis and demonstrated the ability to utilize a wide range of carbohydrates, including α-D-glucose, D-melibiose, D-fructose, L-rhamnose, and various organic acids, such as methyl pyruvate and propionic acid, along with tolerance to fluctuating pH (5 to 10) and salinity (0-4% NaCl). The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine, while fatty acid analysis revealed C12:0, C16:0, C17:0 cyclo, and summed feature 2 (C12:0 aldehyde/unknown) as major components. The respiratory quinones identified were MK-7 and MK-8. These comprehensive phenotypic, chemotaxonomic, and genomic characteristics support the unique taxonomic position of DMV24BSW_DT within the genus Neopusillimonas and the proposal of a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aestuarii sp. nov. (Type strain DMV24BSW_DT = MCC 2506 T = KCTC 72453 T = JCM 34508 T) is proposed.
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Grants
- BT/Coord.II/01/03/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/Coord.II/01/03/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/Coord.II/01/03/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/Coord.II/01/03/2016 Department of Biotechnology, Ministry of Science and Technology, India
- BT/Coord.II/01/03/2016 Department of Biotechnology, Ministry of Science and Technology, India
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Affiliation(s)
- Kiran Kirdat
- National Centre for Cell Science, National Centre for Microbial Resource, University of Pune Campus, Ganeshkhind, Pune, 411007, India
| | - Umera Patwekar
- National Centre for Cell Science, National Centre for Microbial Resource, University of Pune Campus, Ganeshkhind, Pune, 411007, India
| | - Kunal Jain
- Post Graduate Department of Biosciences, Sardar Patel University, Anand, 388315, India
| | - Malad Mubarak
- Ajinkya DY Patil University, Airport Road, Charholi Budruk, Pune, 412105, India
| | - Pradeep Choudhary
- Dr. DY Patil Biotechnology & Bioinformatics Institute, Pimpri-Chinchwad, 411033, India
| | - Lucky Thakkar
- National Centre for Cell Science, National Centre for Microbial Resource, University of Pune Campus, Ganeshkhind, Pune, 411007, India
| | - Vipool Thorat
- National Centre for Cell Science, National Centre for Microbial Resource, University of Pune Campus, Ganeshkhind, Pune, 411007, India
- Central Institute of Medicinal and Aromatic Plants, Kukrail, Lucknow, 226015, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa, 388421, India
| | - Tushar Lodha
- National Centre for Cell Science, National Centre for Microbial Resource, University of Pune Campus, Ganeshkhind, Pune, 411007, India
- Bioenergy Group, Agharkar Research Institute, Shivajinagar, Pune, 411004, India
| | - Amit Yadav
- National Centre for Cell Science, National Centre for Microbial Resource, University of Pune Campus, Ganeshkhind, Pune, 411007, India.
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Pearl S, Anbarasu A. Genomic landscape of nosocomial Acinetobacter baumannii: A comprehensive analysis of the resistome, virulome, and mobilome. Sci Rep 2025; 15:18203. [PMID: 40414962 DOI: 10.1038/s41598-025-03246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Accepted: 05/19/2025] [Indexed: 05/27/2025] Open
Abstract
Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing and capsule typing were performed to investigate the clonal diversity. The genomes were characterized to identify antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements. Further, pangenome analysis was conducted to examine the core and accessory genomes of A. baumannii. Our dataset comprised of 609 genomes deposited from diverse geographic regions worldwide between 2004 and 2024. The genomes showed high clonal heterogeneity, with sequence type ST2 being the predominant sequence type. A total of 185 unique ARGs were identified, with majority of them associated with efflux pump and β-lactamase coding genes. Over 25,000 IS elements were detected, with IS4 family being the prevalent type. High abundance of integron-mediated resistance determinants, especially for aminoglycosides and β-lactams, were identified. The open pangenome window due to its larger accessory genome suggested substantial genome plasticity. Our findings highlight A. baumannii's rapid evolution and resistance potential, emphasizing need for alternative therapeutic strategies. Enhanced surveillance, infection control measures, and antimicrobial stewardship are crucial to combat this persistent threat.
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Affiliation(s)
- Sara Pearl
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India
| | - Anand Anbarasu
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India.
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India.
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Yu J, Ding Y, Zhang X, Fang Y, Tai S, Yuan E, Duan Y. Whole-genome sequencing analysis of Staphylococcus aureus isolated from female patients with mastitis in Henan, China. J Glob Antimicrob Resist 2025:S2213-7165(25)00123-7. [PMID: 40419111 DOI: 10.1016/j.jgar.2025.05.019] [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: 09/17/2024] [Revised: 05/14/2025] [Accepted: 05/22/2025] [Indexed: 05/28/2025] Open
Abstract
OBJECTIVES To study the molecular characteristics, antibiotic resistance profiles and virulence features of Staphylococcus aureus (SA) isolates that cause mastitis. METHODS 117 SA isolates were collected from women with mastitis. Strain identification and antimicrobial susceptibility testing were conducted using the Vitek 2 system. All SA isolates were sequenced on the Illumina HiSeq platform. For multilocus sequence typing, ResFinder, spaTyper, and SCCmecFinder were employed to analyse the strains. RESULTS Thirty-five methicillin-resistant Staphylococcus aureus (MRSA) strains and 82 methicillin-sensitive Staphylococcus aureus (MSSA) strains were isolated from women with acute breast abscesses. The rates of resistance to various antibiotics were significantly higher among MRSA isolates than among MSSA isolates. Twenty-two sequence types (STs), 35 staphylococcal protein A (spa) types, and 4 SCCmec types were identified. ST22, ST59, and ST398 were the major lineages, and t309 and t437 were the most common spa types. SCCmec-IVa was the predominant SCCmec type. Interestingly, toxin gene subtypes A (hlgA, hlgB, hlgC, lukF-PV, lukS-PV, seg, sei, sem, sen, seo, seu, n = 54), B (hlgA, hlgB, hlgC, seb, sek, seq, n = 13), C (hlgA, hlgB, hlgC, lukD, lukE, n = 10), and D (hlgA, hlgB, hlgC, n = 10) accounted for 74.4% (87/117) of all SA isolates, suggesting the high expression of virulence genes. CONCLUSIONS ST22, ST398, and ST59 are the main types that cause mastitis and have different virulence factor profiles. This study provides deeper insights into the molecular epidemiology of SA associated with acute mastitis.
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Affiliation(s)
- Jing Yu
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yanzi Ding
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China
| | - Xue Zhang
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yang Fang
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China
| | - Shuhong Tai
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China
| | - Enwu Yuan
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China.
| | - Yitao Duan
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, Henan, People's Republic of China.
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Lorenzen S, Dieckmann AL, Možina SS, Zelenik K, Marquardt P, Tersteegen A, Kaasch AJ, Bohne W, Zautner AE. Characterization of aquatic clade 2 and 3 Campylobacter coli isolates from Slovenia reveals admixture with other Campylobacter species. BMC Microbiol 2025; 25:322. [PMID: 40413380 DOI: 10.1186/s12866-025-04042-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 05/13/2025] [Indexed: 05/27/2025] Open
Abstract
Campylobacter coli, a significant foodborne pathogen, has undergone extensive genetic exchange with its close relative, Campylobacter jejuni, leading to the emergence of three distinct clades. While clade 1 strains are commonly isolated from clinical and agricultural sources, clades 2 and 3 are primarily found in aquatic environments. This study aimed to enhance our understanding of C. coli clade 2 and 3 isolates through genomic and phenotypic characterization. A total of 48 surface water samples were collected from 19 different water bodies throughout Slovenia, and eleven Campylobacter isolates initially identified as C. coli from clades 2 and 3 were cultured. Whole genome sequencing was then performed on these isolates. Phylogenetic analysis was conducted using core genome multilocus sequence typing (cgMLST) and k-mer analysis. Phenotypic characterization included growth analysis, autoagglutination, biofilm formation, motility, antimicrobial susceptibility, water survival, and metabolic profiling. Genomic analysis revealed significant admixture with other Campylobacter species in the clade 2 and 3 isolates. One isolate was found to represent a new species related to C. coli. Besides C. jejuni and C. lari, this novel species appears to have contributed to introgression in the C. coli clades 2 and 3 isolates. Phenotypic characterization demonstrated diverse growth patterns, motility, autoagglutination abilities, and biofilm formation among the isolates. This study provides new insights into the genetic diversity and phenotypic characteristics of aquatic C. coli clade 2 and 3 isolates from Slovenia. The observed admixture with other Campylobacter species highlights the complex evolutionary history of these environmental strains and underscores the importance of continued surveillance and characterization of Campylobacter isolates from diverse ecological niches.
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Affiliation(s)
- Stephan Lorenzen
- Bioinformatics Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anastasia-Lisa Dieckmann
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Zelenik
- Center for Microbiological Analysis of Food, Water and Other Environmental Samples, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Pauline Marquardt
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Aljoscha Tersteegen
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Achim J Kaasch
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Erich Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany.
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany.
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Astuti RI, Maulana I, Wahyuni WT, Meryandini A. Genetic properties of mercury‑tolerant yeast, Pichia kudriavzevii 1P4. Int Microbiol 2025:10.1007/s10123-025-00666-3. [PMID: 40410606 DOI: 10.1007/s10123-025-00666-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 04/16/2025] [Accepted: 04/30/2025] [Indexed: 05/25/2025]
Abstract
Mercury contamination in commercial products poses serious risks to human health and the environment. The in vitro detection methods using spectroscopy approaches are expensive and have limited practical use. Yeast-based biosensors provide a more affordable and user-friendly alternative. Therefore, the exploration of mercury tolerance yeast is essential to support the sensor properties. In this study, we investigated the mercury tolerance of 10 yeast isolates. Pichia kudriavzevii 1P4 exhibited tolerance up to 1.5 mM HgCl2 while showing slow growth phenotype as grown in 2 mM HgCl2. This is the first report to show the ability of this genus of the yeast Pichia to cope with HgCl2 stress. X-ray spectra showed Hg accumulation in yeast colonies grown in HgCl2, while none was detected in colonies grown without it. This data indicates the capability of 1P4 in the accumulation of Hg as one of the HgCl2-stress tolerance mechanisms. Whole-genome sequencing of isolate 1P4, using the MGI DNBSEQ-G400 platform, revealed a genome size of 10.8 Mbp across five chromosomes, with a GC content of 38.97%. The largest portions of the genome are involved in translation, amino acid transport, metabolism, and protein modification, based on COG analysis. Key genes potentially contributing to mercury tolerance involve efflux/inorganic ion transport system (e.g., FieF, Acr3/B, and CzcO/D-clusters) and glutathione-associated oxidative stress response (e.g., BtuE and LysX, which encoded glutathione peroxidase and glutathione synthase). Those genes were predominant in COG category of inorganic ion transport and metabolism (P) and defense mechanisms (V). The genome of 1P4 was assembled into 4753 gene clusters, where 2222 of which were shared with the other species of yeast, including Pichia membranifaciens, P. kluyveri, P. inconspicua, S. cerevisiae, and C. albicans. Meanwhile, 921 gene clusters were shared among genera of Pichia spp., only. These findings highlight the genetic profile and mercury-tolerance mechanisms of isolate 1P4, supporting its potential application as a mercury biosensor or bioremediation agent.
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Affiliation(s)
- Rika Indri Astuti
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), IPB Dramaga Campus, Bogor City, 16680, Indonesia.
- Biotechnology Research Center, Dramaga Campus, IPB University, West Java, Bogor City, 16680, Indonesia.
| | - Indra Maulana
- IPB Culture Collection, Dramaga Campus, IPB University, West Java, Bogor City, 16680, Indonesia
| | - Wulan Tri Wahyuni
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), IPB Dramaga Campus, Bogor City, 16680, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), IPB Dramaga Campus, Bogor City, 16680, Indonesia
- Biotechnology Research Center, Dramaga Campus, IPB University, West Java, Bogor City, 16680, Indonesia
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40
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Zinger A, Doron-Faigenboim A, Gelbart D, Levin I, Lapidot M. Contribution of the tobamovirus resistance gene Tm-1 to control of tomato brown rugose fruit virus (ToBRFV) resistance in tomato. PLoS Genet 2025; 21:e1011725. [PMID: 40408442 DOI: 10.1371/journal.pgen.1011725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Accepted: 05/13/2025] [Indexed: 05/25/2025] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a rapidly spreading pathogen that poses a significant threat to tomato production worldwide. We previously identified a locus on tomato chromosome 11 controlling tolerance to the virus. We further established that combining this locus with one that maps to the Tm-1 region on chromosome 2 confers resistance to the virus. Here we sought to determine whether, and how, the Tm-1 gene itself is involved in ToBRFV resistance. Overexpression of Tm-1 in a tolerant genotype significantly reduced viral accumulation, conferring resistance to ToBRFV. On the other hand, overexpression of Tm-1 in a susceptible genotype only delayed symptom appearance. Moreover, effective RNAi-silencing of Tm-1 in the resistant genotype yielded susceptible plants. These findings show that the Tm-1 gene interacts genetically with the locus controlling tolerance on chromosome 11 and that this interaction is critical for achieving effective resistance to ToBRFV. In addition, the symptomatic plants obtained following silencing of Tm-1 in the resistant genotype indicate that tolerance is also dependent on normal expression levels of the recessive tm-1 allele.
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Affiliation(s)
- Avner Zinger
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon LeZion, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Doron-Faigenboim
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon LeZion, Israel
| | - Dana Gelbart
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon LeZion, Israel
| | - Ilan Levin
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon LeZion, Israel
| | - Moshe Lapidot
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon LeZion, Israel
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Hetland MAK, Winkler MA, Kaspersen H, Håkonsholm F, Bakksjø RJ, Bernhoff E, Delgado-Blas JF, Brisse S, Correia A, Fostervold A, Lam MMC, Lunestad BT, Marathe NP, Raffelsberger N, Samuelsen Ø, Sunde M, Sundsfjord A, Urdahl AM, Wick RR, Holt KE, Löhr IH. Complete genomes of 568 diverse Klebsiella pneumoniae species complex isolates from humans, animals, and marine sources in Norway from 2001 to 2020. Microbiol Resour Announc 2025:e0093124. [PMID: 40401948 DOI: 10.1128/mra.00931-24] [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: 09/02/2024] [Accepted: 12/02/2024] [Indexed: 05/23/2025] Open
Abstract
We report 578 hybrid genome assemblies (568 complete) of Klebsiella pneumoniae species complex isolates from human, animal, and marine sources in Norway collected from 2001 to 2020, belonging to five phylogroups including K. pneumoniae (n = 492) and K. variicola (n = 69) and 364 unique sequence types.
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Affiliation(s)
- Marit A K Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Biological Sciences, Faculty of Science and Technology, University of Bergen, Bergen, Norway
| | - Mia A Winkler
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Håkon Kaspersen
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Ås, Norway
| | - Fredrik Håkonsholm
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Institute of Marine Research, Bergen, Norway
| | - Ragna-Johanne Bakksjø
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Jose F Delgado-Blas
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Annapaula Correia
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Aasmund Fostervold
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Margaret M C Lam
- Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia
| | - Bjørn-Tore Lunestad
- Department of Biological Sciences, Faculty of Science and Technology, University of Bergen, Bergen, Norway
- Institute of Marine Research, Bergen, Norway
| | | | - Niclas Raffelsberger
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Marianne Sunde
- Section for Bacteriology, Department for Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anne Margrete Urdahl
- Research Section Food Safety and Animal Health, Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Ås, Norway
| | - Ryan R Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia
| | - Iren H Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
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Vazquez-Guillen JM, Palacios-Saucedo GC, Rivera-Morales LG, Caballero-Trejo A, Flores-Flores AS, Quiroga-Garza JM, Chavez-Santoscoy RA, Hernandez-Perez J, Hinojosa-Alvarez SA, Hernandez-Gonzalez JA, Rojas-Contreras M, Vazquez-Juarez R, Valladares-Trujillo R, Alonso-Tellez CA, Treviño-Baez JD, Rivera-Alvarado MA, Tamez-Guerra RS, Rodriguez-Padilla C. Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance. PeerJ 2025; 13:e19454. [PMID: 40416609 PMCID: PMC12103846 DOI: 10.7717/peerj.19454] [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: 10/27/2024] [Accepted: 04/21/2025] [Indexed: 05/27/2025] Open
Abstract
Background Streptococcus agalactiae (Group B Streptococcus, GBS) is an important pathogen associated with neonatal sepsis, pneumonia, and meningitis, which can be transmitted from colonized pregnant women to their newborns. This study aimed to determine the prevalence and characterize the genomic features of S. agalactiae isolates from pregnant women attending a referral hospital in Northeastern Mexico. Methods Vaginal-rectal swabs were collected from pregnant women during routine prenatal care between April 2017 and March 2020. Whole-genome sequencing was conducted to determine sequence type (ST), clonal complex (CC), capsular polysaccharide (Cps) genotype, virulence factors, and antibiotic resistance genes through comparative genome analysis. Results S. agalactiae colonization was detected in 51 (2.7%) of 1,924 pregnant women. The most common STs were ST8 (23.5%) and ST88 (15.7%). Cps genotyping showed high concordance between serological and molecular methods. Genes conferring resistance to tetracyclines (tetM, 60.1%) and macrolides (mreA, 100%) were identified. Key virulence factor genes, including cylE, bca, and scpB, were present in over 90% of the isolates. Conclusion Although GBS colonization prevalence was low, genomic analysis revealed the genetic diversity of S. agalactiae in Northeastern Mexico, emphasizing the importance of molecular techniques for epidemiological surveillance and infection control.
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Affiliation(s)
- Jose Manuel Vazquez-Guillen
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Inmunologia y Virologia, San Nicolas de los Garza, Nuevo Leon, Mexico
| | - Gerardo C. Palacios-Saucedo
- Division de Investigacion en Salud y Division de Auxiliares de Diagnostico, Unidad Medica de Alta Especialidad (UMAE) No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo Leon, Mexico
- Universidad Autonoma de Nuevo Leon, Facultad de Medicina, Departamento de Pediatria, Hospital Universitario “Dr. Jose Eleuterio Gonzalez”, Monterrey, Nuevo Leon, Mexico
| | - Lydia Guadalupe Rivera-Morales
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Inmunologia y Virologia, San Nicolas de los Garza, Nuevo Leon, Mexico
| | - Amilcar Caballero-Trejo
- Departamento de Epidemiologia y Direccion de Educacion e Investigacion, Unidad Medica de Alta Especialidad No. 23 Hospital de Ginecologia y Obstetricia “Dr. Ignacio Morones Prieto”, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, Mexico
| | - Aldo Sebastian Flores-Flores
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Inmunologia y Virologia, San Nicolas de los Garza, Nuevo Leon, Mexico
| | - Juan Manuel Quiroga-Garza
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Inmunologia y Virologia, San Nicolas de los Garza, Nuevo Leon, Mexico
| | - Rocio Alejandra Chavez-Santoscoy
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Instituto Tecnologico y de Estudios Superiores de Monterrey (ITESM), Monterrey, Mexico
| | - Jesus Hernandez-Perez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Instituto Tecnologico y de Estudios Superiores de Monterrey (ITESM), Monterrey, Mexico
| | - Silvia Alejandra Hinojosa-Alvarez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Instituto Tecnologico y de Estudios Superiores de Monterrey (ITESM), Monterrey, Mexico
| | - Julio Antonio Hernandez-Gonzalez
- Laboratorio de Genomica y Bioinformatica, Centro de Investigaciones Biologicas del Noroeste S.C., La Paz, Baja California Sur, Mexico
- Laboratorio de Ciencia y Tecnologia de los Alimentos, Universidad Autonoma de Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Maurilia Rojas-Contreras
- Laboratorio de Ciencia y Tecnologia de los Alimentos, Universidad Autonoma de Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Ricardo Vazquez-Juarez
- Laboratorio de Genomica y Bioinformatica, Centro de Investigaciones Biologicas del Noroeste S.C., La Paz, Baja California Sur, Mexico
| | - Ramon Valladares-Trujillo
- Coordinacion de Educacion e Investigacion en Salud, Hospital General de Zona No. 17, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, Mexico
| | - Cesar Alejandro Alonso-Tellez
- Division de Investigacion en Salud y Division de Auxiliares de Diagnostico, Unidad Medica de Alta Especialidad (UMAE) No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo Leon, Mexico
| | - Joaquin Dario Treviño-Baez
- Departamento de Epidemiologia y Direccion de Educacion e Investigacion, Unidad Medica de Alta Especialidad No. 23 Hospital de Ginecologia y Obstetricia “Dr. Ignacio Morones Prieto”, Instituto Mexicano del Seguro Social, Monterrey, Nuevo León, Mexico
| | - Miguel Angel Rivera-Alvarado
- Division de Investigacion en Salud y Division de Auxiliares de Diagnostico, Unidad Medica de Alta Especialidad (UMAE) No. 25, Instituto Mexicano del Seguro Social, Monterrey, Nuevo Leon, Mexico
| | - Reyes S. Tamez-Guerra
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Inmunologia y Virologia, San Nicolas de los Garza, Nuevo Leon, Mexico
| | - Cristina Rodriguez-Padilla
- Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Biologicas, Laboratorio de Inmunologia y Virologia, San Nicolas de los Garza, Nuevo Leon, Mexico
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Gestels Z, Torfs B, Abdellati S, De Baetselier I, Rombouts C, Dermauw V, Manoharan-Basil SS, Kenyon C. "Acceptable" concentrations of enrofloxacin in food lead to reduced enrofloxacin susceptibility in a mouse model of gastrointestinal Klebsiella pneumoniae. Microbiol Spectr 2025:e0038525. [PMID: 40401967 DOI: 10.1128/spectrum.00385-25] [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: 04/14/2025] [Indexed: 05/23/2025] Open
Abstract
Concentrations of antimicrobials up to 1,000-fold lower than the minimum inhibitory concentration can select for antimicrobial resistance. This generates the hypothesis that the low concentrations of antimicrobials allowed in our food could select for resistance. We assessed if the dose of enrofloxacin allowed in food by the European Medicines Agency (6.2 µg/kg) could decrease susceptibility to enrofloxacin in a strain of Klebsiella pneumoniae colonizing the gastrointestinal tracts of Specific Opportunistic Pathogen-Free Naval Medical Research Institute (NMRI) mice. We found that one-tenth of this dose given daily was able to increase the K. pneumoniae enrofloxacin MIC 8-fold (from 0.047 µg/mL to 0.38 µg/mL). Our findings suggest the need for studies to assess if the same could occur in humans.IMPORTANCEAntimicrobial-resistant infections are responsible for over a million deaths a year. Reducing antimicrobial resistance requires addressing all the sources of unnecessary antimicrobial exposure. Because the antimicrobial concentration in our food frequently approaches or exceeds the maximum allowed limits, it is crucial to ensure that the legal concentrations of antimicrobials in food do not induce antimicrobial resistance. We found that enrofloxacin doses, 10 times lower than those classified as safe, could increase enrofloxacin MICs 8-fold in K. pneumoniae in the gastrointestinal tracts of mice. These findings suggest that we need to consider the induction of antimicrobial resistance when defining safe concentrations of antimicrobials in our food.
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Affiliation(s)
- Zina Gestels
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
| | - Bianca Torfs
- Applied Technology and Production unit, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
| | - Said Abdellati
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
| | - Irith De Baetselier
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
| | - Caroline Rombouts
- Applied Technology and Production unit, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
| | - Veronique Dermauw
- Unit of Zoonoses, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Flanders, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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44
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Darden B, Johnson G, Busch G, Sharma I. Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. Microbiol Resour Announc 2025:e0088224. [PMID: 40401939 DOI: 10.1128/mra.00882-24] [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: 08/13/2024] [Accepted: 04/17/2025] [Indexed: 05/23/2025] Open
Abstract
We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments.
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Rahaman MM, Sadique A, Alam J, Khan F, Ayesha Z, Islam S, Murshid M, Rafsan R, Islam S, Iqbal HB, Das TK, Ahmed O, Rumman K, Sharmin A, Hossain MM, Alam M, Hossain M. Draft genome sequence of Pseudomonas aeruginosa strain maqsudiensis isolated from cattle swab in Dhaka, Bangladesh. Microbiol Resour Announc 2025:e0119024. [PMID: 40396781 DOI: 10.1128/mra.01190-24] [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: 11/07/2024] [Accepted: 02/06/2025] [Indexed: 05/22/2025] Open
Abstract
Here, we present the draft genome sequence of Pseudomonas aeruginosa strain maqsudiensis, isolated from cattle stool swab. The genome was sequenced using the Illumina MiSeq platform, yielding a 6.33 Mb assembly with 5,784 predicted coding sequences. The genome harbors multiple antibiotic-resistance genes and virulence factors, providing insights into P. aeruginosa colonization in livestock and potential implications for antimicrobial resistance dissemination through the food chain.
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Affiliation(s)
- Md Mashiur Rahaman
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Abdus Sadique
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Jahidul Alam
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Fahad Khan
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Zinat Ayesha
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Shoriful Islam
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Monsur Murshid
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Raiyan Rafsan
- Department of Electrical and Computer Engineering, School of Engineering & Physical Sciences, North South University, Dhaka, Bangladesh
| | | | - Humaira Binte Iqbal
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | | | - Oly Ahmed
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Kamruzzaman Rumman
- National Institute of Cancer Research and Hospital (NICRH), Dhaka, Bangladesh
| | - Ayesha Sharmin
- Department of Chemistry, Bangladesh University of Engineering & Technology, Dhaka, Bangladesh
| | - Md Mainul Hossain
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Munirul Alam
- icddr,b, International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Maqsud Hossain
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
- Department of Biochemistry & Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
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46
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Vietmeier A, Valkanas M, Lamagna N, Flett S, Gulliver D, Trun N. Bacterial nitrite production oxidizes Fe(II) bioremediating acidic abandoned coal mine drainage. Appl Environ Microbiol 2025; 91:e0040525. [PMID: 40237488 DOI: 10.1128/aem.00405-25] [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: 02/28/2025] [Accepted: 03/17/2025] [Indexed: 04/18/2025] Open
Abstract
Passive remediation systems (PRSs) treating either acidic or neutral abandoned coal mine drainage (AMD) are colonized by bacteria that can bioremediate iron (Fe) through chemical cycling. Due to the low pH in acidic AMD, iron oxidation from soluble Fe(II) to precipitated Fe(III) is mainly directed by microbial oxidation. Less well described are biotic reactions that lead to iron remediation through abiotic secondary reactions. We describe here iron oxidation in acidic AMD that is mediated by the bacterial reduction of nitrate to nitrite followed by the geochemical oxidation of Fe(II). Within an acidic PRS, 4,560 bacteria cultured from the microbial community were screened for their ability to oxidize iron and to perform nitrate-dependent iron oxidation (NDFO). Iron oxidation in the culturable community was observed in every pond of the system, ranging from 2.1% to 11.4%, and NDFO was observed in every pond, ranging from 1.4% to 6.0% of the culturable bacteria. Five NDFO isolates were purified and identified as Paraburkholderia spp. One of our isolates, Paraburkholderia sp. AV18 was shown to drive NDFO through the bacterial production of nitrite that in turn chemically oxidizes Fe(II) (nitrate reduction-iron oxidation; NRIO). AV18 expressed nitrate reductase, napA, concurrent to nitrite production. Burkholderiales are found by 16S rRNA gene sequencing in every pond of the PRS. The frequency of NDFO metabolism in the culturable microbial community and abundance of Burkholderiales in the PRS suggest nitrite producers contribute to the bioremediation of iron in acidic AMD and may be an unharnessed opportunity to increase iron bioremediation in acidic conditions. IMPORTANCE Our study sheds light on a poorly defined biogeochemical interaction, nitrate-dependent iron oxidation (NDFO), that has been described in several environments. We show that bacterial nitrate reduction produces nitrite, which can chemically oxidize ferrous iron, leading to insoluble ferric iron. We show that bacteria capable of the nitrate reduction-iron oxidation (NRIO) reactions are prevalent throughout multiple passive remediation systems that treat acidic coal mine drainage, indicating this may be a widespread mechanism for iron removal under acidic conditions. In acidic coal mine remediation, iron precipitation has been shown to be solely bacterially mediated, and NRIO provides a simple mechanism for aerobic oxidation of iron in these conditions.
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Affiliation(s)
- Anna Vietmeier
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
- Department of Energy, National Energy Technology Laboratory, Pittsburgh, Pennsylvania, USA
| | - Michelle Valkanas
- Department of Biology, Earth, and Environmental Science, PennWest California, California, Pennsylvania, USA
| | - Natalie Lamagna
- Center for Environmental Research and Education, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Samuel Flett
- Department of Energy, National Energy Technology Laboratory, Pittsburgh, Pennsylvania, USA
| | - Djuna Gulliver
- Department of Energy, National Energy Technology Laboratory, Pittsburgh, Pennsylvania, USA
| | - Nancy Trun
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
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Lysenko YA, Milovanov AV, Kopyltsov SV, Gahurová D, Elisiutikova AV. Draft genome of Lactobacillus amylovorus KSAU with probiotic potential isolated from the gastrointestinal tract of industrial pigs. Microbiol Resour Announc 2025:e0057724. [PMID: 40396734 DOI: 10.1128/mra.00577-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 02/24/2025] [Indexed: 05/22/2025] Open
Abstract
The Lactobacillus amylovorus KSAU strain was isolated from the chyme of the intestinal cecum of an industrial pig. Genes encoding the synthesis of bacteriocins were annotated and suggest their potential to improve the preparation and production of probiotics for pigs.
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Affiliation(s)
- Yuri A Lysenko
- Department of Veterinary Medicine, Russian State Agrarian University Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Alexander V Milovanov
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Sergey V Kopyltsov
- Department of Biotechnology, Biochemistry and Biophysics, Kuban State Agrarian University named after IT Trubilin, Krasnodar, Krasnodar Krai, Russia
| | - Dominika Gahurová
- Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Anastasia V Elisiutikova
- Department of Plant and Animal Genetics, Kuban State Agrarian University named after IT Trubilin, Krasnodar, Krasnodar Krai, Russia
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Brunelli L, Perotti S, Gargari G, De Vitis V, Mantegazza G, Ferrari R, Minuzzo M, Pierallini E, Ricci G, Fiore W, Guglielmetti S. Genetic and phenotypic stability of Lacticaseibacillus paracasei DG (DSM 34154) over 10 years of industrial production. Appl Environ Microbiol 2025; 91:e0239424. [PMID: 40272178 DOI: 10.1128/aem.02394-24] [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: 11/28/2024] [Accepted: 03/25/2025] [Indexed: 04/25/2025] Open
Abstract
The commercialization of a probiotic microorganism requires genetic and phenotypic consistency across production lots. However, the large-scale industrial production of probiotic microbial biomasses over years poses a risk of genetic drift, potentially affecting the probiotic's ability to confer health benefits. This study assessed the stability of Lacticaseibacillus paracasei DG (DSM 34154), a commercial probiotic. Seven isolates from different commercial lots over 10 years, one 8-year-old laboratory subculture, one isolate from human feces, and the DG strain deposited at DSMZ were analyzed. Shotgun and PacBio sequencing were combined to obtain the complete genome of the 10 isolates. Comparative analysis showed that the seven commercial isolates had identical genomes, differing from the DSMZ isolate by one synonymous transition and one non-synonymous transversion. The laboratory subculture strain had two additional mutations. Phenotypic analyses, including antibiotic resistance, carbohydrate fermentation profile, survival to simulated gastrointestinal transit, immunomodulatory capacity, and radical scavenging ability, found no significant differences among isolates. Overall, this study demonstrates the substantial equivalence of L. paracasei DG over 10 years of industrial production, indicating that the current industrial practices help prevent genome alterations that could compromise probiotic performance. Similar studies should be part of continuous monitoring and quality control measures for the probiotic products on the market.IMPORTANCEThe genetic and functional stability of probiotic strains during years of industrial production is essential but has not been clearly demonstrated for many strains. This study shows that careful industrial practices can maintain the genetic integrity and functionality of probiotics. Using advanced genome sequencing and detailed laboratory tests, we confirmed that the probiotic Lacticaseibacillus paracasei DG (DSM 34154) has remained stable over a decade of production, consistently delivering its health-promoting properties. These findings support the quality and reliability of probiotic products, fostering consumer trust and highlighting the importance of continuous monitoring in probiotic manufacturing to sustain quality assurance.
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Affiliation(s)
| | - Susanna Perotti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Giorgio Gargari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | - Giacomo Mantegazza
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
- μbEat lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | | | - Elena Pierallini
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Giovanni Ricci
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | - Simone Guglielmetti
- μbEat lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Horiguchi T, Umeyama T, Tomuro H, Otani A, Shinohara T, Abe M, Takatsuka S, Miyazawa K, Nagi M, Muraosa Y, Hoshino Y, Sakoh T, Araoka H, Uchida N, Kaneko T, Nagano Y, Tsukada H, Miyazaki T, Miyazaki Y. Whole-Genome Sequencing and Comparative Genomic Analysis of Three Clinical Bloodstream Infection Isolates of Trichosporon austroamericanum. J Fungi (Basel) 2025; 11:401. [PMID: 40422735 DOI: 10.3390/jof11050401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2025] [Revised: 05/16/2025] [Accepted: 05/19/2025] [Indexed: 05/28/2025] Open
Abstract
Trichosporon austroamericanum is a recently described yeast species related to Trichosporon inkin and exclusively isolated from clinical specimens. However, its genomic features and pathogenic potential remain poorly understood. In this study, we performed whole-genome sequencing on three blood-derived isolates from patients with invasive fungal infections and comparative analyses with 13 related Trichosporon species. The three isolates yielded high-quality assemblies of 9-10 scaffolds (~21 Mb), facilitating reliable comparisons. While most species had comparable genome sizes, Trichosporon ovoides, Trichosporon coremiiforme, and Cutaneotrichosporon mucoides displayed large, fragmented genomes, suggestive of polyploidy. ANI analysis and phylogenetic trees based on ANI and single-copy orthologs supported the classification of T. austroamericanum as a distinct clade with moderate intraspecific divergence. Using the Galleria mellonella, a model for fungal pathogenicity, all T. austroamericanum strains reduced larval survival, and NIIDF 0077300 exhibited virulence comparable to T. asahii and greater than T. inkin. To explore the gene-level differences associated with pathogenicity, we performed ortholog analysis based on single-copy genes. This revealed a unique Zn(II)2Cys6-type transcription factor gene (OG0010545) present only in NIIDF 0077300 and T. asahii. These findings highlight the genomic diversity and infection-associated traits of T. austroamericanum, providing a framework for future functional studies.
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Affiliation(s)
- Takanori Horiguchi
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
- Division of Respirology, Rheumatology, Infectious Diseases and Neurology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Takashi Umeyama
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Hiroko Tomuro
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Amato Otani
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Takayuki Shinohara
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Masahiro Abe
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Shogo Takatsuka
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Ken Miyazawa
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Minoru Nagi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 189-0002, Japan
| | - Yasunori Muraosa
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Yasutaka Hoshino
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
| | - Takashi Sakoh
- Department of Infectious Diseases, Toranomon Hospital, Tokyo 105-8470, Japan
| | - Hideki Araoka
- Department of Infectious Diseases, Toranomon Hospital, Tokyo 105-8470, Japan
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, Tokyo 105-8470, Japan
| | - Tomoyoshi Kaneko
- The Jikei University School of Medicine Kashiwa Hospital, Chiba 277-8567, Japan
| | - Yuko Nagano
- The Jikei University School of Medicine Kashiwa Hospital, Chiba 277-8567, Japan
| | - Hiroki Tsukada
- The Jikei University School of Medicine Kashiwa Hospital, Chiba 277-8567, Japan
| | - Taiga Miyazaki
- Division of Respirology, Rheumatology, Infectious Diseases and Neurology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yoshitsugu Miyazaki
- Department of Fungal Infection, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo 162-8640, Japan
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50
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Wang Y, Yang L, Wu W, Feng Z, He J, Guo C, He J. Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential. Appl Environ Microbiol 2025; 91:e0245624. [PMID: 40277363 DOI: 10.1128/aem.02456-24] [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: 12/08/2024] [Accepted: 02/18/2025] [Indexed: 04/26/2025] Open
Abstract
Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39T, CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879T, confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.
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Affiliation(s)
- Yuanyuan Wang
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
| | - Luyi Yang
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
| | - Wenbo Wu
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
| | - Zhengqi Feng
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
| | - Jian He
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
| | - Changjun Guo
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- School of Marine Sciences, State Key Laboratory for Biocontrol & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Province Key Laboratory of Aquatic Economic Animals / Guangdong Provincial Observation and Research Station for Marine Ranching of the Lingdingyang Bay, Sun Yat-sen University, Guangzhou, China
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