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Gámbaro F, Pérez AB, Prot M, Agüera E, Baidaliuk A, Sánchez-Seco MP, Martínez-Martínez L, Vázquez A, Fernandez-Garcia MD, Simon-Loriere E. Untargeted metagenomic sequencing identifies Toscana virus in patients with idiopathic meningitis, southern Spain, 2015 to 2019. Euro Surveill 2023; 28:2200913. [PMID: 37943504 PMCID: PMC10636744 DOI: 10.2807/1560-7917.es.2023.28.45.2200913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/15/2023] [Indexed: 11/10/2023] Open
Abstract
BackgroundVarious pathogens, including bacteria, fungi, parasites, and viruses can lead to meningitis. Among viruses causing meningitis, Toscana virus (TOSV), a phlebovirus, is transmitted through sandfly bites. TOSV infection may be suspected if patients with enterovirus- and herpesvirus-negative aseptic (non-bacterial) meningitis recall recent insect bites. Other epidemiological factors (season, rural area) may be considered. The broad range of possible meningitis aetiologies poses considerable diagnosis challenges. Untargeted metagenomic next-generation sequencing (mNGS) can potentially identify pathogens, which are not considered or detected in routine diagnostic panels.AimIn this retrospective, single-centre observational study, we investigated mNGS usefulness to understand the cause of meningitis when conventional approaches fail.MethodsCerebrospinal fluid (CSF) samples from patients hospitalised in southern Spain in 2015-2019 with aseptic meningitis and no aetiology found by conventional testing, were subjected to mNGS. Patients' demographic characteristics had been recorded and physicians had asked them about recent insect bites. Obtained viral genome sequences were phylogenetically analysed.ResultsAmong 23 idiopathic cases, TOSV was identified in eight (all male; median age: 39 years, range: 15-78 years). Five cases lived in an urban setting, three occurred in autumn and only one recalled insect bites. Phylogenetic analysis of TOSV segment sequences supported one intra-genotype reassortment event.ConclusionsOur study highlights the usefulness of mNGS for identifying viral pathogens directly in CSF. In southern Spain, TOSV should be considered regardless of recalling of insect bites or other epidemiological criteria. Detection of a disease-associated reassortant TOSV emphasises the importance of monitoring the spread and evolution of phleboviruses in Mediterranean countries.
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Affiliation(s)
- Fabiana Gámbaro
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ana Belén Pérez
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Eduardo Agüera
- Universidad de Córdoba, Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Artem Baidaliuk
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - María Paz Sánchez-Seco
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Universidad de Córdoba, Córdoba, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Ana Vázquez
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - María Dolores Fernandez-Garcia
- These authors contributed equally to this work and share last authorship and correspondence
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Etienne Simon-Loriere
- These authors contributed equally to this work and share last authorship and correspondence
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
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Charmpi C, Thamsborg KKM, Mikalsen SO, Magnussen E, Sosa Fajardo A, Van der Veken D, Leisner JJ, Leroy F. Bacterial species diversity of traditionally ripened sheep legs from the Faroe Islands (skerpikjøt). Int J Food Microbiol 2023; 386:110023. [PMID: 36463775 DOI: 10.1016/j.ijfoodmicro.2022.110023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/03/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Skerpikjøt is a traditionally ripened sheep leg product from the Faroe Islands, constituting a relatively underexplored microbial ecosystem. The objective of this study is to achieve a deeper understanding of the microbial composition of this artisanal product. Nine ripened hind legs, obtained from three different producers, were assessed regarding their bacterial communities and contents of biogenic amines, including both surface and core samples. Biogenic amine concentrations were generally low, although one sample had a somewhat elevated concentration of cadaverine. Bacterial diversity was investigated by culture-dependent and culture-independent techniques. Gram-positive catalase-positive cocci (GCC) constituted the most abundant group. Within this group, Staphylococcus equorum was the most prevailing species, followed by Kocuria sp., Mammaliicoccus vitulinus, and Staphylococcus saprophyticus. Lactic acid bacteria prevailed in only one sample and were mainly represented by Latilactobacillus curvatus. Enterobacterial communities were characterised by the prevalence of Serratia proteamaculans. Despite the majority of GCC, Clostridium putrefaciens was the most abundant bacterial species in some core samples. Taken together, the culture-dependent and culture-independent identification methods gave complementary results.
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Affiliation(s)
- Christina Charmpi
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Belgium
| | - Kristian Key Milan Thamsborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark
| | - Svein-Ole Mikalsen
- Faculty of Science and Technology, University of the Faroe Islands, Vestarabryggja 15, FO-100 Tórshavn, Faroe Islands
| | - Eyðfinn Magnussen
- Faculty of Science and Technology, University of the Faroe Islands, Vestarabryggja 15, FO-100 Tórshavn, Faroe Islands
| | - Ana Sosa Fajardo
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Belgium
| | - David Van der Veken
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Belgium
| | - Jørgen J Leisner
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg C, Denmark
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Elsene, Belgium.
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Soler P, Moreno-Mesonero L, Zornoza A, Macián VJ, Moreno Y. Characterization of eukaryotic microbiome and associated bacteria communities in a drinking water treatment plant. Sci Total Environ 2021; 797:149070. [PMID: 34303230 DOI: 10.1016/j.scitotenv.2021.149070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The effectiveness of drinking water treatment is critical to achieve an optimal and safe drinking water. Disinfection is one of the most important steps to eliminate the health concern caused by the microbial population in this type of water. However, no study has evaluated the changes in its microbiome, specially the eukaryotic microbiome, and the fates of opportunistic pathogens generated by UV disinfection with medium-pressure mercury lamps in drinking water treatment plants (DWTPs). In this work, the eukaryotic community composition of a DWTP with UV disinfection was evaluated before and after a UV disinfection treatment by means of Illumina 18S rRNA amplicon-based sequencing. Among the physicochemical parameters analysed, flow and nitrate appeared to be related with the changes in the eukaryotic microbiome shape. Public health concern eukaryotic organisms such as Blastocystis, Entamoeba, Acanthamoeba, Hartmannella, Naegleria, Microsporidium or Caenorhabditis were identified. Additionally, the relation between the occurrence of some human bacterial pathogens and the presence of some eukaryotic organisms has been studied. The presence of some human bacterial pathogens such as Arcobacter, Mycobacterium, Pseudomonas and Parachlamydia were statistically correlated with the presence of some eukaryotic carriers showing the public health risk due to the bacterial pathogens they could shelter.
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Affiliation(s)
- Patricia Soler
- Empresa Mixta Valenciana de Aguas, S.A. (EMIVASA), Av. del Regne de València, 28, 46005, Valencia, Spain.
| | - Laura Moreno-Mesonero
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Andrés Zornoza
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; H2OCITIES, SL. Arte Mayor de la Seda, 15, 46950 Xirivella, Valencia, Spain.
| | - V Javier Macián
- Empresa Mixta Valenciana de Aguas, S.A. (EMIVASA), Av. del Regne de València, 28, 46005, Valencia, Spain; Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Yolanda Moreno
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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Du G, Liu L, Guo Q, Cui Y, Chen H, Yuan Y, Wang Z, Gao Z, Sheng Q, Yue T. Microbial community diversity associated with Tibetan kefir grains and its detoxification of Ochratoxin A during fermentation. Food Microbiol 2021; 99:103803. [PMID: 34119096 DOI: 10.1016/j.fm.2021.103803] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
Tibetan kefir grains (TKG) are multi-functional starter cultures used in foods and have been applied in various fermentation systems. This study aimed to investigate the microbial community composition of TKG, the detoxification abilities of TKG and their isolates towards common mycotoxins, and the potential for applying TKG and their associated microbial populations to avoid mycotoxin contamination in dairy products. Cultivation-independent high-throughput sequencing of bacterial and fungal rDNA genes indicated that Lactobacillus kefiranofaciens and Kazachstania turicensis were the most abundant bacterial and fungal taxa, respectively. In addition, 27 total isolates were obtained using cultivation methods. TKG removed more than 90% of the Ochratoxin A (OTA) after 24 h, while the isolate Kazachstania unisporus AC-2 exhibited the highest removal capacity (~46.1%). Further, the isolate exhibited good resistance to acid and bile salts environment. Analysis of the OTA detoxification mechanism revealed that both adsorption and degradation activities were exhibited by TKG, with adsorption playing a major detoxification role. Furthermore, the addition of OTA did not affect the microbial community structure of TKG. These results indicate that TKG-fermented products can naturally remove mycotoxin contamination of milk and could potentially be practically applied as probiotics in fermentation products.
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Affiliation(s)
- Gengan Du
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Lin Liu
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Qi Guo
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Yuanyuan Cui
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Hong Chen
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Zhenpeng Gao
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China
| | - Qinlin Sheng
- College of Food Science and Engineering, Northwest University, Xi'an, 710069, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (Yangling), Ministry of Agriculture, Yangling, 712100, China; College of Food Science and Engineering, Northwest University, Xi'an, 710069, China.
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Bo B, Kim SA, Han NS. Bacterial and fungal diversity in Laphet, traditional fermented tea leaves in Myanmar, analyzed by culturing, DNA amplicon-based sequencing, and PCR-DGGE methods. Int J Food Microbiol 2020; 320:108508. [PMID: 31986350 DOI: 10.1016/j.ijfoodmicro.2020.108508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/19/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023]
Abstract
Laphet is a traditional fermented food in Myanmar, made from tea leaves (Camellia sinensis) by fermentation with limited air passage. We performed microbial diversity analyses on 14 Laphet products collected from different locations in Myanmar. Amplicon-based sequencing results revealed Lactobacillus and Acetobacter were abundant bacteria and Candida, Pichia, Cyberlindnera, and Debaryomyces were abundant yeast. Using selective media, eight species of lactic acid bacteria and nine species of yeast were isolated; Lactobacillus plantarum and L. collinoides were dominant bacteria and Pichia manshurica, Candida boidinii, and Cyberlindnera jadinii were major yeasts. PCR-DGGE analysis confirmed that most of the dominant bacterial and yeast species found in culture dependent analysis were present in Laphet samples. Microbial diversity and pH of Laphet were different between samples from tea plantation area and local markets due to possible differences in incubation time periods. When tannase activity was tested, 23 among 29 bacterial isolates and two among 36 yeast isolates showed positive activities. These findings provide new insights into microbial diversity of Laphet and increased our understanding of the core bacterial and yeast species involved in the manufacture of Laphet.
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Affiliation(s)
- Bo Bo
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea; Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Division, Myanmar
| | - Seul-Ah Kim
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea.
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Zucca S, Villaraggia M, Gagliardi S, Grieco GS, Valente M, Cereda C, Magni P. Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management. BMC Bioinformatics 2016; 17:339. [PMID: 28185542 PMCID: PMC5123238 DOI: 10.1186/s12859-016-1189-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Amplicon-based targeted resequencing is a commonly adopted solution for next-generation sequencing applications focused on specific genomic regions. The reliability of such approaches rests on the high specificity and deep coverage, although sequencing artifacts attributable to PCR-like amplification can be encountered. Between these artifacts, allele drop-out, which is the preferential amplification of one allele, causes an artificial increase in homozygosity when heterozygous mutations fall on a primer pairing region. Here, a procedure to manage such artifacts, based on a pipeline composed of two steps of alignment and variant calling, is proposed. This methodology has been compared to the Illumina Custom Amplicon workflow, available on Illumina MiSeq, on the analysis of data obtained with four newly designed TruSeq Custom Amplicon gene panels. RESULTS Four gene panels, specific for Parkinson disease, for Intracerebral Hemorrhage Diseases (COL4A1 and COL4A2 genes) and for Familial Hemiplegic Migraine (CACNA1A and ATP1A2 genes) were designed. A total of 119 samples were re-sequenced with Illumina MiSeq sequencer and panel characterization in terms of coverage, number of variants found and allele drop-out potential impact has been carried out. Results show that 14 % of identified variants is potentially affected by allele drop-out artifacts and that both the Custom Amplicon workflow and the procedure proposed here could correctly identify them. Furthermore, a more complex configuration in presence of two mutations was simulated in silico. In this configuration, our proposed methodology outperforms Custom Amplicon workflow, being able to correctly identify two mutations in all the studied configurations. CONCLUSIONS Allele drop-out plays a crucial role in amplicon-based targeted re-sequencing and specific procedures in data analysis of amplicon data should be adopted. Although a consensus has been established in the elimination of primer sequences from aligned data (e.g., via primer sequence trimming or soft clipping), more complex configurations need to be managed in order to increase the retrieved information from available data. Our method shows how to manage one of these complex configurations, when two mutations occur.
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Affiliation(s)
- Susanna Zucca
- Department of Electrical, Computer and Biomedical engineering, University of Pavia, Pavia, 27100, Italy. .,Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy.
| | - Margherita Villaraggia
- Department of Electrical, Computer and Biomedical engineering, University of Pavia, Pavia, 27100, Italy
| | - Stella Gagliardi
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Gaetano Salvatore Grieco
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Marialuisa Valente
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Cristina Cereda
- Center of Genomics and post-Genomics, IRCCS National Institute of Neurology Foundation "C. Mondino", Pavia, 27100, Italy
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical engineering, University of Pavia, Pavia, 27100, Italy
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