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838 results on '"Zomer, Aldert"'

101. The Equine Faecal Microbiota of Healthy Horses and Ponies in The Netherlands: Impact of Host and Environmental Factors

Author

Equine Internal Medicine, dES AVR, dI&I I&I-4, Klinische infectiologie en microb. lab., dIRAS RA-I&I I&I, CS_Welfare & emerging diseases, Theelen, Mathijs J P, Luiken, Roosmarijn E C, Wagenaar, Jaap A, Sloet van Oldruitenborgh-Oosterbaan, Marianne M, Rossen, John W A, Zomer, Aldert L, Equine Internal Medicine, dES AVR, dI&I I&I-4, Klinische infectiologie en microb. lab., dIRAS RA-I&I I&I, CS_Welfare & emerging diseases, Theelen, Mathijs J P, Luiken, Roosmarijn E C, Wagenaar, Jaap A, Sloet van Oldruitenborgh-Oosterbaan, Marianne M, Rossen, John W A, and Zomer, Aldert L

Published
2021

102. Absence of Host-Specific Genes in Canine and Human Staphylococcus pseudintermedius as Inferred from Comparative Genomics

Author

dI&I I&I-4, Klinische infectiologie en microb. lab., Wegener, Alice, Broens, Els M, van der Graaf-van Bloois, Linda, Zomer, Aldert L, Visser, Caroline E, van Zeijl, Jan, van der Meer, Coby, Kusters, Johannes G, Friedrich, Alex W, Kampinga, Greetje A, Sips, Gregorius J, Smeets, Leonard, van Kerckhoven, Manfred E J, Timmerman, Arjen J, Wagenaar, Jaap A, Duim, Birgitta, dI&I I&I-4, Klinische infectiologie en microb. lab., Wegener, Alice, Broens, Els M, van der Graaf-van Bloois, Linda, Zomer, Aldert L, Visser, Caroline E, van Zeijl, Jan, van der Meer, Coby, Kusters, Johannes G, Friedrich, Alex W, Kampinga, Greetje A, Sips, Gregorius J, Smeets, Leonard, van Kerckhoven, Manfred E J, Timmerman, Arjen J, Wagenaar, Jaap A, and Duim, Birgitta

Published
2021

103. Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Patel, Shriram, Vlasblom, Abel A, Verstappen, Koen M, Zomer, Aldert L, Fluit, Ad C, Rogers, Malbert R C, Wagenaar, Jaap A, Claesson, Marcus J, Duim, Birgitta, Klinische infectiologie en microb. lab., dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Patel, Shriram, Vlasblom, Abel A, Verstappen, Koen M, Zomer, Aldert L, Fluit, Ad C, Rogers, Malbert R C, Wagenaar, Jaap A, Claesson, Marcus J, and Duim, Birgitta

Published
2021

104. Complete Genome Sequence of a Clinical Campylobacter Isolate Identical to a Novel Campylobacter Species

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Duim, Birgitta, van der Graaf-van Bloois, Linda, Timmerman, Arjen, Wagenaar, Jaap A, Flipse, Jacky, Wallinga, Janny, Bloembergen, Peter, Miller, William G, Zomer, Aldert L, Klinische infectiologie en microb. lab., dI&I I&I-4, Duim, Birgitta, van der Graaf-van Bloois, Linda, Timmerman, Arjen, Wagenaar, Jaap A, Flipse, Jacky, Wallinga, Janny, Bloembergen, Peter, Miller, William G, and Zomer, Aldert L

Published
2021

105. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Moreno-Indias, Isabel, Lahti, Leo, Nedyalkova, Miroslava, Elbere, Ilze, Roshchupkin, Gennady, Adilovic, Muhamed, Aydemir, Onder, Bakir-Gungor, Burcu, Santa Pau, Enrique Carrillo-de, D’Elia, Domenica, Desai, Mahesh S., Falquet, Laurent, Gundogdu, Aycan, Hron, Karel, Klammsteiner, Thomas, Lopes, Marta B., Marcos-Zambrano, Laura Judith, Marques, Cláudia, Mason, Michael, May, Patrick, Pašić, Lejla, Pio, Gianvito, Pongor, Sándor, Promponas, Vasilis J., Przymus, Piotr, Saez-Rodriguez, Julio, Sampri, Alexia, Shigdel, Rajesh, Stres, Blaz, Suharoschi, Ramona, Truu, Jaak, Truică, Ciprian-Octavian, Vilne, Baiba, Vlachakis, Dimitrios, Yilmaz, Ercument, Zeller, Georg, Zomer, Aldert L., Gómez-Cabrero, David, Claesson, Marcus J., Klinische infectiologie en microb. lab., dI&I I&I-4, Moreno-Indias, Isabel, Lahti, Leo, Nedyalkova, Miroslava, Elbere, Ilze, Roshchupkin, Gennady, Adilovic, Muhamed, Aydemir, Onder, Bakir-Gungor, Burcu, Santa Pau, Enrique Carrillo-de, D’Elia, Domenica, Desai, Mahesh S., Falquet, Laurent, Gundogdu, Aycan, Hron, Karel, Klammsteiner, Thomas, Lopes, Marta B., Marcos-Zambrano, Laura Judith, Marques, Cláudia, Mason, Michael, May, Patrick, Pašić, Lejla, Pio, Gianvito, Pongor, Sándor, Promponas, Vasilis J., Przymus, Piotr, Saez-Rodriguez, Julio, Sampri, Alexia, Shigdel, Rajesh, Stres, Blaz, Suharoschi, Ramona, Truu, Jaak, Truică, Ciprian-Octavian, Vilne, Baiba, Vlachakis, Dimitrios, Yilmaz, Ercument, Zeller, Georg, Zomer, Aldert L., Gómez-Cabrero, David, and Claesson, Marcus J.

Published
2021

106. Sources and transmission routes of campylobacteriosis: a combined analysis of genome and exposure data

Author

IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, LS IRAS EEPI GRA (Gezh.risico-analyse), Dep Infectieziekten Immunologie, Klinische infectiologie en microb. lab., dI&I I&I-4, LS IRAS VPH VV (veterinaire volksgezh.), Dep IRAS, Mughini-Gras, Lapo, Pijnacker, Roan, Coipan, Claudia, Mulder, Annemieke C., Veludo, Adriana Fernandes, de Rijk, Sharona, van Hoek, Angela H.A.M., Buij, Ralph, Muskens, Gerard, Koene, Miriam, Veldman, Kees, Duim, Birgitta, Graaf-van Bloois, Linda van der, van der Weijden, Coen, Kuiling, Sjoerd, Verbruggen, Anjo, van der Giessen, Joke, Opsteegh, Marieke, van der Voort, Menno, Castelijn, Greetje A.A., Schets, Franciska M., Blaak, Hetty, Wagenaar, Jaap A., Zomer, Aldert L., Franz, Eelco, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, LS IRAS EEPI GRA (Gezh.risico-analyse), Dep Infectieziekten Immunologie, Klinische infectiologie en microb. lab., dI&I I&I-4, LS IRAS VPH VV (veterinaire volksgezh.), Dep IRAS, Mughini-Gras, Lapo, Pijnacker, Roan, Coipan, Claudia, Mulder, Annemieke C., Veludo, Adriana Fernandes, de Rijk, Sharona, van Hoek, Angela H.A.M., Buij, Ralph, Muskens, Gerard, Koene, Miriam, Veldman, Kees, Duim, Birgitta, Graaf-van Bloois, Linda van der, van der Weijden, Coen, Kuiling, Sjoerd, Verbruggen, Anjo, van der Giessen, Joke, Opsteegh, Marieke, van der Voort, Menno, Castelijn, Greetje A.A., Schets, Franciska M., Blaak, Hetty, Wagenaar, Jaap A., Zomer, Aldert L., and Franz, Eelco

Published
2021

107. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Institute of Health - LIH [research center], COST Action CA1813, CORE grant (C18/BM/12585940) [sponsor], Moreno-Indias, Isabel, Lahti, Leo, Nedyalkova, Miroslava, Elbere, Ilze, Roshchupkin, Gennady, Adilovic, Muhamed, Aydemir, Onder, Bakir-Gungor, Burcu, Santa Pau, Enrique Carrillo-De, D’Elia, Domenica, Desai, Mahesh, Falquet, Laurent, Gundogdu, Aycan, Hron, Karel, Klammsteiner, Thomas, Lopes, Marta B., Marcos-Zambrano, Laura Judith, Marques, Cláudia, Mason, Michael, May, Patrick, Pašić, Lejla, Pio, Gianvito, Pongor, Sándor, Promponas, Vasilis J., Przymus, Piotr, Saez-Rodriguez, Julio, Sampri, Alexia, Shigdel, Rajesh, Stres, Blaz, Suharoschi, Ramona, Truu, Jaak, Truică, Ciprian-Octavian, Vilne, Baiba, Vlachakis, Dimitrios, Yilmaz, Ercument, Zeller, Georg, Zomer, Aldert L., Gómez-Cabrero, David, Claesson, Marcus J., Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Luxembourg Institute of Health - LIH [research center], COST Action CA1813, CORE grant (C18/BM/12585940) [sponsor], Moreno-Indias, Isabel, Lahti, Leo, Nedyalkova, Miroslava, Elbere, Ilze, Roshchupkin, Gennady, Adilovic, Muhamed, Aydemir, Onder, Bakir-Gungor, Burcu, Santa Pau, Enrique Carrillo-De, D’Elia, Domenica, Desai, Mahesh, Falquet, Laurent, Gundogdu, Aycan, Hron, Karel, Klammsteiner, Thomas, Lopes, Marta B., Marcos-Zambrano, Laura Judith, Marques, Cláudia, Mason, Michael, May, Patrick, Pašić, Lejla, Pio, Gianvito, Pongor, Sándor, Promponas, Vasilis J., Przymus, Piotr, Saez-Rodriguez, Julio, Sampri, Alexia, Shigdel, Rajesh, Stres, Blaz, Suharoschi, Ramona, Truu, Jaak, Truică, Ciprian-Octavian, Vilne, Baiba, Vlachakis, Dimitrios, Yilmaz, Ercument, Zeller, Georg, Zomer, Aldert L., Gómez-Cabrero, David, and Claesson, Marcus J.

Abstract

The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 “ML4Microbiome” that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.

Published
2021

108. Biomolecule sulphation and novel methylations related to guillain-barré syndrome-associated campylobacter jejuni serotype hs:19

Author

Heikema, Astrid P., Strepis, Nikolaos, Horst-Kreft, Deborah, Huynh, Steven, Zomer, Aldert, Kelly, David J., Cooper, Kerry K., Parker, Craig T., Heikema, Astrid P., Strepis, Nikolaos, Horst-Kreft, Deborah, Huynh, Steven, Zomer, Aldert, Kelly, David J., Cooper, Kerry K., and Parker, Craig T.

Abstract

Campylobacter jejuni strains that produce sialylated lipooligosaccharides (LOS) can cause the immune-mediated disease Guillain-Barré syndrome (GBS). The risk of GBS after infection with C. jejuni Penner serotype HS:19 is estimated to be at least six times higher than the average risk. Aside from LOS biosynthesis genes, genomic characteristics that promote an increased risk for GBS following C. jejuni HS:19 infection, remain uncharacterized. We hypothesized that strains with the HS:19 serotype have unique genomic features that explain the increased risk for GBS. We performed genome sequencing, alignments, single nucleotide polymorphisms' analysis and methylome characterization on a subset, and pan-genome analysis on a large number of genomes to compare HS:19 with non-HS:19 C. jejuni genome sequences. Comparison of 36 C. jejuni HS:19 with 874 C. jejuni non-HS:19 genome sequences led to the identification of three single genes and ten clusters containing contiguous genes that were significantly associated with C. jejuni HS:19. One gene cluster of seven genes, localized downstream of the capsular biosynthesis locus, was related to sulphation of biomolecules. This cluster also encoded the campylobacter sialyl transferase Cst-I. Interestingly, sulphated bacterial biomolecules such as polysaccharides can promote immune responses and, therefore, (in the presence of sialic acid) may play a role in the development of GBS. Additional gene clusters included those involved in persistence-mediated pathogenicity and gene clusters involved in restriction-modification systems. Furthermore, characterization of methylomes of two HS:19 strains exhibited novel methylation patterns (5′-CATG-3 and 5′-m6AGTNNNNNNRTTG-3) that could differentially effect gene-expression patterns of C. jejuni HS:19 strains. Our study provides novel insight into specific genetic features and possible virulence factors of C. jejuni associated with the HS:19 serotype that may explain the increased

Published
2021

109. Differential analysis of longitudinal methicillin-resistant staphylococcus aureus colonization in relation to microbial shifts in the nasal microbiome of neonatal piglets

Author

Patel, Shriram, Vlasblom, Abel A., Verstappen, Koen M., Zomer, Aldert L., Fluit, Ad C., Rogers, Malbert R.C., Wagenaar, Jaap A., Claesson, Marcus J., Duim, Birgitta, Patel, Shriram, Vlasblom, Abel A., Verstappen, Koen M., Zomer, Aldert L., Fluit, Ad C., Rogers, Malbert R.C., Wagenaar, Jaap A., Claesson, Marcus J., and Duim, Birgitta

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen and often colonizes pigs. To lower the risk of MRSA transmission to humans, a reduction of MRSA prevalence and/or load in pig farms is needed. The nasal microbiome contains commensal species that may protect against MRSA colonization and may be used to develop competitive exclusion strategies. To obtain a comprehensive understanding of the species that compete with MRSA in the developing porcine nasal microbiome, and the moment of MRSA colonization, we analyzed nasal swabs from piglets in two litters. The swabs were taken longitudinally, starting directly after birth until 6 weeks. Both 16S rRNA and tuf gene sequencing data with different phylogenetic resolutions and complementary culture-based and quantitative real-time PCR (qPCR)-based MRSA quantification data were collected. We employed a compositionally aware bioinformatics approach (CoDaSeq 1 rmcorr) for analysis of longitudinal measurements of the nasal microbiota. The richness and diversity in the developing nasal microbiota increased over time, albeit with a reduction of Firmicutes and Actinobacteria, and an increase of Proteobacteria. Coabundant groups (CAGs) of species showing strong positive and negative correlation with colonization of MRSA and S. aureus were identified. Combining 16S rRNA and tuf gene sequencing provided greater Staphylococcus species resolution, which is necessary to inform strategies with potential protective effects against MRSA colonization in pigs.

Published
2021

110. Identification of conditionally essential genes for Streptococcus suis infection in pigs

Author

Arenas, Jesús, Zomer, Aldert, Harders-Westerveen, Jose, Bootsma, Hester J, De Jonge, Marien I, Stockhofe-Zurwieden, Norbert, Smith, Hilde E, De Greeff, Astrid, Klinische infectiologie en microb. lab., dI&I I&I-4, Klinische infectiologie en microb. lab., and dI&I I&I-4

Subjects
Microbiology (medical), transposon mutagenesis, Streptococcus suis, Immunology, Mutant, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Tn-Seq, Virulence, Infectious and parasitic diseases, RC109-216, Microbiology, Genome, Sepsis, 03 medical and health sciences, Immune system, medicine, Gene, 030304 developmental biology, Host Pathogen Interaction & Diagnostics, 0303 health sciences, biology, 030306 microbiology, pathogenesis, Bacteriologie, Wild type, streptococcus suis, zoonotic pathogen, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, medicine.disease, biology.organism_classification, Host Pathogen Interactie & Diagnostiek, infection, Infectious Diseases, Bacteriologie, Host Pathogen Interactie & Diagnostiek, tn-seq, Parasitology
Abstract

Streptococcus suis is a Gram-positive bacterium and zoonotic pathogen that causes meningitis and sepsis in pigs and humans. The aim of this study was to identify genes required for S. suis infection. We created Tn-Seq libraries in a virulent S. suis strain 10, which was used to inoculate pigs in an intrathecal experimental infection. Comparative analysis of the relative abundance of mutants recovered from different sites of infection (blood, cerebrospinal fluid, and meninges of the brain) identified 361 conditionally essential genes, i.e. required for infection, which is about 18% of the genome. The conditionally essential genes were primarily involved in metabolic and transport processes, regulation, ribosomal structure and biogenesis, transcription, and cell wall membrane and envelope biogenesis, stress defenses, and immune evasion. Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in ex vivo models. Mutants showed different levels of sensitivity to survival in whole blood, serum, cerebrospinal fluid, thermic shock, and stress conditions, as compared to the wild type. Additionally, the role of three selected mutants was validated in co-infection experiments in which pigs were infected with both wild type and isogenic mutant strains. The genetic determinants of infection identified in this work contribute to novel insights in S. suis pathogenesis and could serve as targets for novel vaccines or antimicrobial drugs.

Published
2020

111. An interactive regulatory network controls stress response in Bifidobacterium breve UCC2003

Author

Zomer, Aldert, Fernandez, Matilde, Kearney, Breda, Fitzgerald, Gerald F., Ventura, Marco, and van Sinderen, Douwe

Subjects
Bifidobacterium -- Health aspects, Bifidobacterium -- Research, Gastrointestinal system -- Physiological aspects, Gastrointestinal system -- Research, Biological sciences
Abstract

Members of the genus Bifidobacterium are gram-positive bacteria that commonly are found in the gastrointestinal tract (GIT) of mammals, including humans. Because of their perceived probiotic properties, they frequently are incorporated as functional ingredients in food products. From probiotic production to storage and GIT delivery, bifidobacteria encounter a plethora of stresses. To cope with these environmental challenges, they need to protect themselves through stress-induced adaptive responses. We have determined the response of B. breve UCC2003 to various stresses (heat, osmotic, and solvent) using transcriptome analysis, DNA-protein interactions, and GusA reporter fusions, and we combined these with results from an in silico analysis. The integration of these results allowed the formulation of a model for an interacting regulatory network for stress response in B. breve UCC2003 where HspR controls the SOS response and the CIgR regulon, which in turn regulates and is regulated by HrcA. This model of an interacting regulatory network is believed to represent the paradigm for stress adaptation in bifidobacteria. doi: 10.1128/JB.00897-09

Published
2009

112. A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans

Author

Flipse, Jacky, Duim, Birgitta, Wallinga, Janny A., de Wijkerslooth, Laetitia R. H., Graaf-van Bloois, Linda van der, Timmerman, Arjen J., Zomer, Aldert L., Veldman, Kees T., Wagenaar, Jaap A., Bloembergen, Peter, Klinische infectiologie en microb. lab., dI&I I&I-4, Klinische infectiologie en microb. lab., and dI&I I&I-4

Subjects
Microbiology (medical), Tetracycline, Epidemiology, Bioinformatica & Diermodellen, lcsh:Medicine, Campylobacter spp, Case Report, medicine.disease_cause, Azithromycin, Microbiology, Bio-informatics & Animal models, non-jejuni/coli infection, medicine, Immunology and Allergy, Epidemiology, Bio-informatics & Animal models, Molecular Biology, culture versus PCR, Epidemiologie, General Immunology and Microbiology, business.industry, Lymphogranuloma venereum, Campylobacter, lcsh:R, 16S ribosomal RNA, medicine.disease, Lymphoma, Ciprofloxacin, Infectious Diseases, Epidemiologie, Bioinformatica & Diermodellen, Candidatus, business, medicine.drug
Abstract

A man with a well-controlled HIV infection, previously diagnosed with lymphogranuloma venereum and treated for Hodgkin’s lymphoma, was suffering from chronic diarrhea. He travelled to Indonesia in the month prior to the start of complaints. Over a 15-month period, sequences related to Campylobactertroglodytis/upsaliensis, C. pinnepediorum/mucosalis/concisus and C. hominis were detected by 16S rRNA qPCR-based assays in various stool samples and in a colon biopsy. Culture revealed the first isolation of “candidatus Campylobacter infans”, a species identified recently by molecular methods only. The patient was treated with azithromycin, ciprofloxacin and tetracycline. To identify potential continuous exposure of the patient to Campylobacter, stool samples of the partner and the cat of the patient were analyzed and C. pinnepediorum/mucosalis/concisus and C. helveticus, respectively, were detected. The diversity in detected species in this immunocompromised patient with a lack of repeatedly consistent findings resulted in the conclusion that not any of the Campylobacter species was the primary cause of the clinical condition. This study shows the challenges in detection and interpretation of diagnostic results regarding Campylobacter.

Published
2020

113. After the bite: bacterial transmission from grey seals ( Halichoerus grypus ) to harbour porpoises ( Phocoena phocoena )

Author

Gilbert, Maarten J., IJsseldijk, Lonneke L., Rubio-García, Ana, Gröne, Andrea, Duim, Birgitta, Rossen, John, Zomer, Aldert L., Wagenaar, Jaap A., dI&I I&I-4, VPDC pathologie, dPB CR, VP pathologie, dPB I&I, Klinische infectiologie en microb. lab., dI&I I&I-4, VPDC pathologie, dPB CR, VP pathologie, dPB I&I, Klinische infectiologie en microb. lab., and Microbes in Health and Disease (MHD)

Subjects
Epidemiology, Bioinformatica & Diermodellen, Zoology, microbiome, Phocoena, Oral cavity, bacterial transmission, Phoca, Seal (mechanical), 03 medical and health sciences, MARINE MAMMALS, FEVER, biology.animal, Bio-informatics & Animal models, INFECTION, Epidemiology, Bio-informatics & Animal models, harbour porpoise, North sea, lcsh:Science, CLINICAL SPECIMENS, 030304 developmental biology, computer.programming_language, Epidemiologie, 0303 health sciences, Multidisciplinary, STREPTOCOCCUS-PHOCAE, biology, 030306 microbiology, Transmission (medicine), Genetics and Genomics, biology.organism_classification, common seal, SP NOV, Epidemiologie, Bioinformatica & Diermodellen, Harbour, lcsh:Q, computer, Porpoise, Research Article, grey seal
Abstract

Recent population growth of the harbour porpoise ( Phocoena phocoena ), grey seal ( Halichoerus grypus ) and common seal ( Phoca vitulina ) in the North Sea has increased potential interaction between these species. Grey seals are known to attack harbour porpoises. Some harbour porpoises survive initially, but succumb eventually, often showing severely infected skin lesions. Bacteria transferred from the grey seal oral cavity may be involved in these infections and eventual death of the animal. In humans, seal bites are known to cause severe infections. In this study, a 16S rRNA-based microbiome sequencing approach is used to identify the oral bacterial diversity in harbour porpoises, grey seals and common seals; detect the potential transfer of bacteria from grey seals to harbour porpoises by biting and provide insights in the bacteria with zoonotic potential present in the seal oral cavity. β-diversity analysis showed that 12.9% (4/31) of the harbour porpoise skin lesion microbiomes resembled seal oral microbiomes, while most of the other skin lesion microbiomes also showed seal-associated bacterial species, including potential pathogens. In conclusion, this study shows that bacterial transmission from grey seals to harbour porpoises by biting is highly likely and that seal oral cavities harbour many bacterial pathogens with zoonotic potential.

Published
2020

114. Incompatibility and phylogenetic relationship of I-complex plasmids

Author

Rozwandowicz, Marta, Hordijk, Joost, Bossers, Alex, Zomer, Aldert, Wagenaar, Jaap A, Mevius, Dik J, Brouwer, Michael S M, dI&I I&I-4, Klinische infectiologie en microb. lab., dI&I I&I-4, and Klinische infectiologie en microb. lab.

Subjects
DNA Replication, Cell division, Epidemiology, Bioinformatica & Diermodellen, Population, Biology, medicine.disease_cause, Plasmid, Genomic Instability, Bacterial cell structure, 03 medical and health sciences, IncZ, Drug Resistance, Bacterial, Bio-informatics & Animal models, Escherichia coli, medicine, Epidemiology, Bio-informatics & Animal models, Dislodgement, education, Molecular Biology, Phylogeny, 030304 developmental biology, Genetics, Host Pathogen Interaction & Diagnostics, Epidemiologie, 0303 health sciences, education.field_of_study, 030306 microbiology, Electroporation, Bacteriologie, Incompatibility IncB/O, Bacteriology, Genomics, Sequence Analysis, DNA, Bacteriology, Host Pathogen Interaction & Diagnostics, Phenotype, Host Pathogen Interactie & Diagnostiek, Mutagenesis, Conjugation, Genetic, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Transformation, Bacterial, Phylogenetic relationship, Plasmids
Abstract

Plasmid incompatibility is the inability of two plasmids to be stably maintained in one cell, resulting in loss of one of the plasmids in daughter cells. Dislodgement is a phenotypically distinct form of incompatibility, described as an imperfect reproduction, manifesting in rapid exclusion of a resident plasmid after superinfection. The relationship between plasmids of the phenotypic incompatibility groups IncB/O and IncZ is unclear. Their inability to co-exist was initially referred to as dislodgement while other research reached the conclusion that IncB/O and IncZ plasmids are incompatible. In this manuscript we re-evaluated the relationship between IncB/O and IncZ plasmids to settle these conflicting conclusions. We performed dislodgement testing of R16Δ (IncB/O) and pSFE-059 (IncZ) plasmids by electroporation in a bacterial cell and checked their stability. Stability tests of the obtained plasmid pair showed that the IncB/O plasmid was exclusively and almost completely lost from the heteroplasmid Escherichia coli population. Other IncB/O - IncZ pairs could not form a heteroplasmid population, using conjugation or electroporation. Our data supports the previous suggestion that IncB/O and IncZ plasmids may be considered phenotypically incompatible.

Published
2020

115. Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363

Author

Wegmann, Udo, O'Connell-Motherway, Mary, Zomer, Aldert, Buist, Girbe, Shearman, Claire, Canchaya, Carlos, Ventura, Marco, Goesmann, Alexander, Gasson, Michael J., Kuipers, Oscar P., van Sinderen, Douwe, and Kok, Jan

Subjects
Genomes -- Research, Lactococcus -- Genetic aspects, Lactococcus -- Research, Lactic acid -- Research, Streptococcus -- Genetic aspects, Streptococcus -- Research, Biological sciences
Abstract

Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp, cremoris MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category 'carbohydrate metabolism and transport,' by far the largest category of novel proteins in comparison with L. lactis subsp, lactis IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56.kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the 'lateral gene transfer hot spot' in the genome of Streptococcus thermophilus. Although the parent of L. lactis MG1363 was used to demonstrate lysogeny in Lactococcus, L. lactis MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research.

Published
2007

116. Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363

Author

Zomer, Aldert L., Buist, Girbe, Larsen, Rasmus, Kok, Jan, and Kuipers, Oscar P.

Subjects
Gene expression -- Research, Lactococcus -- Genetic aspects, Lactococcus -- Research, Protein-protein interactions -- Research, Biological sciences
Abstract

Carbon catabolite control protein A (CcpA) is the main regulator involved in carbon catabolite repression in gram-positive bacteria. Time series gene expression analyses of Lactococcus lactis MG1363 and L. lactis MG1363[DELTA]ccpA using DNA microarrays were used to define the CcpA regulon of L. lactis. Based on a comparison of the transcriptome data with putative CcpA binding motifs (cre sites) in promoter sequences in the genome of L. lactis, 82 direct targets of CcpA were predicted. The main differences in time-dependent expression of CcpA-regulated genes were differences between the exponential and transition growth phases. Large effects were observed for carbon and nitrogen metabolic genes in the exponential growth phase. Effects on nucleotide metabolism genes were observed primarily in the transition phase. Analysis of the positions of putative cre sites revealed that there is a link between either repression or activation and the location of the cre site within the promoter region. Activation was observed when putative cre sites were located upstream of the hexameric -35 sequence at an average position of -56.5 or further upstream with decrements of 10.5 bp. Repression was observed when the cre site was located in or downstream of putative -35 and -10 sequences. The highest level of repression was observed when the cre site was present at a defined side of the DNA helix relative to the canonical -10 sequence. Gel retardation experiments, Northern blotting, and enzyme assays showed that CcpA represses its own expression and activates the expression of the divergently oriented prolidase-encoding pepQ gene, which constitutes a link between regulation of carbon metabolism and regulation of nitrogen metabolism.

Published
2007

117. Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

Author

Castellanos, L.R., Graaf-Van Bloois, Linda, Van Der, Donado-Godoy, Pilar, Veldman, K.T., Duarte, Francisco, Acuña, María T., Jarquín, Claudia, Weill, Francois Xavier, Mevius, D.J., Wagenaar, J.A., Hordijk, Joost, Zomer, Aldert L., Castellanos, L.R., Graaf-Van Bloois, Linda, Van Der, Donado-Godoy, Pilar, Veldman, K.T., Duarte, Francisco, Acuña, María T., Jarquín, Claudia, Weill, Francois Xavier, Mevius, D.J., Wagenaar, J.A., Hordijk, Joost, and Zomer, Aldert L.

Abstract

Salmonella enterica serovar Paratyphi B variant Java sequence type 28 is prevalent in poultry and poultry meat. We investigated the evolutionary relatedness between sequence type 28 strains from Europe and Latin America using time-resolved phylogeny and principal component analysis. We sequenced isolates from Colombia, Guatemala, Costa Rica, and the Netherlands and complemented them with publicly available genomes from Europe, Africa, and the Middle East. Phylogenetic time trees and effective population sizes (Ne) showed separate clustering of strains from Latin America and Europe. The separation is estimated to have occurred during the 1980s. Ne of strains increased sharply in Europe around 1995 and in Latin America around 2005. Principal component analysis on noncore genes showed a clear distinction between strains from Europe and Latin America, whereas the plasmid gene content was similar. Regardless of the evolutionary separation, similar features of resistance to β-lactams and quinolones/fluoroquinolones indicated parallel evolution of antimicrobial resistance in both regions

Published
2020

118. Supplementary material from 'After the bite: bacterial transmission from grey seals (Halichoerus grypus) to harbour porpoises (Phocoena phocoena)'

Author

Gilbert, Maarten J., IJsseldijk, Lonneke L., Rubio-García, Ana, Gröne, Andrea, Duim, Birgitta, Rossen, John, Zomer, Aldert L., Wagenaar, Jaap A., Gilbert, Maarten J., IJsseldijk, Lonneke L., Rubio-García, Ana, Gröne, Andrea, Duim, Birgitta, Rossen, John, Zomer, Aldert L., and Wagenaar, Jaap A.

Abstract

Recent population growth of the harbour porpoise (Phocoena phocoena), grey seal (Halichoerus grypus) and common seal (Phoca vitulina) in the North Sea has increased potential interaction between these species. Grey seals are known to attack harbour porpoises. Some harbour porpoises survive initially, but succumb eventually, often showing severely infected skin lesions. Bacteria transferred from the grey seal oral cavity may be involved in these infections and eventual death of the animal. In humans, seal bites are known to cause severe infections. In this study, a 16S rRNA-based microbiome sequencing approach is used to identify the oral bacterial diversity in harbour porpoises, grey seals and common seals; detect the potential transfer of bacteria from grey seals to harbour porpoises by biting and provide insights in the bacteria with zoonotic potential present in the seal oral cavity. β-diversity analysis showed that 12.9% (4/31) of the harbour porpoise skin lesion microbiomes resembled seal oral microbiomes, while most of the other skin lesion microbiomes also showed seal-associated bacterial species, including potential pathogens. In conclusion, this study shows that bacterial transmission from grey seals to harbour porpoises by biting is highly likely and that seal oral cavities harbour many bacterial pathogens with zoonotic potential.

Published
2020

119. A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Flipse, Jacky, Duim, Birgitta, Wallinga, Janny A., de Wijkerslooth, Laetitia R. H., Graaf-van Bloois, Linda van der, Timmerman, Arjen J., Zomer, Aldert L., Veldman, Kees T., Wagenaar, Jaap A., Bloembergen, Peter, Klinische infectiologie en microb. lab., dI&I I&I-4, Flipse, Jacky, Duim, Birgitta, Wallinga, Janny A., de Wijkerslooth, Laetitia R. H., Graaf-van Bloois, Linda van der, Timmerman, Arjen J., Zomer, Aldert L., Veldman, Kees T., Wagenaar, Jaap A., and Bloembergen, Peter

Published
2020

120. Tracing the animal sources of surface water contamination with Campylobacter jejuni and Campylobacter coli

Author

LS IRAS EEPI GRA (Gezh.risico-analyse), Klinische infectiologie en microb. lab., dI&I I&I-4, Dep IRAS, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Mulder, Annemieke C., Franz, Eelco, de Rijk, Sharona, Versluis, Moyke A.J., Coipan, Claudia, Buij, Ralph, Müskens, Gerard, Koene, Miriam, Pijnacker, Roan, Duim, Birgitta, Bloois, Linda van der Graaf van, Veldman, Kees, Wagenaar, Jaap A., Zomer, Aldert L., Schets, Franciska M., Blaak, Hetty, Mughini-Gras, Lapo, LS IRAS EEPI GRA (Gezh.risico-analyse), Klinische infectiologie en microb. lab., dI&I I&I-4, Dep IRAS, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Mulder, Annemieke C., Franz, Eelco, de Rijk, Sharona, Versluis, Moyke A.J., Coipan, Claudia, Buij, Ralph, Müskens, Gerard, Koene, Miriam, Pijnacker, Roan, Duim, Birgitta, Bloois, Linda van der Graaf van, Veldman, Kees, Wagenaar, Jaap A., Zomer, Aldert L., Schets, Franciska M., Blaak, Hetty, and Mughini-Gras, Lapo

Published
2020

121. Genomic analysis of European bovine Staphylococcus aureus from clinical versus subclinical mastitis

Author

dFAH I&I, Klinische infectiologie en microb. lab., dI&I I&I-4, Immunologie, dI&I RA-I&I I&I, LS Immunologie, FAH veterinaire epidemiologie, dFAH AVR, Hoekstra, Jurriaan, Zomer, Aldert L, Rutten, Victor P M G, Benedictus, Lindert, Stegeman, Arjan, Spaninks, Mirlin P, Bennedsgaard, Torben W, Biggs, Andrew, De Vliegher, Sarne, Mateo, Demetrio Herrera, Huber-Schlenstedt, Reglindis, Katholm, Jørgen, Kovács, Péter, Krömker, Volker, Lequeux, Guillaume, Moroni, Paolo, Pinho, Luís, Smulski, Sebastian, Supré, Karlien, Swinkels, Jantijn M, Holmes, Mark A, Lam, Theo J G M, Koop, Gerrit, dFAH I&I, Klinische infectiologie en microb. lab., dI&I I&I-4, Immunologie, dI&I RA-I&I I&I, LS Immunologie, FAH veterinaire epidemiologie, dFAH AVR, Hoekstra, Jurriaan, Zomer, Aldert L, Rutten, Victor P M G, Benedictus, Lindert, Stegeman, Arjan, Spaninks, Mirlin P, Bennedsgaard, Torben W, Biggs, Andrew, De Vliegher, Sarne, Mateo, Demetrio Herrera, Huber-Schlenstedt, Reglindis, Katholm, Jørgen, Kovács, Péter, Krömker, Volker, Lequeux, Guillaume, Moroni, Paolo, Pinho, Luís, Smulski, Sebastian, Supré, Karlien, Swinkels, Jantijn M, Holmes, Mark A, Lam, Theo J G M, and Koop, Gerrit

Published
2020

123. Identification of conditionally essential genes for Streptococcus suis infection in pigs

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Arenas, Jesús, Zomer, Aldert, Harders-Westerveen, Jose, Bootsma, Hester J, De Jonge, Marien I, Stockhofe-Zurwieden, Norbert, Smith, Hilde E, De Greeff, Astrid, Klinische infectiologie en microb. lab., dI&I I&I-4, Arenas, Jesús, Zomer, Aldert, Harders-Westerveen, Jose, Bootsma, Hester J, De Jonge, Marien I, Stockhofe-Zurwieden, Norbert, Smith, Hilde E, and De Greeff, Astrid

Published
2020

124. Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Castellanos, L Ricardo, van der Graaf-van Bloois, Linda, Donado-Godoy, Pilar, Veldman, Kees, Duarte, Francisco, Acuña, María T, Jarquín, Claudia, Weill, François-Xavier, Mevius, Dik J, Wagenaar, Jaap A, Hordijk, Joost, Zomer, Aldert L, Klinische infectiologie en microb. lab., dI&I I&I-4, Castellanos, L Ricardo, van der Graaf-van Bloois, Linda, Donado-Godoy, Pilar, Veldman, Kees, Duarte, Francisco, Acuña, María T, Jarquín, Claudia, Weill, François-Xavier, Mevius, Dik J, Wagenaar, Jaap A, Hordijk, Joost, and Zomer, Aldert L

Published
2020

125. Incompatibility and phylogenetic relationship of I-complex plasmids

Author

dI&I I&I-4, Klinische infectiologie en microb. lab., Rozwandowicz, Marta, Hordijk, Joost, Bossers, Alex, Zomer, Aldert, Wagenaar, Jaap A, Mevius, Dik J, Brouwer, Michael S M, dI&I I&I-4, Klinische infectiologie en microb. lab., Rozwandowicz, Marta, Hordijk, Joost, Bossers, Alex, Zomer, Aldert, Wagenaar, Jaap A, Mevius, Dik J, and Brouwer, Michael S M

Published
2020

126. After the bite: bacterial transmission from grey seals ( Halichoerus grypus ) to harbour porpoises ( Phocoena phocoena )

Author

dI&I I&I-4, VPDC pathologie, dPB CR, VP pathologie, dPB I&I, Klinische infectiologie en microb. lab., Gilbert, Maarten J., IJsseldijk, Lonneke L., Rubio-García, Ana, Gröne, Andrea, Duim, Birgitta, Rossen, John, Zomer, Aldert L., Wagenaar, Jaap A., dI&I I&I-4, VPDC pathologie, dPB CR, VP pathologie, dPB I&I, Klinische infectiologie en microb. lab., Gilbert, Maarten J., IJsseldijk, Lonneke L., Rubio-García, Ana, Gröne, Andrea, Duim, Birgitta, Rossen, John, Zomer, Aldert L., and Wagenaar, Jaap A.

Published
2020

127. Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes

Author

Kooyman, Frans N J, Wagenaar, Jaap A, Zomer, Aldert, LS Klinisch Onderzoek Wagenaar, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, and dI&I I&I-4

Subjects
Epidemiology, Bioinformatica & Diermodellen, parasitology, medicine.disease_cause, Genome, DNA sequencing, diplomonad, Bio-informatics & Animal models, parasitic diseases, medicine, Giardia lamblia, heterozygosity, Epidemiology, Bio-informatics & Animal models, cathepsin, Gene, Epidemiologie, Whole genome sequencing, Genetics, biology, synteny, Multiple displacement amplification, Giardia, General Medicine, multiple displacement amplification, biology.organism_classification, Diplomonad, Epidemiologie, Bioinformatica & Diermodellen
Abstract

Giardia duodenalis (syn. Giardia intestinalis or Giardia lamblia) infSAects over 280 million people each year and numerous animals. G. duodenalis can be subdivided into eight assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study, we isolated single and pooled cysts of assemblages C and D from dog faeces by FACS, and sequenced them using multiple displacement amplification and Illumina paired-end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99 % marker genes observed) and the allelic sequence heterozygosity (ASH) values of assemblages C and D were 0.89 and 0.74 %, respectively. These ASH values were slightly higher than for assemblage B (>0.43 %) and much higher than for assemblages A and E, which ranged from 0.002 to 0.037 %. The flavohaemoglobin and 4Fe-4S binding domain family encoding genes involved in O2 and NO detoxification were only present in assemblages A, B and E. Cathepsin B orthologs were found in all genomes. Six clades of cathepsin B orthologs contained one gene of each genome, while in three clades not all assemblages were represented. We conclude that whole-genome sequencing from a single Giardia cyst results in complete draft genomes, making the genomes of unculturable Giardia assemblages accessible. Observed differences between the genomes of assemblages C and D on one hand and the assemblages A, B and E on the other hand are possibly associated with host specificity.

Published
2019

128. Short-Term Hypoxia Dampens Inflammation in vivo via Enhanced Adenosine Release and Adenosine 2B Receptor Stimulation

Author

Kiers, Dorien, Wielockx, Ben, Peters, Esther, van Eijk, Lucas T, Gerretsen, Jelle, John, Aaron, Janssen, Emmy, Groeneveld, Rianne, Peters, Mara, Damen, Lars, Meneses, Ana M, Krüger, Anja, Langereis, Jeroen D, Zomer, Aldert L, Blackburn, Michael R, Joosten, Leo A, Netea, Mihai G, Riksen, Niels P, van der Hoeven, Johannes G, Scheffer, Gert-Jan, Eltzschig, Holger K, Pickkers, Peter, Kox, Matthijs, LS Klinisch Onderzoek Wagenaar, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, and dI&I I&I-4

Subjects
0301 basic medicine, Adenosine, medicine.medical_treatment, Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], lcsh:Medicine, Inflammation, Pharmacology, Systemic inflammation, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Mice, 0302 clinical medicine, All institutes and research themes of the Radboud University Medical Center, Endotoxin, medicine, Animals, Humans, Hypoxia, Adenosine 2B receptor, lcsh:R5-920, business.industry, lcsh:R, Receptors, Purinergic P1, Interleukin, Vascular damage Radboud Institute for Molecular Life Sciences [Radboudumc 16], General Medicine, Hypoxia (medical), Purinergic signalling, Hypoxia-Inducible Factor 1, alpha Subunit, Endotoxemia, 3. Good health, Interleukin-10, Up-Regulation, Interleukin 10, Disease Models, Animal, 030104 developmental biology, Cytokine, Reconstructive and regenerative medicine Radboud Institute for Molecular Life Sciences [Radboudumc 10], Cytokines, medicine.symptom, business, lcsh:Medicine (General), 030217 neurology & neurosurgery, medicine.drug, Research Paper
Abstract

Hypoxia and inflammation are closely intertwined phenomena. Critically ill patients often suffer from systemic inflammatory conditions and concurrently experience short-lived hypoxia. We evaluated the effects of short-term hypoxia on systemic inflammation, and show that it potently attenuates pro-inflammatory cytokine responses during murine endotoxemia. These effects are independent of hypoxia-inducible factors (HIFs), but involve augmented adenosine levels, in turn resulting in an adenosine 2B receptor-mediated post-transcriptional increase of interleukin (IL)-10 production. We translated our findings to humans using the experimental endotoxemia model, where short-term hypoxia resulted in enhanced plasma concentrations of adenosine, augmentation of endotoxin-induced circulating IL-10 levels, and concurrent attenuation of the pro-inflammatory cytokine response. Again, HIFs were shown not to be involved. Taken together, we demonstrate that short-term hypoxia dampens the systemic pro-inflammatory cytokine response through enhanced purinergic signaling in mice and men. These effects may contribute to outcome and provide leads for immunomodulatory treatment strategies for critically ill patients., Highlights • Short-term hypoxia attenuates the systemic pro-inflammatory cytokine response in vivo in both mice and men • The underlying mechanism involves adenosine 2B receptor-mediated enhanced production of anti-inflammatory interleukin-10 • These effects may contribute to outcome and provide leads for novel treatment strategies for critically ill patients Inflammation and short bouts of low oxygen levels are frequently encountered phenomena in severely ill patients admitted to the Intensive Care unit. This study investigated the effect of short-term low oxygen levels on the inflammatory response in both mice and humans. The results show that a short period of low levels of oxygen potently dampens inflammation, and identify the underlying mechanisms. These effects of low oxygen levels may contribute to the outcome of severely ill patients. Furthermore, the increased understanding of the underlying mechanisms provided by this study can be used to develop therapies to dampen inflammation in patients.

Published
2018

129. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Author

Moreno-Indias, Isabel, primary, Lahti, Leo, additional, Nedyalkova, Miroslava, additional, Elbere, Ilze, additional, Roshchupkin, Gennady, additional, Adilovic, Muhamed, additional, Aydemir, Onder, additional, Bakir-Gungor, Burcu, additional, Santa Pau, Enrique Carrillo-de, additional, D’Elia, Domenica, additional, Desai, Mahesh S., additional, Falquet, Laurent, additional, Gundogdu, Aycan, additional, Hron, Karel, additional, Klammsteiner, Thomas, additional, Lopes, Marta B., additional, Marcos-Zambrano, Laura Judith, additional, Marques, Cláudia, additional, Mason, Michael, additional, May, Patrick, additional, Pašić, Lejla, additional, Pio, Gianvito, additional, Pongor, Sándor, additional, Promponas, Vasilis J., additional, Przymus, Piotr, additional, Saez-Rodriguez, Julio, additional, Sampri, Alexia, additional, Shigdel, Rajesh, additional, Stres, Blaz, additional, Suharoschi, Ramona, additional, Truu, Jaak, additional, Truică, Ciprian-Octavian, additional, Vilne, Baiba, additional, Vlachakis, Dimitrios, additional, Yilmaz, Ercument, additional, Zeller, Georg, additional, Zomer, Aldert L., additional, Gómez-Cabrero, David, additional, and Claesson, Marcus J., additional

Published
2021
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130. Tracing the animal sources of surface water contamination with Campylobacter jejuni and Campylobacter coli

Author

Mulder, Annemieke C., primary, Franz, Eelco, additional, de Rijk, Sharona, additional, Versluis, Moyke A.J., additional, Coipan, Claudia, additional, Buij, Ralph, additional, Müskens, Gerard, additional, Koene, Miriam, additional, Pijnacker, Roan, additional, Duim, Birgitta, additional, Bloois, Linda van der Graaf-van, additional, Veldman, Kees, additional, Wagenaar, Jaap A., additional, Zomer, Aldert L., additional, Schets, Franciska M., additional, Blaak, Hetty, additional, and Mughini-Gras, Lapo, additional

Published
2020
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133. Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

Author

Castellanos, L. Ricardo, primary, van der Graaf-van Bloois, Linda, additional, Donado-Godoy, Pilar, additional, Veldman, Kees, additional, Duarte, Francisco, additional, Acuña, María T., additional, Jarquín, Claudia, additional, Weill, François-Xavier, additional, Mevius, Dik J., additional, Wagenaar, Jaap A., additional, Hordijk, Joost, additional, and Zomer, Aldert L., additional

Published
2020
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136. Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes

Author

Nebenzahl-Guimaraes, Hanna, van Laarhoven, Arjan, Farhat, Maha R, Koeken, Valerie Acm, Mandemakers, Jornt, Zomer, Aldert, van Hijum, Sacha Aft, Netea, Mihai G, Murray, Megan, van Crevel, Reinout, van Soolingen, Dick, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Social Networks, Solidarity and Inequality, Universidade do Minho, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, and Social Networks, Solidarity and Inequality

Subjects
Genetic Markers, 0301 basic medicine, Pulmonary and Respiratory Medicine, Tuberculosis, Bacterial genomes, Medicina Básica [Ciências Médicas], Immunology, 030106 microbiology, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Virulence, WASS, Sociology of Consumption and Households, Critical Care and Intensive Care Medicine, Mycobacterium tuberculosis, immunology, 03 medical and health sciences, Immune system, Genetic variation, medicine, Transmission, Immunity, Cellular, Science & Technology, biology, Transmission (medicine), Strain (biology), Editorials, transmission, biology.organism_classification, medicine.disease, 3. Good health, bacterial genomes, Sociologie van Consumptie en Huishoudens, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], Phenotype, 030104 developmental biology, tuberculosis, Genetic marker, Ciências Médicas::Medicina Básica
Abstract

Successful transmission of tuberculosis depends on the interplay of human behavior, host immune responses, and Mycobacterium tuberculosis virulence factors. Previous studies have been focused on identifying host risk factors associated with increased transmission, but the contribution of specific genetic variations in mycobacterial strains themselves are still unknown., This study was funded by the Portuguese Foundation for Science and Technology (FCT) (SFRH/BD/33902/2009 [H.N.-G.]).

Published
2017

138. Draft Genome Sequence of Streptococcus suis S10, a Virulent Strain Used in Experimental Pig Infections

Author

Gaiser, Rogier A., Zomer, Aldert L., Wells, Jerry M., van Baarlen, Peter, LS Klinisch Onderzoek Wagenaar, and dI&I I&I-4

Subjects
Serotype, Whole genome sequencing, 0303 health sciences, Strain (biology), Genome Sequences, 030302 biochemistry & molecular biology, Virulence, Streptococcus suis, Biology, biology.organism_classification, Genome, 3. Good health, Microbiology, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), WIAS, Genetics, Life Science, Host-Microbe Interactomics, Molecular Biology, Gene, Prophage, VLAG, 030304 developmental biology
Abstract

Here, we report the draft whole-genome sequence of Streptococcus suis strain S10, isolated from the tonsils of a healthy pig. S. suis S10 belongs to the highly virulent serotype 2, which includes isolates that cause infectious diseases, including meningitis, in pigs and human., Here, we report the draft whole-genome sequence of Streptococcus suis strain S10, isolated from the tonsils of a healthy pig. S. suis S10 belongs to the highly virulent serotype 2, which includes isolates that cause infectious diseases, including meningitis, in pigs and human. The genome contains a complete prophage that encodes a candidate virulence gene.

Published
2019

139. Phylogenomic investigation of IncI1-I plasmids harboring blaCMY-2 and blaSHV-12 in salmonella enterica and Escherichia coli in multiple countries

Author

Castellanos, Luis Ricardo, van der Graaf-van Bloois, Linda, Donado-Godoy, Pilar, Mevius, Dik J, Wagenaar, Jaap A, Hordijk, Joost, Zomer, Aldert, LS Klinisch Onderzoek Wagenaar, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, and dI&I I&I-4

Subjects
Epidemiology, Salmonella Paratyphi B var. JAva, medicine.disease_cause, Genome, Salmonella Paratyphi B var. Java, Plasmid, Pharmacology (medical), Phylogeny, DeoR, Genetics, 0303 health sciences, sugE, biology, Broiler, Salmonella enterica, Chicken, SugE, Infectious Diseases, Blc, Plasmids, IS26, Bioinformatica & Diermodellen, chicken, Coronacrisis-Taverne, broiler, deoR, beta-Lactamases, 03 medical and health sciences, Mechanisms of Resistance, S. Heidelberg, blc, Bio-informatics & Animal models, medicine, Escherichia coli, Epidemiology, Bio-informatics & Animal models, Tn1721, Gene, 030304 developmental biology, Pharmacology, Epidemiologie, 030306 microbiology, ISEcp1, Sequence types, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, bacterial infections and mycoses, Epidemiologie, Bioinformatica & Diermodellen, IS1294
Abstract

The objective of this study was to elucidate the genetic and evolutionary relatedness of bla(CMY-2)- and bla(SHV-12)-carrying IncI1-Iγ plasmids. Phylogenomic analysis based on core genome alignments and gene presence/absence was performed for different IncI1-Iγ sequence types (STs). Most IncI1-Iγ/ST12 and IncI1-Iγ/ST231 plasmids had near-identical core genomes. The data suggest that widely occurring bla(CMY-2)-carrying IncI1-Iγ/ST12 plasmids originate from a common ancestor. In contrast, bla(SHV-12) was inserted independently into different IncI1-Iγ/ST231-related plasmids.

Published
2019

142. Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes

Author

Kooyman, Frans N.J., Wagenaar, Jaap A., Zomer, Aldert, Kooyman, Frans N.J., Wagenaar, Jaap A., and Zomer, Aldert

Abstract

Giardia duodenalis (syn. Giardia intestinalis or Giardia lamblia) infSAects over 280 million people each year and numerous animals. G. duodenalis can be subdivided into eight assemblages with different host specificity. Unculturable assemblages have so far resisted genome sequencing efforts. In this study, we isolated single and pooled cysts of assemblages C and D from dog faeces by FACS, and sequenced them using multiple displacement amplification and Illumina paired-end sequencing. The genomes of assemblages C and D were compared with genomes of assemblages A and B from humans and assemblage E from ruminants and pigs. The genomes obtained from the pooled cysts and from the single cysts were considered complete (>99 % marker genes observed) and the allelic sequence heterozygosity (ASH) values of assemblages C and D were 0.89 and 0.74 %, respectively. These ASH values were slightly higher than for assemblage B (>0.43 %) and much higher than for assemblages A and E, which ranged from 0.002 to 0.037 %. The flavohaemoglobin and 4Fe-4S binding domain family encoding genes involved in O2 and NO detoxification were only present in assemblages A, B and E. Cathepsin B orthologs were found in all genomes. Six clades of cathepsin B orthologs contained one gene of each genome, while in three clades not all assemblages were represented. We conclude that whole-genome sequencing from a single Giardia cyst results in complete draft genomes, making the genomes of unculturable Giardia assemblages accessible. Observed differences between the genomes of assemblages C and D on one hand and the assemblages A, B and E on the other hand are possibly associated with host specificity.

Published
2019

143. Zoonotic Endocarditis in a Man, the Netherlands

Author

dES AVR, Sub Ambulante kliniek, Applied Veterinary Research, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Sleutjens, Janneke, Meijer, Dennie, Meregalli, Paola G, Bakker, Leendert, Wagenaar, Jaap A, Duim, Birgitta, Zomer, Aldert, dES AVR, Sub Ambulante kliniek, Applied Veterinary Research, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Sleutjens, Janneke, Meijer, Dennie, Meregalli, Paola G, Bakker, Leendert, Wagenaar, Jaap A, Duim, Birgitta, and Zomer, Aldert

Published
2019

148. The Contribution of Genetic Variation of Streptococcus Pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease

Author

dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Cremers, Amelieke J H, Mobegi, Fredrick M, van der Gaast-de Jongh, Christa E, van Weert, Michelle, van Opzeeland, Fred J, Vehkala, Minna, Knol, Mirjam J, Bootsma, Hester J, Välimäki, Niko, Croucher, Nicholas J, Meis, Jacques F, Bentley, Stephen D, van Hijum, Sacha A F T, Corander, Jukka, Zomer, Aldert L, Ferwerda, Gerben, de Jonge, Marien I, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Cremers, Amelieke J H, Mobegi, Fredrick M, van der Gaast-de Jongh, Christa E, van Weert, Michelle, van Opzeeland, Fred J, Vehkala, Minna, Knol, Mirjam J, Bootsma, Hester J, Välimäki, Niko, Croucher, Nicholas J, Meis, Jacques F, Bentley, Stephen D, van Hijum, Sacha A F T, Corander, Jukka, Zomer, Aldert L, Ferwerda, Gerben, and de Jonge, Marien I

Published
2019

149. Living in cold blood: Arcobacter, Campylobacter, and Helicobacter in reptiles

Author

Gilbert, Maarten J., Duim, Birgitta, Zomer, Aldert L., Wagenaar, Jaap A., Gilbert, Maarten J., Duim, Birgitta, Zomer, Aldert L., and Wagenaar, Jaap A.

Abstract

Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.

Published
2019

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