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6. Harbor Porpoise Deaths Associated with Erysipelothrix rhusiopathiae, the Netherlands, 2021

Author

IJsseldijk, Lonneke L., Begeman, Lineke, Duim, Birgitta, Grone, Andrea, Kik, Marja J.L., Klijnstra, Mirjam D., Lakemeyer, Jan, Leopold, Mardik F., Munnink, Bas B. Oude, Doeschate, Mariel ten, van Schalkwijk, Linde, Zomer, Aldert, Bloois, Linda van der Graaf-van, and Broens, Els M.

Subjects
Porpoises -- Diseases -- Causes of, Wildlife diseases -- Causes of, Gram-positive bacterial infections -- Causes of, Emerging communicable diseases -- Causes of, Health
Abstract

Erysipelothrix bacteria cause infections in humans and other species after contact with infected animals or environmental sources (1). Illness ranges from mild to systemic, which can include septicemia and endocarditis. [...]

Published
2023

8. Targeted isolation of bacteria with potential to competitively excludeStaphylococcus aureusin the upper respiratory tract of pigs

Author

Vlasblom, Abel A., primary, Patel, Shriram, additional, Lawlor, Peadar G., additional, Claesson, Marcus J., additional, Crespo-Piazuelo, Daniel, additional, Eckenberger, Julia, additional, Huseyin, Chloe Elizabeth, additional, Elend, Christian, additional, Wagenaar, Jaap A, additional, Zomer, Aldert L., additional, and Duim, Birgitta, additional

Published
2024
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12. Extended period of selection for antimicrobial resistance due to recirculation of persistent antimicrobials in broilers.

Author

Swinkels, Aram F, Berendsen, Bjorn J A, Fischer, Egil A J, Zomer, Aldert L, and Wagenaar, Jaap A

Subjects
DRUG resistance in bacteria, ESCHERICHIA coli, DRUG resistance in microorganisms, ANIMAL behavior, FLUOROQUINOLONES
Abstract

Objectives Antimicrobials can select for antimicrobial-resistant bacteria. After treatment the active compound is excreted through urine and faeces. As some antimicrobials are chemically stable, recirculation of subinhibitory concentrations of antimicrobials may occur due to coprophagic behaviour of animals such as chickens. Methods The persistence of three antimicrobials over time and their potential effects on antimicrobial resistance were determined in four groups of broilers. Groups were left untreated (control) or were treated with amoxicillin (unstable), doxycycline or enrofloxacin (stable). Antimicrobials were extracted from the faecal samples and were measured by LC-MS/MS. We determined the resistome genotypically using shotgun metagenomics and phenotypically by using Escherichia coli as indicator microorganism. Results Up to 37 days after treatment, doxycycline and enrofloxacin had concentrations in faeces equal to or higher than the minimal selective concentration (MSC), in contrast to the amoxicillin treatment. The amoxicillin treatment showed a significant difference (P  ≤ 0.01 and P  ≤ 0.0001) in the genotypic resistance only directly after treatment. On the other hand, the doxycycline treatment showed approximately 52% increase in phenotypic resistance and a significant difference (P  ≤ 0.05 and P  ≤ 0.0001) in genotypic resistance throughout the trial. Furthermore, enrofloxacin treatment resulted in a complete non-WT E. coli population but the quantity of resistance genes was similar to the control group, likely because resistance is mediated by point mutations. Conclusions Based on our findings, we suggest that persistence of antimicrobials should be taken into consideration in the assessment of priority classification of antimicrobials in livestock. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Prevotella timonensis degrades the vaginal epithelial glycocalyx through high fucosidase and sialidase activities

Author

Infectiebiologie, Sub Molecular Microbiology, Klinische infectiologie en microb. lab., Molecular Microbiology, Infectious Diseases and Immunology - Infection Biology, Infectious Diseases and Immunology - KLIF, Perez, Celia Segui, Jongh, Rivka De, Jonkergouw, Robin, Pelayo, Paula, Balskus, Emily P., Zomer, Aldert, Strijbis, Karin, Infectiebiologie, Sub Molecular Microbiology, Klinische infectiologie en microb. lab., Molecular Microbiology, Infectious Diseases and Immunology - Infection Biology, Infectious Diseases and Immunology - KLIF, Perez, Celia Segui, Jongh, Rivka De, Jonkergouw, Robin, Pelayo, Paula, Balskus, Emily P., Zomer, Aldert, and Strijbis, Karin

Published
2024

16. A Systematic Review of the Effect of Macrolide Use in Food Producing Animals and its Impact on Rates of Human Carriage and Disease of Macrolide-Resistant Bacteria

Author

Rittscher, Anne, Zomer, Aldert (Thesis Advisor), Rittscher, Anne, and Zomer, Aldert (Thesis Advisor)

Abstract

Layman's Summary: Campylobacteriosis is a common illness caused by Campylobacter spp.. which causes a global loss in nearly the in nearly 33 million healthy human life years globally annually (the World Health Organization (WHO)). The main antibiotics used to treat campylobacteriosis are macrolides, which are in the highest priority group on both the WHO’s Critically Important Antimicrobials list and the World Organization for Animal Health (WOAH) critically important veterinary antimicrobials list. Macrolides are important drugs to both human and animal health and are used to treat common illnesses where there are few alternatives. The WHO cites the burden of disease and evidence of macrolide resistance in Campylobacter species and resistance genes in Enterococcus species which could be transferred from animals to humans as reasons for macrolides' high ranking in both lists. This systematic review aims to examine whether use of macrolides in food animals impacts the rate of human carriage and disease by macrolide-resistant bacteria, namely Campylobacter species and Enterococcus species of bacteria. I divided this question into 5 sub-questions; 1) the first asks if the use of macrolides in food animals is associated with carriage of macrolide-resistant bacteria in these animals; and 2) if the presence of resistant bacteria in food animals leads to resistant bacteria in food; 3) next, whether macrolide resistant bacteria can be transmitted from animals to humans via occupational and 4) community exposure was analyzed; 5) finally, data was collected to investigate if the carriage of macrolide resistant bacteria leads to illness in people. I performed a systematic literature search of Scopus and Web of Science for articles published between 1999 and September 2022. Quantitative analysis was performed when there was enough data in a category to make comparisons, otherwise a qualitative analysis was done. 59 papers were included. More data was available to address the fi

Published
2024

17. Integrative and Conjugative Elements and Prophage DNA as Carriers of Resistance Genes in Erysipelothrix rhusiopathiae Strains from Domestic Geese in Poland

Author

Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Dec, Marta, Zomer, Aldert, Webster, John, Nowak, Tomasz, Stępień-Pyśniak, Dagmara, Urban-Chmiel, Renata, Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Dec, Marta, Zomer, Aldert, Webster, John, Nowak, Tomasz, Stępień-Pyśniak, Dagmara, and Urban-Chmiel, Renata

Published
2024

19. Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.

Author

Zomer, Aldert, Ingham, Colin J., von Meijenfeldt, F. A. Bastiaan, Doncel, Álvaro Escobar, van de Kerkhof, Gea T., Hamidjaja, Raditijo, Schouten, Sanne, Schertel, Lukas, Müller, Karin H., Catón, Laura, Hahnke, Richard L., Bolhuis, Henk, Vignolini, Silvia, and Dutilh, Bas E.

Subjects
*STRUCTURAL colors, *BACTERIAL genomes, *NANOSTRUCTURED materials, *MULTICELLULAR organisms, *SEAWATER
Abstract

Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

Author

Castellanos, L. Ricardo, Bloois, Linda van der Graaf-van, Donado-Godoy, Pilar, Veldman, Kees, Duarte, Francisco, Acuna, Maria T., Jarquin, Claudia, Weill, Francois-Xavier, Mevius, Dik J., Wagenaar, Jaap A., Hordijk, Joost, and Zomer, Aldert L.

Subjects
Genomics, Drug resistance in microorganisms, Genomes, Poultry industry, Phylogeny, Salmonella, Health
Abstract

The d-Tartrate fermenting, nonparatyphoidal variant of Salmonella enterica serovar Paratyphi B, contemporarily known as variant Java, was first reported in 1935 by De Moor (1). From then until recently, Salmonella [...]

Published
2020
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27. Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

Author

D’Elia, Domenica, primary, Truu, Jaak, additional, Lahti, Leo, additional, Berland, Magali, additional, Papoutsoglou, Georgios, additional, Ceci, Michelangelo, additional, Zomer, Aldert, additional, Lopes, Marta B., additional, Ibrahimi, Eliana, additional, Gruca, Aleksandra, additional, Nechyporenko, Alina, additional, Frohme, Marcus, additional, Klammsteiner, Thomas, additional, Pau, Enrique Carrillo-de Santa, additional, Marcos-Zambrano, Laura Judith, additional, Hron, Karel, additional, Pio, Gianvito, additional, Simeon, Andrea, additional, Suharoschi, Ramona, additional, Moreno-Indias, Isabel, additional, Temko, Andriy, additional, Nedyalkova, Miroslava, additional, Apostol, Elena-Simona, additional, Truică, Ciprian-Octavian, additional, Shigdel, Rajesh, additional, Telalović, Jasminka Hasić, additional, Bongcam-Rudloff, Erik, additional, Przymus, Piotr, additional, Jordamović, Naida Babić, additional, Falquet, Laurent, additional, Tarazona, Sonia, additional, Sampri, Alexia, additional, Isola, Gaetano, additional, Pérez-Serrano, David, additional, Trajkovik, Vladimir, additional, Klucar, Lubos, additional, Loncar-Turukalo, Tatjana, additional, Havulinna, Aki S., additional, Jansen, Christian, additional, Bertelsen, Randi J., additional, and Claesson, Marcus Joakim, additional

Published
2023
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29. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition

Author

Stege, Paul B., primary, Hordijk, Joost, additional, Sandholt, Arnar K. S., additional, Zomer, Aldert L., additional, Viveen, Marco C., additional, Rogers, Malbert R. C., additional, Salomons, Moniek, additional, Wagenaar, Jaap A., additional, Mughini-Gras, Lapo, additional, Willems, Rob J. L., additional, and Paganelli, Fernanda L., additional

Published
2023
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30. Genomic analysis of European bovine Staphylococcus aureus from clinical versus subclinical mastitis

Author

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
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32. Molecular Characterization and Clinical Relevance of Taxonomic Reassignment of Staphylococcus schleiferi Subspecies into Two Separate Species, Staphylococcus schleiferi and Staphylococcus coagulans

Author

Naing, Soe Yu, primary, Duim, Birgitta, additional, Broens, Els M., additional, Schweitzer, Valentijn, additional, Zomer, Aldert, additional, van der Graaf-van Bloois, Linda, additional, van der Meer, Coby, additional, Stellingwerff, Luutsen, additional, Fluit, Ad C., additional, and Wagenaar, Jaap A., additional

Published
2023
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34. Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome

Author

CS_Welfare & emerging diseases, Equine Internal Medicine, Klinische infectiologie en microb. lab., Farm Animal Health, FAH voeding, Theelen, Mathijs J P, Luiken, Roosmarijn E C, Wagenaar, Jaap A, Sloet van Oldruitenborgh-Oosterbaan, Marianne M, Rossen, John W A, Schaafstra, Femke J W C, van Doorn, David A, Zomer, Aldert L, CS_Welfare & emerging diseases, Equine Internal Medicine, Klinische infectiologie en microb. lab., Farm Animal Health, FAH voeding, Theelen, Mathijs J P, Luiken, Roosmarijn E C, Wagenaar, Jaap A, Sloet van Oldruitenborgh-Oosterbaan, Marianne M, Rossen, John W A, Schaafstra, Femke J W C, van Doorn, David A, and Zomer, Aldert L

Published
2023

36. Harbor Porpoise Deaths Associated with Erysipelothrix rhusiopathiae, the Netherlands, 2021

Author

VPDC pathologie, Klinische infectiologie en microb. lab., IJsseldijk, Lonneke L, Begeman, Lineke, Duim, Birgitta, Gröne, Andrea, Kik, Marja J L, Klijnstra, Mirjam D, Lakemeyer, Jan, Leopold, Mardik F, Munnink, Bas B Oude, Ten Doeschate, Mariel, van Schalkwijk, Linde, Zomer, Aldert, der Graaf-van Bloois, Linda van, Broens, Els M, VPDC pathologie, Klinische infectiologie en microb. lab., IJsseldijk, Lonneke L, Begeman, Lineke, Duim, Birgitta, Gröne, Andrea, Kik, Marja J L, Klijnstra, Mirjam D, Lakemeyer, Jan, Leopold, Mardik F, Munnink, Bas B Oude, Ten Doeschate, Mariel, van Schalkwijk, Linde, Zomer, Aldert, der Graaf-van Bloois, Linda van, and Broens, Els M

Published
2023

37. Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution

Author

Klinische infectiologie en microb. lab., van der Graaf-van Bloois, Linda, Duim, Birgitta, Looft, Torey, Veldman, Kees T, Zomer, Aldert L, Wagenaar, Jaap A, Klinische infectiologie en microb. lab., van der Graaf-van Bloois, Linda, Duim, Birgitta, Looft, Torey, Veldman, Kees T, Zomer, Aldert L, and Wagenaar, Jaap A

Published
2023

38. Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics

Author

Klinische infectiologie en microb. lab., Bloomfield, Samuel J., Zomer, Aldert L., O'grady, Justin, Kay, Gemma L., Wain, John, Janecko, Nicol, Palau, Raphaëlle, Mather, Alison E., Klinische infectiologie en microb. lab., Bloomfield, Samuel J., Zomer, Aldert L., O'grady, Justin, Kay, Gemma L., Wain, John, Janecko, Nicol, Palau, Raphaëlle, and Mather, Alison E.

Published
2023

39. Global Distribution of O Serotypes and Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Collected From the Blood of Patients With Bacteremia Across Multiple Surveillance Studies

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Weerdenburg, Eveline, Davies, Todd, Morrow, Brian, Zomer, Aldert L, Hermans, Peter, Go, Oscar, Spiessens, Bart, van den Hoven, Thijs, van Geet, Gunter, Aitabi, Moussa, DebRoy, Chitrita, Dudley, Edward G, Bonten, Marc, Poolman, Jan, Geurtsen, Jeroen, Klinische infectiologie en microb. lab., dI&I I&I-4, Weerdenburg, Eveline, Davies, Todd, Morrow, Brian, Zomer, Aldert L, Hermans, Peter, Go, Oscar, Spiessens, Bart, van den Hoven, Thijs, van Geet, Gunter, Aitabi, Moussa, DebRoy, Chitrita, Dudley, Edward G, Bonten, Marc, Poolman, Jan, and Geurtsen, Jeroen

Published
2023

40. Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation

Author

Klinische infectiologie en microb. lab., Infectious Diseases and Immunology, Infectious Diseases and Immunology - KLIF, Rubio-Garcia, Ana, Zomer, Aldert L, Guo, Ruoshui, Rossen, John W A, van Zeijl, Jan H, Wagenaar, Jaap A, Luiken, Roosmarijn E C, Klinische infectiologie en microb. lab., Infectious Diseases and Immunology, Infectious Diseases and Immunology - KLIF, Rubio-Garcia, Ana, Zomer, Aldert L, Guo, Ruoshui, Rossen, John W A, van Zeijl, Jan H, Wagenaar, Jaap A, and Luiken, Roosmarijn E C

Published
2023

41. Safety Evaluation of an Intranasally Applied Cocktail of Lactococcus lactis Strains in Pigs

Author

Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Rattigan, Ruth, Wajda, Lukasz, Vlasblom, Abel A, Wolfe, Alan, Zomer, Aldert L, Duim, Birgitta, Wagenaar, Jaap A, Lawlor, Peadar G, Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Rattigan, Ruth, Wajda, Lukasz, Vlasblom, Abel A, Wolfe, Alan, Zomer, Aldert L, Duim, Birgitta, Wagenaar, Jaap A, and Lawlor, Peadar G

Published
2023

42. Quantifying fluoroquinolone resistance-inducing point mutations from metagenomics data

Author

Cernat, Simona, Zomer, Aldert (Thesis Advisor), Cernat, Simona, and Zomer, Aldert (Thesis Advisor)

Abstract

Bacterial resistance to fluoroquinolones primary arises from chromosomal point mutations in the gyrA and parC genes. Currently, bioinformatics tools designed for measuring resistance from metagenomics data are not able to detect resistance arising from point mutations. To address this gap, two methods for quantifying fluoroquinolone resistance-inducing SNPs from metagenomic reads were created.GyrAPointCounter is a software which can analyze the presence and abundance of point mutations present on gyrA that cause resistance and infer the relative proportion of reads carrying potential resistance causing sequences vs wildtype sequences. Additionally, we developed a classification tree machine learning model, which was trained using the physicochemical proprieties of amino acids. Both methods form their decision rules by using the available sequences and the mutational patterns of fluoroquinolone-resistant GyrAs present in the CARD database. The two methods were validated using an Escherichia coli (E. coli) WGS dataset (n = 201) and an external dataset comprised of gyrA sequences (n = 40) belonging to species distinct from those present in the training data. The results of the analyses show that both methods display excellent concordance with the phenotypic data for E. coli sequences. The classification performance for novel species for GyrAPointCounter and the supervised learning model showed a True Positive Rate (TPR) of 0.87 and 1 and True Negative Rate (TNR) of 0.75 and 0.68 respectively. An in-house shotgun time series metagenomomics datatset containing Illumina short-reads from farm animals treated with enrofloxacin was submitted for the analysis with our two methods. The enrofloxacin-treated samples displayed higher average resistance levels compared to the control groups for both methods. Conclusions: This research introduced the first version of GyrAPointCounter, which is a promising tool for monitoring the resistance levels from metagenomics data. However, st

Published
2023

43. Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action

Author

Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, D'Elia, Domenica, Truu, Jaak, Lahti, Leo, Berland, Magali, Papoutsoglou, Georgios, Ceci, Michelangelo, Zomer, Aldert, Lopes, Marta B, Ibrahimi, Eliana, Gruca, Aleksandra, Nechyporenko, Alina, Frohme, Marcus, Klammsteiner, Thomas, Pau, Enrique Carrillo-de Santa, Marcos-Zambrano, Laura Judith, Hron, Karel, Pio, Gianvito, Simeon, Andrea, Suharoschi, Ramona, Moreno-Indias, Isabel, Temko, Andriy, Nedyalkova, Miroslava, Apostol, Elena-Simona, Truică, Ciprian-Octavian, Shigdel, Rajesh, Telalović, Jasminka Hasić, Bongcam-Rudloff, Erik, Przymus, Piotr, Jordamović, Naida Babić, Falquet, Laurent, Tarazona, Sonia, Sampri, Alexia, Isola, Gaetano, Pérez-Serrano, David, Trajkovik, Vladimir, Klucar, Lubos, Loncar-Turukalo, Tatjana, Havulinna, Aki S, Jansen, Christian, Bertelsen, Randi J, Claesson, Marcus Joakim, Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, D'Elia, Domenica, Truu, Jaak, Lahti, Leo, Berland, Magali, Papoutsoglou, Georgios, Ceci, Michelangelo, Zomer, Aldert, Lopes, Marta B, Ibrahimi, Eliana, Gruca, Aleksandra, Nechyporenko, Alina, Frohme, Marcus, Klammsteiner, Thomas, Pau, Enrique Carrillo-de Santa, Marcos-Zambrano, Laura Judith, Hron, Karel, Pio, Gianvito, Simeon, Andrea, Suharoschi, Ramona, Moreno-Indias, Isabel, Temko, Andriy, Nedyalkova, Miroslava, Apostol, Elena-Simona, Truică, Ciprian-Octavian, Shigdel, Rajesh, Telalović, Jasminka Hasić, Bongcam-Rudloff, Erik, Przymus, Piotr, Jordamović, Naida Babić, Falquet, Laurent, Tarazona, Sonia, Sampri, Alexia, Isola, Gaetano, Pérez-Serrano, David, Trajkovik, Vladimir, Klucar, Lubos, Loncar-Turukalo, Tatjana, Havulinna, Aki S, Jansen, Christian, Bertelsen, Randi J, and Claesson, Marcus Joakim

Published
2023

44. Development of Kaptive databases for Vibrio parahaemolyticus O-and K-antigen genotyping

Author

van der Graaf-Van Bloois, Linda, Chen, Hongyou, Wagenaar, Jaap A., Zomer, Aldert L., van der Graaf-Van Bloois, Linda, Chen, Hongyou, Wagenaar, Jaap A., and Zomer, Aldert L.

Abstract

Vibrio parahaemolyticus is an important food-borne human pathogen and presents immunogenic surface polysaccharides, which can be used to distinguish problematic and disease-causing lineages. V. parahaemolyticus is divided in 16 O-serotypes (O-antigen) and 71 K-serotypes (K-antigen). Agglutination tests are still the gold standard for serotyping, but many V. parahaemolyticus isolates are not typable by agglutination. An alternative for agglutination tests is genotyping using whole-genome sequencing data, by which K-and O-genotypes have been curated and identified previously for other clinically relevant organisms with the software tool Kaptive. In this study, V. parahaemolyticus isolates were serotyped and sequenced, and all known and several novel O-and K-loci were identified. We developed Kaptive databases for all O-and K-loci after manual curation of the loci. In our study, we could genotype the O-and K-loci of 98 and 93% of the genomes, respectively, with a Kaptive confidence score higher than ‘none’. The newly developed Kaptive databases with the identified V. parahaemolyticus O-and K-loci can be used to identify the O-and K-genotypes of V. parahaemolyticus isolates from genome sequences.

Published
2023

45. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition

Author

Infectious Diseases and Immunology, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., IRAS – One Health Microbial, Infectious Diseases and Immunology - KLIF, Stege, Paul B, Hordijk, Joost, Sandholt, Arnar K S, Zomer, Aldert L, Viveen, Marco C, Rogers, Malbert R C, Salomons, Moniek, Wagenaar, Jaap A, Mughini-Gras, Lapo, Willems, Rob J L, Paganelli, Fernanda L, Infectious Diseases and Immunology, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., IRAS – One Health Microbial, Infectious Diseases and Immunology - KLIF, Stege, Paul B, Hordijk, Joost, Sandholt, Arnar K S, Zomer, Aldert L, Viveen, Marco C, Rogers, Malbert R C, Salomons, Moniek, Wagenaar, Jaap A, Mughini-Gras, Lapo, Willems, Rob J L, and Paganelli, Fernanda L

Published
2023

46. Molecular Characterization and Clinical Relevance of Taxonomic Reassignment of Staphylococcus schleiferi Subspecies into Two Separate Species, Staphylococcus schleiferi and Staphylococcus coagulans.

Author

Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Naing, Soe Yu, Duim, Birgitta, Broens, Els M, Schweitzer, Valentijn, Zomer, Aldert, van der Graaf-van Bloois, Linda, van der Meer, Coby, Stellingwerff, Luutsen, Fluit, Ad C, Wagenaar, Jaap A, Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Naing, Soe Yu, Duim, Birgitta, Broens, Els M, Schweitzer, Valentijn, Zomer, Aldert, van der Graaf-van Bloois, Linda, van der Meer, Coby, Stellingwerff, Luutsen, Fluit, Ad C, and Wagenaar, Jaap A

Published
2023

47. Harbor Porpoise Deaths Associated with Erysipelothrix rhusiopathiae, the Netherlands, 2021

Author

IJsseldijk, Lonneke L.I., Begeman, Lineke, Duim, Birgitta, Gröne, Andrea, Kik, Marja J.L., Klijnstra, Mirjam D., Lakemeyer, Jan, Leopold, Mardik F., Munnink, Bas B.Oude, ten Doeschate, Mariel, van Schalkwijk, Linde, Zomer, Aldert, van der Graaf-Van Bloois, Linda, Broens, Els M., IJsseldijk, Lonneke L.I., Begeman, Lineke, Duim, Birgitta, Gröne, Andrea, Kik, Marja J.L., Klijnstra, Mirjam D., Lakemeyer, Jan, Leopold, Mardik F., Munnink, Bas B.Oude, ten Doeschate, Mariel, van Schalkwijk, Linde, Zomer, Aldert, van der Graaf-Van Bloois, Linda, and Broens, Els M.

Abstract

In August 2021, a large-scale mortality event affected harbor porpoises (Phocoena phocoena) in the Netherlands. Pathology and ancillary testing of 22 animals indicated that the most likely cause of death was Erysipelothrix rhusiopathiae infection. This zoonotic agent poses a health hazard for cetaceans and possibly for persons handling cetacean carcasses.

Published
2023

48. Harbor Porpoise Deaths Associated with Erysipelothrix rhusiopathiae, the Netherlands, 2021

Author

IJsseldijk, Lonneke, Begeman, Lineke, Duim, Birgitta, Gröne, Andrea, Kik, Marja J.L., Klijnstra, Mirjam D., Lakemeyer, Jan, Leopold, Mardik F., Oude Munnink, Bas B., ten Doeschate, Mariel, van Schalkwijk, Linde, Zomer, Aldert, van der Graaf-Van Bloois, Linda, Broens, Els M., IJsseldijk, Lonneke, Begeman, Lineke, Duim, Birgitta, Gröne, Andrea, Kik, Marja J.L., Klijnstra, Mirjam D., Lakemeyer, Jan, Leopold, Mardik F., Oude Munnink, Bas B., ten Doeschate, Mariel, van Schalkwijk, Linde, Zomer, Aldert, van der Graaf-Van Bloois, Linda, and Broens, Els M.

Abstract

In August 2021, a large-scale mortality event affected harbor porpoises (Phocoena phocoena) in the Netherlands. Pathology and ancillary testing of 22 animals indicated that the most likely cause of death was Erysipelothrix rhusiopathiae infection. This zoonotic agent poses a health hazard for cetaceans and possibly for persons handling cetacean carcasses.

Published
2023

49. Antimicrobial resistance in Campylobacter fetus : Emergence and genomic evolution

Author

van der Graaf-van Bloois, Linda, Duim, Birgitta, Looft, Torey, Veldman, Kees T., Zomer, Aldert L., Wagenaar, Jaap A., van der Graaf-van Bloois, Linda, Duim, Birgitta, Looft, Torey, Veldman, Kees T., Zomer, Aldert L., and Wagenaar, Jaap A.

Abstract

Campylobacter fetus is a pathogen, which is primarily associated with fertility problems in sheep and cattle. In humans, it can cause severe infections that require antimicrobial treatment. However, knowledge on the development of antimicrobial resistance in C. fetus is limited. Moreover, the lack of epidemiological cut-off values (ECOFFs) and clinical breakpoints for C. fetus hinders consistent reporting about wild-type and non-wild-type susceptibility. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus and to determine the C. fetus resistome [the collection of all antimicrobial resistance genes (ARGs) and their precursors] to describe the genomic basis of antimicrobial resistance in C. fetus isolates over time. Whole-genome sequences of 295 C. fetus isolates, including isolates that were isolated in the period 1939 till the mid 1940s, before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers, and phenotypic antimicrobial susceptibility was obtained for a selection of 47 isolates. C. fetus subspecies fetus (Cff) isolates showed multiple phenotypic antimicrobial resistances compared to C. fetus subspecies venerealis (Cfv) isolates that were only intrinsic resistant to nalidixic acid and trimethoprim. Cff isolates showed elevated minimal inhibitory concentrations for cefotaxime and cefquinome that were observed in isolates from 1943 onwards, and Cff isolates contained gyrA substitutions, which conferred resistance to ciprofloxacin. Resistances to aminoglycosides, tetracycline and phenicols were linked to acquired ARGs on mobile genetic elements. A plasmid-derived tet(O) gene in a bovine Cff isolate in 1999 was the first mobile genetic element observed, followed by detection of mobile elements containing tet(O)-aph(3')-III and tet(44)-ant(6)-Ib genes, and a plasmid from a single human isolate in 2003, carrying aph(3')-III-ant(6)-Ib and a chloramphenicol resistance gene (cat). The presen

Published
2023

50. Bacterial GWAS: A Comprehensive Assessment of Challenges, Methods and Alternatives

Author

Vermeulen, Sander, Zomer, Aldert (Thesis Advisor), Vermeulen, Sander, and Zomer, Aldert (Thesis Advisor)

Abstract

Genome-wide association studies (GWAS) have proven to be a successful method for identifying associations between human genotypes and phenotypes. Due to advances in sequencing technologies and the subsequent growth of bacterial datasets, bacterial GWAS is increasingly becoming a viable research method for identifying bacterial genotype-phenotype associations. However, bacterial GWAS cannot be performed using established methods used in human GWAS due to genomic differences. Specialized software to perform bacterial GWAS has been developed, utilizing regression models, phylogenetic trees, and machine learning to overcome the unique genomic challenges. Here, we will discuss these challenges of bacterial GWAS, the software methods that have been developed and our recommendations on their usage, and discuss alternative methods for identifying genotype-phenotype associations in bacteria.

Published
2023

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