Biology subjects

Bossers, A.

Publications and source records attributed to Bossers, A..

4 recordsLinked to original sources

bioRxiv2025

CArP - CApture-based sequencing for Pathogen surveillance in complex matrices

This study highlights the development and application of a novel capture-based long-read sequencing approach, CArP, designed to benefit pathogen surveillance. This combines targeted gene enrichment with the contextual insights of long-read sequencing, providing a highly efficient and flexible approach for pathogen detection. In this initial version, antimicrobial resistance (AMR) genes are utilized as marker genes that improve sequencing sensitivity. This allowed the detection of bacteria in broiler caecal content samples that carried resistance genes for critical antibiotics, including macrolides and quinolones. These specific AMR genes would have remained undetected when traditional metagenomic shotgun sequencing would have been applied, as it failed to detect these genes and therefore putative pathogens. This demonstrates the potential to detect and characterize pathogens more effectively compared to traditional sequencing strategies. The modular design of CArP furthermore demonstrates expansion with additional marker genes, such as viral or fungal markers, that can enable broader pathogen coverage. Taken together, this approach allows to advance pathogen detection and can contribute to global efforts in pandemic preparedness and the subsequent response.

genomics↗

bioRxiv2023

Impact of diet on jejunal microbiota composition during broiler development with special focus on Enterococcus hirae and Enterococcus faecium

Modern broiler breeds allow for high feed efficiency and rapid growth, but come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are furthermore affected by the composition of the gut microbiota, which in turn is influenced by diet composition. In this study we therefore assessed how diet composition alters the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content jejunum was used for metagenomic shotgun sequencing to determine the microbiota composition on species level. Among all diet groups, a total of 104 differential abundant bacterial species were detected. Most notably were the changes in the jejunal microbiota induced by butyrate supplementation when compared to the control diet, resulting in the reduced relative abundance of mainly Enterococcus faecium and the opportunistic pathogen Enterococcus hirae in broilers 4 days post-hatch. At this early stage of development, the immune system is still immature thereby highlighting the importance to study the relation of diet and the jejunal microbiota. Future studies should furthermore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.

microbiology↗

bioRxiv2023

Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens.

The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria similar to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed on the day of hatch (day 0) over 12 pens. On day 5, half of the chickens in each pen were orally inoculated with 5{middle dot}102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). Amoxicillin drinking water treatment was given twice daily in 6 of the 12 pens from days 2 to 6 to evaluate the effect of antibiotic treatment on the transmission rates. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2 to 6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.

microbiology↗

bioRxiv2017

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

EFFORT groupHaitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzynska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stark.\n\nAbstractAntimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. Use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and countries. We found that the total acquired AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. Novel, functionally-determined AMR genes were, however, not associated with total drug use.

microbiology↗