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Harders, F.

Publications and source records attributed to Harders, F..

8 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↗
bioRxiv2024

Bluetongue virus serotype 12 in the Netherlands in 2024 - A BTV serotype reported in Europe for the first time

Bluetongue (BT) is a viral midge borne disease primarily affecting ruminants such as sheep, cattle, and goats. In 2023, the Netherlands reported the first case of bluetongue virus serotype 3 (BTV-3), after being BTV free for eleven years. Since May 2024, vaccination with inactivated BT vaccines for serotype 3 was applied in the Netherlands. Nonetheless, in late June/July 2024, BTV-3 re-emerged and spread over large parts of Europe. In October 2024, BTV-12 was identified by follow-up diagnostics after a BTV-3 vaccinated sheep with signs of BT was tested positive for BTV but negative for serotype 3. This marks a significant event, as BTV-12 had never been reported in Europe. Screening of farms in close proximity to the sheep farm and retrospective analysis of previously BTV PCR positive tested clinical suspicions, resulted in nine BTV-12 affected farms in total. The emergence of BTV-12 in the Netherlands raises important questions about the route of introduction of BT in the Netherlands and mechanisms of viral spread of this specific serotype. Possible adaptation of new BTV serotypes to the European climatic and husbandry conditions prompts reconsideration of surveillance, prevention, and control strategies in relation to changing ecological conditions and vector dynamics. The initial findings, respective studies as well as the initial attempts to trace the origin of BTV-12 are described.

zoology↗
bioRxiv2023

Emergence of bluetongue virus serotype 3 in the Netherlands in September 2023

Since 1998, WOAH-notifiable bluetongue virus (BTV) serotype 1, 2, 3, 4, 6, 8, 9, 11, and 16 have been reported in Europe. In mid-August, 2006, a BTV-8 outbreak started in Northwestern Europe. The Netherlands was declared BT-free again in February 2012 and annual monitoring demonstrated BT-freedom up to 2023. On September 3rd 2023, clinical manifestations in sheep typical for BT were notified to the Dutch Food and Product Safety Consumer Authority. Laboratory diagnosis confirmed BTV-infection on September 6 and the first notifications of clinical signs in cattle were also reported. Two days later, the virus was identified as serotype 3 by whole genome sequencing. Clinical signs were like these of BTV-8 outbreak and were most serious in sheep. Retrospective analysis revealed no earlier circulation of BTV. It was concluded that the BTV-3 outbreak was detected shortly after introduction, while the virus source and route of introduction remains unknown. Article summary lineDuring September 2023, a novel serotype 3 Bluetongue virus (BTV) emerged in the Netherlands which affected sheep and cattle.

microbiology↗
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↗
bioRxiv2020

Chlamydia gallinacea: genetically armed as a pathogen however a phenotypical commensal?

Chlamydia gallinacea is an obligate intracellular bacterium that has recently been added to the family of Chlamydiaceae. C. gallinacea is genetically diverse, widespread in poultry and a suspected cause of pneumonia in slaughterhouse workers. In poultry, C. gallinacea infections appear asymptomatic, but studies about the pathogenic potential are limited. In this study two novel sequence types of C. gallinacea were isolated from apparently healthy chickens. Both isolates (NL_G47 and NL_F725) were closely related to each other and showed 99.1% DNA sequence identity to C. gallinacea Type strain 08-1274/3. To gain further insight in the pathogenic potential, infection experiments in embryonated chicken eggs and comparative genomics with Chlamydia psittaci were performed. C. psittaci is an ubiquitous zoonotic pathogen of birds and mammals, and infection in poultry can result in severe systemic illness. In experiments with embryonated chicken eggs C. gallinacea induced mortality was observed, potentially strain dependent but lower compared to C. psittaci induced mortality. Comparative analyses confirmed all currently available C. gallinacea genomes possess the hallmark genes coding for known and potential virulence factors as found in C. psittaci albeit to a reduced number of orthologues or paralogs. The presence of (potential) virulence factors and the observed mortality in embryonated eggs indicates C. gallinacea should rather be considered as a (conditional) pathogen than an innocuous commensal. ImportanceChlamydiaceae are a family of bacteria comprising human and animal pathogens including the recently recognized Chlamydia gallinacea. C. gallinacea is widespread in poultry without causing clinical signs, which raises questions about its pathogenic potential. To assess this potential, two novel C. gallinacea strains were isolated, tested in infection experiments in embryonated chicken eggs and compared to C. psittaci. C. psittaci infection in poultry can result in severe systemic illness, depending on the conditions, and infections can be transmitted to humans. In the experiments C. gallinacea infection induced mortality of the embryo, but to a lower extent than infection with C. psittaci. Subsequent genome comparisons confirmed both C. gallinacea strains possess potential virulence genes typical for chlamydia, but fewer than C. psittaci. These results indicate C. gallinacea does have a pathogenic potential which warrants further research to elucidate its role as a poultry pathogen.

microbiology↗
bioRxiv2020

Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms

The zoonotic origin of the SARS-CoV-2 pandemic is still unknown. Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation of outbreaks on 16 mink farms and humans living or working on these farms, using whole genome sequencing. We conclude that the virus was initially introduced from humans and has evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission. We also describe the first animal to human transmissions of SARS-CoV-2 in mink farms. One sentence summarySARS-CoV-2 transmission on mink farms.

genomics↗
bioRxiv2020

SARS-CoV2 infection in farmed mink, Netherlands, April 2020

In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.

microbiology↗