Biology subjects

Kipp, E. J.

Publications and source records attributed to Kipp, E. J..

7 recordsLinked to original sources

bioRxiv2025

Evaluating the diagnostic capabilities of nanopore sequencing for Borrelia burgdorferi detection in blacklegged ticks

Ticks pose substantial threats to public health. Blacklegged ticks (Ixodes scapularis) are responsible for most tick-borne diseases in the US, transmitting seven human pathogens. Molecular surveillance for tick-borne pathogens has been outpaced by their emergence, revealing a critical need to develop agnostic strategies that characterize emerging and putative pathogens. Oxford Nanopore Technologys nanopore adaptive sampling (NAS), an approach that selectively enriches or depletes for target genomes or genetic loci, provides an opportunity to generate real-time genomic insights into tick-borne pathogens. In the current study, we performed PCR and NAS on pooled Borrelia burgdorferi-infected and -uninfected ticks to evaluate the diagnostic capability of NAS. We found that NAS generates extensive datasets on tick-borne pathogens from individual ticks that aid in distinguishing true and false positive samples. Using a pooled approach consisting of whole genomic DNA from 168 total ticks multiplexed over seven sequencing experiments, our results indicated that NAS is extremely specific (0.97 [95% CI: 0.93, 1.00]) with moderate sensitivity (0.48 [95% CI: 0.41, 0.55]), suggesting a strong capacity to confirm B. burgdorferi when present at the expense of an elevated false-negative rate. We found that quality-based filtering of sequence data has a profound influence on diagnostic metrics, emphasizing the need to optimize pooling strategy, wet-lab procedures, and bioinformatic pipelines to enhance the sensitivity of NAS for detecting tick-borne pathogens. Author summaryTicks pose substantial threats to public health. In the United States, the blacklegged tick (Ixodes scapularis) can transmit seven (known) human pathogens and is responsible for most tick-borne disease cases. The most prevalent tick-borne pathogen, Borrelia burgdorferi, causes Lyme disease, which is consequently the most common tick-borne disease in the United States. As blacklegged ticks continue to expand across the United States, it is imperative to develop rapid molecular surveillance tools that agnostically detect emerging and putative pathogens. In the current study, we employ Oxford Nanopore Technologys nanopore adaptive sampling on PCR-infected and PCR-uninfected blacklegged ticks to determine the diagnostic capability of this technology for rapid Borrelia burgdorferi detection. Our results suggest that nanopore adaptive sampling can generate extensive sequence datasets on user-specified target reference genomes. We demonstrate that nanopore adaptive sampling is extremely specific, capable of confirming B. burgdorferi presence when detected, yet lacks sensitivity, leading to a high false negative rate. We highlight the methodological limitations that undoubtedly led to this lower sensitivity and provide future research directions for enhancing nanopore adaptive sampling as a real-time, unbiased molecular tool for tick-borne pathogen surveillance.

molecular biology↗

bioRxiv2023

Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling

AO_SCPLOWBSTRACTC_SCPLOWAccurate species identification is essential to mammalogy. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for non-invasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a PCR-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from nine mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS-barcoding of non-invasive samples. By mapping to the entire National Center for Biotechnology Information (NCBI) mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all of our fecal samples. Eight of nine species identifications matched previous PCR or animal/fecal morphological identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications, particularly field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts causes changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies.

genomics↗

bioRxiv2023

The Genome of the Soybean Gall Midge (Resseliella maxima)

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagne, is a recently discovered insect that feeds on soybean plants in the Midwest US. Resseliella maxima larvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae (Wood-Mason). The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

genomics↗

bioRxiv2021

Nanopore adaptive sampling for mitogenome sequencing and bloodmeal identification in hematophagous insects

Blood-feeding insects are important vectors for an array of zoonotic pathogens. Despite significant research focused on well-documented insect vectors of One Health importance, resources for molecular species identification of a large number of hematophagous arthropods are limited. Advancements in next-generation sequencing technologies provide opportunities for targeting mitochondrial genomes of blood-feeding insects, as well as their bloodmeal hosts. This dual approach holds great promise for elucidating complex disease transmission pathways and enhancing the molecular resources for the identification of cryptic insect species. To this end, we leveraged the newly developed Oxford Nanopore Adaptive Sampling (NAS) pipeline to dually sequence the mitogenomes of hematophagous insects and their bloodmeals. Using NAS, we sequenced the entire mitogenomes of Aedes vexans, Culex restuans, Culex territans, and Chrysops niger and successfully identified bloodmeal hosts of Chrysops niger, Culex restuans, and Aedes trivittatus. We show that NAS has the utility to simultaneously molecularly identify blood-feeding insects and characterize disease transmission pathways through bloodmeal host identification. Moreover, our data indicate NAS can facilitate a wide array of molecular systematic studies through novel phylogenetic capture methods. We conclude the NAS approach has great potential for informing global One Health initiatives centered on the mitigation of vector-borne disease through dual vector and bloodmeal identification.

genomics↗

bioRxiv2021

Enabling metagenomic surveillance for bacterial tick-borne pathogens using nanopore sequencing with adaptive sampling

Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing platforms can be bioinformatically leveraged, in real-time, for enhanced biosurveillance of a vast array of zoonoses. The recently released nanopore adaptive sampling (NAS) pipeline facilitates immediate mapping of individual nucleotide molecules (i.e., DNA, cDNA, and RNA) to a given reference as each molecule is sequenced. User-defined thresholds then allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. Here, we show how NAS can be used to selectively sequence entire genomes of bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis. The NAS method provided a two-fold increase in targeted pathogen sequences, successfully enriching for Borrelia (Borreliella) burgdorferi s.s.; Borrelia (Borrelia) miyamotoi; Anaplasma phagocytophilum; and Ehrlichia muris eauclairensis genomic DNA within our I. scapularis samples. Our results indicate that NAS has strong potential for real-time sequence-based pathogen surveillance.

microbiology↗

bioRxiv2021

Molecular surveillance of zoonotic bacterial pathogens in farm dwelling peridomestic rodents across the upper Midwest, USA

The effective control of rodent populations on farms is a critical component of food- safety, as rodents are reservoirs and vectors for many foodborne pathogens in addition to several zoonotic pathogens. The functional role of rodents in the amplification and transmission of pathogens is likely underappreciated. Clear links have been identified between rodents and outbreaks of pathogens throughout Europe and Asia, however, comparatively little research has been devoted to studying this rodent-agricultural interface in the USA, particularly across the Midwest. Here, we address this existing knowledge gap by characterizing the metagenomic communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of the putative zoonotic food- borne and other human pathogens. Rodents (mice and rats) were live trapped from three dairy and mixed animal farms. Tissues and fecal samples were collected from all rodents. DNA extraction was performed on 90 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed with the MinION. Our data suggests the presence of putative foodborne pathogens including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many important mastitis pathogens. A critically important observation is that we discovered these pathogens within all five species of rodents (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and shrew (Blarina brevicauda) in varying abundances. Interestingly, we observed a higher abundance of enteric pathogens (e.g. Salmonella) in shrew feces compared to the rodents analyzed in our study, however more data is required to establish that connection. Knowledge gained from our research efforts will directly inform and improve upon farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

microbiology↗

bioRxiv2020

Integrating indigenous knowledge, ontology, and molecular barcoding to characterize spider monkey (Ateles paniscus) filariasis

Zoonotic disease risk is greatly influenced by cultural practices and belief systems. Yet, few studies have integrated traditional ecological knowledge and ontology with western ways of knowing to better understand potential zoonoses. Here, we integrate molecular phylogenetics, histopathology, and ethnography to characterize a filarial nematode found within the abdominal cavity of spider monkeys (Ateles paniscus). The filarid is recognized as spider monkey cotton by indigenous Waiwai in the Konashen Community Owned Conservation Area, Guyana. Ethnographic data revealed that the Waiwai perceive of spider monkey cotton as a normal characteristic within the spider monkey person. Further, the Waiwai indicated that cotton was ubiquitous with spider monkeys and is not understood to be infectious nor zoonotic. This distinction is in contrast to other internal parasites found within spider monkeys that the Waiwai know to cause disease in both monkeys and humans. Our morphological and molecular characterization support the classification of the filarid as Dipetalonema caudispina, a minimally studied and seemingly non-zoonotic parasite, consistent with Waiwai beliefs. Thus, our findings allow us to establish commensurability between scientific knowledge and indigenous ontology. More broadly, this work highlights the importance of integrating multiple knowledge systems and leveraging advanced genomics to better understand and prevent emerging zoonotic diseases.

evolutionary biology↗