Browsing by Author "Lahmers, Kevin K."

Now showing 1 - 20 of 35
  • Thumbnail Image
    Characterization of Deoxycholate-Responsive Genes Utilized by  Brucella abortus 2308 During Oral Infection
    Lehman, Christian Ryan (Virginia Tech, 2017-07-17)
    Brucellosis is a chronic, recurring disease caused by the bacterium Brucella abortus, along with other species of the genus Brucella, and is one of the most common bacterial zoonosis worldwide. The bacteria preferentially infect and reside within host macrophages, causing an undulant fever, joint pain, and other flu-like symptoms, in addition to more severe problems like hepatosplenomegaly and endocarditis. Brucella infection is most often acquired via inhalation through the respiratory route, or via consumption of unpasteurized dairy products. Although ingestion is a major route of infection, the transcriptional response of B. abortus during oral infection remains poorly characterized. In this project, RNA sequencing was used to discover genes with the greatest transcriptional changes in B. abortus subjected to deoxycholate, a host bile acid encountered by bacteria during oral infection. Gene deletion strains of B. abortus were then created and tested for susceptibility to pH and bile acid stress, along with their ability to invade and replicate within macrophages. If the genes of interest are important for the oral infection process, B. abortus strains lacking these genes will likely be more susceptible to pH and deoxycholate stress and may exhibit attenuation in the macrophage infection model. Determination of genes important for the oral infection process would further elucidate the molecular mechanisms by which B. abortus invades the host, and could help lead to future treatments and novel therapeutics.
  • Thumbnail Image
    Characterizing a Small Regulatory RNA in Brucella abortus Linked to Outer Membrane Stress Resistance
    Stoyanof, Stephen Tristan (Virginia Tech, 2023-12-14)
    Brucella abortus is a bacterial species that infects cattle, elk, and bison herds worldwide and is a causative agent of brucellosis. B. abortus is a common form of zoonosis, as incidental spillover into the human population results in millions of infections annually. Current treatment options are limited to culling infected animals and treating humans with a rigorous antibiotic regimen, which still results in up to a 30% relapse rate. Detection of the pathogen is difficult due to the replicative niche residing within the host's immune cells, specifically macrophages and dendritic cells. Numerous small regulatory RNAs (sRNAs) were found to be expressed by B. abortus, and it was hypothesized that they may be important for virulence. One sRNA, when deleted, was shown to be linked to outer membrane stress resistance and was named MssR (membrane sensitivity sRNA). When the ΔmssR strain was tested in both macrophage and mouse models of infection, there were no virulence defects. Additionally, proteomic and transcriptomic studies of the ΔmssR strain showed very few dysregulated targets. Expression of mssR was tested under numerous biologically relevant conditions, and it was shown to be expressed significantly more during exponential phase of growth, compared to stationary phase. Initial microscopical analysis of mutant cells after treatment with sodium dodecyl sulfate (SDS_ did not reveal any morphological differences. It is unknown what contributes to the observed phenotypes and additional experiments are required to determine what is causing the perturbations in the outer membrane of the ΔmssR strain.
  • Thumbnail Image
    Complete Genome Sequence of Curtobacterium sp. Isolated from Surface-Sterilized Germinating Alfalfa Seeds
    Compton, K. Karl; Jensen, Roderick, V; Lahmers, Kevin K.; Scharf, Birgit E. (American Society for Microbiology, 2022-02)
    We reported the complete genome sequence of a member of the pathogenic Curtobacterium genus. The sample includes a circular 3955-kb chromosome, a 164-kb megaplasmid and a 42-kb plasmid. This strain was isolated from surface-sterilized alfalfa seeds.
  • Thumbnail Image
    Complete Genome Sequence of Providencia stuartii CMC-4104, Isolated from a Human Splenic Abscess, Containing Multiple Copies of NDM-1 and PER-1 Carbapenem Resistance Genes
    Rao, Jayasimha; Stornelli, Nicholas K.; Everson, Nathan A.; McDaniel, Lauren F.; Gomez De La Espriella, Mariana; Faulhaber, Jason R.; Todd, S. Michelle; Lahmers, Kevin K.; Jensen, Roderick V. (American Society for Microbiology, 2022-08-04)
    We report the complete genome sequence of a clinical isolate of Providencia stuartii strain CMC-4104, isolated from a splenic abscess. Oxford Nanopore Technologies (ONT) and Illumina sequencing reads were assembled using Geneious to generate a 4,504,925-bp circular chromosome containing multiple copies of the NDM-1 and PER-1 genes in a genomic resistance island.
  • Thumbnail Image
    Diagnostic accuracy of stereotactic brain biopsy for intracranial neoplasia in dogs: Comparison of biopsy, surgical resection, and necropsy specimens
    Kani, Yukitaka; Cecere, Thomas E.; Lahmers, Kevin K.; LeRoith, Tanya; Zimmerman, Kurt L.; Isom, Scott; Hsu, Fang-Chi; Debinski, Waldemar; Robertson, John L.; Rossmeisl, John H. Jr. (American College of Veterinary Internal Medicine, 2019-05)
    Background Stereotactic brain biopsy (SBB) is a technique that allows for definitive diagnosis of brain lesions. Little information is available regarding the diagnostic utility of SBB in dogs with intracranial diseases. Objective To investigate the diagnostic accuracy (DA) of SBB in dogs with brain tumors. Animals Thirty-one client-owned dogs that underwent SBB followed by surgical resection or necropsy examinations. Methods Retrospective observational study. Two pathologists blinded to SBB and reference standard diagnoses reviewed histologic specimens and typed and graded tumors according to World Health Organization and revised canine glioma classification criteria. Agreement between tumor type and grade from SBB were compared to reference standards and assessed using kappa statistics. Patient and technical factors associated with agreement also were examined. Results Stereotactic brain biopsy specimens were obtained from 24 dogs with gliomas and 7 with meningiomas. Tumor type agreement between SBB and the reference standard was observed in 30/31 cases (kappa = 0.95). Diagnostic concordance was perfect for meningiomas. Grade agreement among gliomas was observed in 18/23 cases (kappa = 0.47). Stereotactic brain biopsy underrepresented the reference standard glioma grade in cases with disagreement. The DA of SBB was 81%, with agreement noted in 56/69 biopsy samples. Smaller tumors and fewer SBB specimens obtained were significantly associated with diagnostic discordance. Conclusions and Clinical Importance The DA of SBB readily allows for the diagnosis of common brain tumors in dogs. Although glioma grade discordance was frequent, diagnoses obtained from SBB are sufficient to currently inform therapeutic decisions. Multiple SBB specimens should be collected to maximize DA.
  • Thumbnail Image
    Discovery and Characterization of a Novel Regulatory Small RNA, VcrS, Required for Virulence in Brucella abortus
    King, Kellie Alexandra (Virginia Tech, 2022-02-01)
    Brucella abortus is a facultative, intracellular, zoonotic pathogen that resides inside macrophages during infection. This is a specialized niche where B. abortus encounters various stresses, such as acidic conditions and reactive oxygen species, as it navigates through the macrophage. In order to survive this harsh environment, B. abortus utilizes post-transcriptional regulation through the use of small regulatory RNAs (sRNAs). sRNAs bind to messenger RNA (mRNA) targets via complementary base pairing. sRNAs are a class of regulatory molecules in bacteria that elicit rapid post-transcriptional regulation. sRNA-mRNA binding can positively or negatively influence gene expression. Positive regulation can occur through sRNA binding to protect the mRNA from RNases. sRNA binding can also alleviate the secondary structure and reveal the ribosomal binding site. Alternatively, sRNA-mRNA interactions can have negative consequences on gene expression through degradation via RNases or sRNA binding can occlude the ribosomal binding site. Although some sRNAs have been discovered in B. abortus, few have been characterized in regards to virulence. In this study, B. abortus was stressed in conditions relevant to the macrophage, including, including low pH, oxidative stress, and nutrient limitation. Transcriptomic analysis revealed high levels of transcripts in intergenic regions, a hallmark of sRNAs, which led to the discovery of VcrS for virulence and cell wall regulating sRNA. A ΔvcrS was engineered and this mutant was used to infect both naïve murine macrophages, as well as BALB/c mice. Both virulence studies demonstrated significantly decreased bacterial recovery of ΔvcrS compared to the wildtype strain. Quantitative proteomics revealed that one protein, BAB1_1454, is 30-fold over-produced in ΔvcrS compared to wildtype. This essential protein encodes MurF, which catalyzes the final cytoplasmic step of generating the mura-pentapeptide precursor for peptidoglycan synthesis. VcrS is hypothesized to interact with murF mRNA and interfere with translation initiation. Sequence data indicates a putative 6 nucleotide motif in VcrS that has complementarity to the ribosomal binding site of murF. Identification of the binding site and further characterization of VcrS will showcase the importance of sRNA regulation in the virulence of B. abortus.
  • Thumbnail Image
    Distribution of Theileria orientalis in Virginia Market Cattle, 2018-2020
    Telionis, Alex; Lahmers, Kevin K.; Todd, Michelle; Carbonello, Amanda; Broaddus, Charles C.; Bissett, Carolynn J.; Hungerford, Laura L. (MDPI, 2022-11-15)
    Theileria orientalis, genotype Ikeda, was recently detected in North America. Determining the emerging distribution of this pathogen is critical for understanding spread and developing management strategies. Whole blood samples were collected from cattle at Virginia livestock markets from September 2018 through December 2020. Animals were tested for T. orientalis using a universal and then genotype specific real-time PCR based on the MPSP gene. Prevalence for each genotype was analyzed for temporal trends and mapped by county. Spatial patterns were compared between genotypes and assessed for associations with habitat features, cattle movements through cattle markets and county proximity. Overall, 212 of 1980 samples tested positive for T. orientalis with an overall prevalence of 8.7% (172/1980) for genotype Ikeda, 1.8% (36/1980) for genotype Chitose, 0.2% (3/1980) for genotype Buffeli. The Ikeda genotype increased over time in northern and southwestern Virginia markets. The Ikeda and Chitose genotypes occurred in different regions, with little overlap, but for each genotype, spatial distribution was associated with a combination of cattle movements and environmental factors. Genotype specific qPCR testing and surveillance of cattle from across a wide area of Virginia are providing information on temporal, spatial, and other patterns for this emerging disease.
  • Thumbnail Image
    Epizootic pneumonia of bighorn sheep following experimental exposure to Mycoplasma ovipneumoniae.
    Besser, Thomas E.; Cassirer, E. Frances; Potter, E. Frances; Lahmers, Kevin K.; Oaks, J. Lindsay; Shanthalingam, Sudarvili; Srikumaran, Subramaniam; Foreyt, William J. (2014)
    BACKGROUND: Bronchopneumonia is a population limiting disease of bighorn sheep (Ovis canadensis). The cause of this disease has been a subject of debate. Leukotoxin expressing Mannheimia haemolytica and Bibersteinia trehalosi produce acute pneumonia after experimental challenge but are infrequently isolated from animals in natural outbreaks. Mycoplasma ovipneumoniae, epidemiologically implicated in naturally occurring outbreaks, has received little experimental evaluation as a primary agent of bighorn sheep pneumonia. METHODOLOGY/PRINCIPAL FINDINGS: In two experiments, bighorn sheep housed in multiple pens 7.6 to 12 m apart were exposed to M. ovipneumoniae by introduction of a single infected or challenged animal to a single pen. Respiratory disease was monitored by observation of clinical signs and confirmed by necropsy. Bacterial involvement in the pneumonic lungs was evaluated by conventional aerobic bacteriology and by culture-independent methods. In both experiments the challenge strain of M. ovipneumoniae was transmitted to all animals both within and between pens and all infected bighorn sheep developed bronchopneumonia. In six bighorn sheep in which the disease was allowed to run its course, three died with bronchopneumonia 34, 65, and 109 days after M. ovipneumoniae introduction. Diverse bacterial populations, predominantly including multiple obligate anaerobic species, were present in pneumonic lung tissues at necropsy. CONCLUSIONS/SIGNIFICANCE: Exposure to a single M. ovipneumoniae infected animal resulted in transmission of infection to all bighorn sheep both within the pen and in adjacent pens, and all infected sheep developed bronchopneumonia. The epidemiologic, pathologic and microbiologic findings in these experimental animals resembled those seen in naturally occurring pneumonia outbreaks in free ranging bighorn sheep.
  • Thumbnail Image
    Equine Herpesvirus Type 1: Filling Gaps Toward Improved Outbreak Management
    Saklou, Nadia Talal (Virginia Tech, 2023-09-06)
    Equine herpesvirus type 1 (EHV-1) is a common pathogen of horses that typically causes upper respiratory disease, however is also associated with late-term abortion, neonatal foal death and neurologic disease. Once a horse is infected, the virus concentrates to local lymphoid tissue, where it becomes latent. The virus can recrudesce during times of stress, which can lead to the initiation of devastating outbreaks. Some variants of EHV-1 have been associated with more severe disease outcomes. Appropriate outbreak management focuses on minimizing the movement of potentially exposed horses. This approach lacks a strategy for prevention at the level of latency largely due to a knowledge paucity in regards to carriage rate of latent EHV-1. Biosecurity decisions are also dependent on awaiting currently-available diagnostic testing that often take several days for results. Thus, our work has been focused on understanding the carriage rate of the latent virus in different geographic regions as well as improving diagnostic efficiency, both of which are essential for improving the management of EHV-1 disease. Loop mediated isothermal amplification (LAMP) is a method that amplifies nucleic acid rapidly at a constant temperature and is minimally affected by inhibitors that are often found in clinical samples. This procedure can be followed by multiple detection methods. A new, efficient sequencing method, called nanopore sequencing, has been developed in a handheld device, called MinION, that provides thorough output in a timely manner. When combined with LAMP, it has been referred to as LAMPore. The first objective of our work was to estimate the prevalence of latent EHV-1 and compare the frequency of each variant in the submandibular lymph nodes from horses in Virginia. Our second objective was to perform direct DNA sequencing of EHV-1 using the mobile MinION sequencer in combination with LAMP viral enrichment. Our findings demonstrated a low apparent prevalence of latent EHV-1 DNA in submandibular lymph nodes in this population of horses in Virginia as well as successful detection and identification of EHV-1 in equine nasal swab samples using LAMPore sequencing.
  • Thumbnail Image
    Establishment of a Long Term Cell Culture Model for Testing Anti-Infectives against Mycobacterium avium subsp. paratuberculosis
    Kimsawatde, Gade Carolyn (Virginia Tech, 2015-05-05)
    Mycobacterium avium subsp. paratuberculosis (MAP) is a very slow growing bacterium that is the causative agent of Johne's disease (JD) in ruminants and has long been suggested to be associated with complications of Crohn's disease (CD) in humans. Although there is no direct evidence that MAP is the primary etiological agent for CD, most CD patients are found to have MAP in their intestinal tissues. The current control measures for JD in cattle, sheep, and goats have only been minimally effective, and there are only medications to treat the symptoms of mycobacterial infections associated with CD in humans. Along with not being able to cure MAP infections, there is no established laboratory animal model for testing therapeutics. When mice are infected with MAP they develop systemic infection and do not mimic disease observed in ruminants. J774A.1 murine macrophages typically have a very short lifespan of about 4-6 days, however MAP infected cell cultures can survive up to about 10 days. Using a modified protocol of Estrella et al. (2011), we have been able to establish a 45-60 day long-term MAP infected J774A.1 murine macrophage cell culture model. With the addition of retinoic acid (RA), vitamin D (VD), and phorbol myristate acetate (PMA) in combination in cell culture, we were able to screen novel therapeutics before embarking on in vivo testing in animals. This is a significant step forward in Crohn's and Johne's disease treatment research. We are not only able to test various drugs against specific strains of MAP to determine susceptibility, but we are also able to test a wide variety of drugs at the same time, with relatively minimal cost. We have evaluated the efficacy of clarithromycin, azithromycin, isoniazid, amikacin, ethambutol, ciprofloxacin, levofloxacin, rifampicin, clofazimine, as well as a combination of clarithromycin, rifampicin, and clofazimine using our MAP infected macrophage cell culture model. We were able to determine the drugs' differential ability to kill intracellular MAP in the early stages of infection, versus chronic stages of infection, and against two different strains of MAP, 43015 and 19698 that affect humans and cattle respectively. The minimal inhibitory concentration (MIC) of each drug was determined as per NCCLS protocol in vitro, and the drugs were tested at the MIC value, along with one concentration above and below the MIC in our cell culture model. The antimicrobials were found to be effective at different stages of cell culture infection and in different strains of MAP. Some drugs were more effective at early stages of MAP infection, whereas others were more effective in chronic or latent stages of infections. It is important to note that although a drug may be effective at a certain stage of infection, it may not necessarily be effective against all strains of MAP. The most promising results were seen with a combination of clarithromycin, clofazimine, and rifampicin, which was effective at all stages of infection with both strains of MAP tested. This long term cell culture model will provide researchers with important screening tools for evaluating new therapeutics before embarking on costly in vivo testing, and allow the assessment of therapeutics at different stages of MAP infection but also against an array of intracellular pathogens.
  • Thumbnail Image
    Evaluating the Prevalence of Tick-Borne Viruses Circulating in Virginia Using a One-Health Approach
    Garba, Ahmed Oladayo (Virginia Tech, 2023-07-03)
    Ticks are hematophagous ectoparasites capable of transmitting various pathogens, including bacteria, protozoa, and viruses, to vertebrates. In the United States, tick-borne pathogens are responsible for around 95% of arthropod-borne diseases. Lyme disease is the most common tick-borne illness. However, emerging tick-borne viruses such as Bourbon virus (BRBV), Powassan virus (POWV), and Heartland virus (HRTV) can cause more severe health problems, including death and neurological abnormalities. The reports of molecular detection of viral RNA in field-collected ticks and serological evidence in a pilot study of wildlife species suggest the presence of these emerging viruses in Virginia. The presence poses a serious health threat, but the extent of their presence or circulation in Virginia is unknown. The objectives of the research are (1) to determine the evidence of circulation of POWV, HRTV, and BRBV in Virginia through serological assessment of domestic and wild animals in Virginia and (2) estimate transmission parameters and the basic reproduction number underlying tick-borne virus distribution and prevalence via a mathematical model. Here, we discuss the known literature relevant to tick-borne virus emergence; we assessed the presence of specific neutralizing antibodies against POWV, HRTV, and BRBV in wildlife and livestock sera collected from different health planning regions in Virginia. We used a susceptible-infected-susceptible (SIS) ordinary differential equation model to estimate transmission parameters that best describe the disease dynamics of emerging tick-borne viruses in Virginia. In our study, wildlife sera were seropositive against POWV (18%), BRBV (8%), and HRTV (5%). A wide range of different wildlife species were shown to be exposed to each virus examined. Livestock are also exposed to tick-borne viruses, with seroprevalences of 1%, 1.2%, and 8% detected in cattle for POWV, BRBV, and HRTV, respectively. We estimated the transmission rate and basic reproduction number to be 1.57 and 0.645, respectively. In conclusion, there is a widespread circulation of tick-borne viruses in western and northern Virginia within diverse species of animal populations.
  • Thumbnail Image
    Evaluation of Tumor Grade and Proliferation Indices before and after Short-Course Anti-Inflammatory Prednisone Therapy in Canine Cutaneous Mast Cell Tumors: A Pilot Study
    Klahn, Shawna L.; Dervisis, Nikolaos G.; Lahmers, Kevin K.; Benitez, Marian (MDPI, 2022-06-07)
    Glucocorticoid administration is a common clinical practice that attempts to decrease the inflammation associated with and improve the resectability of canine mast cell tumors (MCTs). However, the impact of neoadjuvant glucocorticoids on the histological features and proliferation indices of canine MCTs is unknown. The objective of this study was to evaluate changes in tumor grade, mitotic count, Ki67, AgNOR, and AgNORxKi67 scores following short-course anti-inflammatory neoadjuvant prednisone in canine patients with MCTs. This was a prospective single-arm pilot study. Client-owned dogs with treatment-naïve cytologically confirmed MCTs were enrolled. Patients underwent an initial incisional biopsy followed by a 10–14-day course of anti-inflammatory prednisone and surgical resection. All histological samples were randomized, masked, and evaluated by a single pathologist. Unstained paired pre- and post-treatment samples were submitted to a commercial laboratory for Ki67 and AgNOR immunohistochemical analysis. There were 11 dogs enrolled with 11 tumors. There were no statistical differences between the pre- and post-treatment histological parameters of mitotic index, Ki67, AgNOR, or Ki67xAgNOR. There were no clinically significant alterations between pre-treatment and post-treatment in the assignment of tumor grades. A short course of anti-inflammatory prednisone does not appear to alter the histological parameters that affect grade determination or significantly alter the proliferation indices in canine MCTs.
  • Thumbnail Image
    Frame-Based Stereotactic Biopsy of Canine Brain Masses: Technique and Clinical Results in 26 Cases
    Rossmeisl, John H. Jr.; Andriani, Rudy T.; Cecere, Thomas E.; Lahmers, Kevin K.; LeRoith, Tanya; Zimmerman, Kurt L.; Gibo, Denise M.; Debinski, Waldemar (2015)
    This report describes the methodology, diagnostic yield, and adverse events (AE) associated with frame-based stereotactic brain biopsies (FBSB) obtained from 26 dogs with solitary forebrain lesions. Medical records were reviewed from dogs that underwent FBSB using two stereotactic headframes designed for use in small animals and compatible with computed tomographic (CT) and magnetic resonance (MR) imaging. Stereotactic plans were generated from MR and CT images using commercial software, and FBSB performed both with (14/26) and without intraoperative image guidance. Records were reviewed for diagnostic yield, defined as the proportion of biopsies producing a specific neuropathological diagnosis, AE associated with FBSB, and risk factors for the development of AE. Postprocedural AE were evaluated in 19/26 dogs that did not proceed to a therapeutic intervention immediately following biopsy. Biopsy targets included intra-axial telencephalic masses (24/26), one intra-axial diencephalic mass, and one extra-axial parasellar mass. The median target volume was 1.99 cm(3). No differences in patient, lesion, or outcome variables were observed between the two headframe systems used or between FBSB performed with or without intraoperative CT guidance. The diagnostic yield of FBSB was 94.6%. Needle placement error was a significant risk factor associated with procurement of non-diagnostic biopsy specimens. Gliomas were diagnosed in 24/26 dogs, and meningioma and granulomatous meningoencephalitis in 1 dog each. AE directly related to FBSB were observed in a total of 7/26 (27%) of dogs. Biopsy-associated clinical morbidity, manifesting as seizures and transient neurological deterioration, occurred in 3/19 (16%) of dogs. The case fatality rate was 5.2% (1/19 dogs), with death attributable to intracranial hemorrhage. FBSB using the described apparatus was relatively safe and effective at providing neuropathological diagnoses in dogs with focal forebrain lesions.
  • Thumbnail Image
    Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction
    Todd, S. Michelle; Settlage, Robert E.; Lahmers, Kevin K.; Slade, Daniel J. (American Society for Microbiology, 2018)
    Understanding the virulence mechanisms of human pathogens from the genus Fusobacterium has been hindered by a lack of properly assembled and annotated genomes. Here we report the first complete genomes for seven Fusobacterium strains, as well as resequencing of the reference strain Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (total of seven species; total of eight genomes). A highly efficient and cost-effective sequencing pipeline was achieved using sample multiplexing for short-read Illumina (150 bp) and long-read Oxford Nanopore Min- ION (80 kbp) platforms, coupled with genome assembly using the open-source software Unicycler. Compared to currently available draft assemblies (previously 24 to 67 contigs), these genomes are highly accurate and consist of only one complete chromosome. We present the complete genome sequence of F. nucleatum subsp. nucleatum ATCC 23726, a genetically tractable and biomedically important strain and, in addition, reveal that the previous F. nucleatum subsp. nucleatum ATCC 25586 genome assembly contains a 452-kb genomic inversion that has been corrected using our sequencing and assembly pipeline. To enable genomic analyses by the scientific community, we concurrently used these genomes to launch FusoPortal, a repository of interactive and downloadable genomic data, genome maps, gene annotations, and protein functional analyses and classifications. In summary, this report provides detailed methods for accurately sequencing, assembling, and annotating Fusobacterium genomes, while focusing on using open-source software to foster the availability of reproducible and open data. This resource will enhance efforts to properly identify virulence proteins that may contribute to a repertoire of diseases that includes periodontitis, preterm birth, and colorectal cancer.
  • Thumbnail Image
    Identifying and Tracking the Evolution of Mutations in the SARS-CoV-2 Virus
    Venkatesan, Lavanya (Virginia Tech, 2021-06-21)
    SARS-CoV-2 is caused by a pathogenic and highly transmissible beta coronavirus leading to severe infections in immuno-compromised individuals. This study first evaluates the primers used in the Reverse Transcription Polymerase Chain Reaction (RT-PCR) to detect SARS-CoV-2 by understanding how mutations might affect the primer efficiency with the SARS-CoV-2 sequences. Mutations on the Spike protein of SARS-CoV-2 are the most important as the spike protein mediates the viral entry into host cells. This study tracks the course of mutations on the spike protein by focusing on the haplogroups of the sequences across the world. A comprehensive database linking three important, currently available databases is curated as part of this study to fill the gaps caused by sequencing errors. Further, this study exploits the data generated by the Illumina and Oxford Nanopore next generation sequencing methods to study the evolution of mutations in a single Septuagenarian patient over an infection period of 102 days using the gene analysis software Geneious Prime.
  • Thumbnail Image
    Mixed Strain Identification of Porcine Reproductive and Respiratory Syndrome Virus in Multiplexed Samples using Nanopore Sequencing
    Buman Ruiz Diaz, Maria Paz (Virginia Tech, 2024-01-08)
    For over thirty years, Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) has been a major contributor to morbidity and mortality in the commercial swine industry across the globe. This highly mutagenic RNA virus causes significant economic losses wherever it is prevalent, leading to $664 million in annual losses in the United States. Unfortunately, the current prevention and diagnostic techniques available have proven to be insufficient in controlling the spread of this disease. We describe an alternative diagnostic method exploiting the rapid turnaround time and long-read capacity of Oxford Nanopore Technology's MinION next-generation sequencer. We have developed a novel primer set designed to span Open Reading Frames 3 through 7 of the PRRSV genome, which has allowed for multiplexing of samples, thus reducing individual cost of testing, while yielding significantly more information than previously available. This novel primer pair and sequencing technique have distinguished mixed infections within individual animals and may be used to determine vaccination status. This new approach will help producers and veterinarians make better-informed decisions about co-mingling of animals and vaccination strategies, thus reducing the emergence of new, pathogenic strains of PRRSV.
  • Thumbnail Image
    Multistate Infestation with the Exotic Disease-Vector Tick Haemaphysalis longicornis - United States, August 2017-September 2018
    Ben Beard, C.; Occi, James; Bonilla, Denise L.; Egizi, Andrea M.; Fonseca, Dina M.; Mertins, James W.; Backenson, Bryon P.; Bajwa, Waheed I.; Barbarin, Alexis M.; Bertone, Matthew A.; Brown, Justin; Connally, Neeta P.; Connell, Nancy D.; Eisen, Rebecca J.; Falco, Richard C.; James, Angela M.; Krell, Rayda K.; Lahmers, Kevin K.; Lewis, Nicole; Little, Susan E.; Neault, Michael; de Leon, Adalberto A. Perez; Randall, Adam R.; Ruder, Mark G.; Saleh, Meriam N.; Schappach, Brittany L.; Schroeder, Betsy A.; Seraphin, Leslie L.; Wehtje, Morgan; Wormser, Gary P.; Yabsley, Michael J.; Halperin, William (Centers for Disease Control and Prevention, 2018-11-30)
    Haemaphysalis longicornis is a tick indigenous to eastern Asia and an important vector of human and animal disease agents, resulting in such outcomes as human hemorrhagic fever and reduction of production in dairy cattle by 25%. H. longicornis was discovered on a sheep in New Jersey in August 2017 (1). This was the first detection in the United States outside of quarantine. In the spring of 2018, the tick was again detected at the index site, and later, in other counties in New Jersey, in seven other states in the eastern United States, and in Arkansas. The hosts included six species of domestic animals, six species of wildlife, and humans. To forestall adverse consequences in humans, pets, livestock, and wildlife, several critical actions are indicated, including expanded surveillance to determine the evolving distribution of H. longicornis, detection of pathogens that H. longicornis currently harbors, determination of the capacity of H. longicornis to serve as a vector for a range of potential pathogens, and evaluation of effective agents and methods for the control of H. longicornis.
  • Thumbnail Image
    Necrotizing hepatitis caused by Clostridium novyi type B in a dog with no predisposing liver lesions: a case report
    Trusiano, Brie; Todd, S. M.; Barrett, Sarah; Ciepluch, Michael; Fox, Alexandra; McClendon, Diamond; Lahmers, Kevin K.; Oakes, Vanessa J.; Carvallo, Francisco R.; Corrigan, Virginia; LeCuyer, Tessa E. (2022-10-05)
    Background Infectious necrotic hepatitis (INH) is typically a disease of ruminants caused by Clostridium novyi type B. Growth of the causative agent is supported by development of an anaerobic environment within the liver. In dogs, C. novyi is rare and has only been previously reported as a post-mortem diagnosis. In one case, infection was secondary to metastatic pancreatic adenocarcinoma and the other was presumptively diagnosed on histopathology of a hepatic lesion in a dog initially presented for acute collapse. Case presentation An 8-year-old spayed, female mixed breed dog was presented for acute onset of hyporexia and vomiting. Serum biochemistry revealed elevated hepatocellular injury and cholestatic liver enzymes. Ultrasound revealed peritoneal fluid accumulation and multiple hepatic masses. Cytologic examination of liver aspirates and peritoneal fluid revealed frequent 4 × 1 μm bacilli with a terminal endospore. Anaerobic bacterial growth isolated from the fluid sample could not be identified using typical laboratory identification techniques. Long-read, whole genome sequencing was performed, and the organism was identified as Clostridium novyi type B. Antimicrobial and hepatic support treatment were initiated. The patient re-presented 27 days later, and the follow up liver aspirate with cytology revealed no appreciable bacteria and anaerobic culture was negative. The patient was presented four months later and a large hepatic mass and peritoneal fluid were again identified on abdominal ultrasound. Cytologic examination of the peritoneal fluid revealed bacilli similar to those identified on initial presentation. The patient was euthanized. The most significant finding on necropsy was necrotizing hepatitis with intralesional endospore-forming bacilli compatible with recurrence of Clostridium novyi type B. There was no identifiable cause of an anaerobic insult to the liver. Conclusions This case demonstrates the diagnostic utility of using cytology as part of the initial diagnostic work up for infectious hepatitis. The cytologic findings coupled with whole genome sequencing and anaerobic culture were crucial for the identification and classification of the organism identified on fine needle aspirate. Clostridium novyi type B should be considered when bacilli organisms containing a terminal endospore are identified on liver aspirates collected from canine patients.
  • Thumbnail Image
    Optimizing Pooled Testing for Estimating the Prevalence of Multiple Diseases
    Warasi, Md S.; Hungerford, Laura L.; Lahmers, Kevin K. (Springer, 2022-08-12)
    Pooled testing can enhance the efficiency of diagnosing individuals with diseases of low prevalence. Often, pooling is implemented using standard groupings (2, 5, 10, etc.). On the other hand, optimization theory can provide specific guidelines in finding the ideal pool size and pooling strategy. This article focuses on optimizing the precision of disease prevalence estimators calculated from multiplex pooled testing data. In the context of a surveillance application of animal diseases, we study the estimation efficiency (i.e., precision) and cost efficiency of the estimators with adjustments for the number of expended tests. This enables us to determine the pooling strategies that offer the highest benefits when jointly estimating the prevalence of multiple diseases, such as theileriosis and anaplasmosis. The outcomes of our work can be used in designing pooled testing protocols, not only in simple pooling scenarios but also in more complex scenarios where individual retesting is performed in order to identify positive cases. A software application using the shiny package in R is provided with this article to facilitate implementation of our methods. Supplementary materials accompanying this paper appear online.
  • Thumbnail Image
    Phase I Clinical Trial of Recombinant Oncolytic Newcastle Disease Virus for Intracranial Meningioma
    King, Jamie N. (Virginia Tech, 2017-07-14)
    Meningioma is one of the most commonly diagnosed intracranial tumors in dogs and humans. Treatment failures resulting in local recurrence and death remain common in tumors of high grade, prompting a need for additional therapeutic options that are both effective and affordable. Genetic modification of the LaSota strain of Newcastle Disease Virus (rLAS) has allowed the virus' fusion protein cleavage site to be replaced with that belonging to urokinase plasminogen activator (rLAS-uPA). This site is cleavable exclusively by the uPA receptor (uPAR), which is overexpressed in canine meningioma. The rLAS-uPA represents a targeted therapy that has the potential to be efficacious against meningioma when administered systemically. A Phase I clinical trial was designed to evaluate the safety and preliminary efficacy of rLAS-uPA administered to dogs with presumptive intracranial meningioma. The primary endpoint was to define the safety of rLAS-uPA, as determined by serial clinical and laboratory assessments during and after viral administration, using standard toxicity metrics defined by the Veterinary Cooperative Oncology Group (VCOG). Secondary end-points included anti-tumor activity quantified by magnetic resonance imaging (MRI) assessment of tumor size, and characterization of immune responses to the rLAS-uPA. Four dogs completed the trial without significant toxicity. No objective tumor responses were noted on MRI from any dog. All dogs produced antiviral antibodies and increased circulating cytokines during the course of treatment. No virus was recovered from plasma, urine, or cerebrospinal fluid. These results indicate that further investigation into the rLAS-uPA dose intensity and interval are required to further develop this therapy.