Biology subjects

Cole, S. D.

Publications and source records attributed to Cole, S. D..

6 recordsLinked to original sources

bioRxiv2026

Clade 2.3.4.4b H5N1 influenza virus and SARS-CoV-2 seroprevalence among owned and feral cats in Philadelphia and surrounding communities

Clade 2.3.4.4b H5NX influenza viruses have spread widely in birds since 2020. In addition to causing disease in birds, these viruses have infected a variety of mammals, including humans. Clade 2.3.4.4b H5N1 viruses are currently causing an outbreak among dairy cattle in the United States, and it is important to determine if other mammals have been exposed to H5NX viruses. Cats, specifically outdoor and feral cats, frequently predate wild birds. Recent studies have shown that cats living on dairy cattle farms can be infected with H5N1. Here, we completed serological studies to determine if owned and feral cats living in an urban environment in the United States have evidence of past H5N1 exposures. We used multianalyte bead-based assays to measure clade 2.3.4.4b hemagglutinin (HA) antibody levels in serum samples collected in July 2023 to June 2025 from 417 feral and 228 owned cats from the greater Philadelphia area. We also measured antibody levels against a panel of HAs from other human and non-human influenza viruses, and the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We completed additional H5N1 and SARS-CoV-2 neutralization assays using samples that had detectable antibodies in the multianalyte bead-based assays. One cat (0.16%) was positive for H5 antibodies and twenty cats (3.1%) were positive for SARS-CoV-2 antibodies in both binding and neutralization assays. These data suggest that cats in the Philadelphia area have not been routinely exposed to clade 2.3.4.4b H5N1 viruses but have been more commonly exposed to SARS-CoV-2. ImportanceHighly pathogenic H5NX avian influenza viruses have caused widespread disease and mortality in both wild and domestic birds, and have infected marine mammals, cattle, and humans. Recent studies have demonstrated that cats can also be infected with H5NX viruses, but it is unknown if these infections are common. In this report, we completed a seroprevalence study and found that H5NX exposure in feral and owned cats in the Philadelphia area appears to be rare. We also completed SARS-CoV-2 serological experiments and found that 3.1% of cats possessed antibodies reactive to this virus.

microbiology↗

bioRxiv2025

Breaking the culture habit: metagenomic diagnosis of companion animal skin infections

BackgroundSkin infections have been described as the primary cause for presentation in veterinary small animal practices and they frequently result in prescription of both topical and systemic antibiotics. Because such infections are often secondary complications of other underlying pathologies, recurrent infections are common and can lead to multiple antibiotic exposures. This scenario creates steady selection pressure toward antibiotic resistance at the confluence of the skin (the largest mammalian organ), the bloodstream, and shared human and animal environments. This case study compares metagenomic (MGX) data with aerobic culture to evaluate diagnostic utility for simultaneous identification and characterization of pathogens, microbiomes, and resistomes of companion animal skin infections. ResultsOne feline and eight canine skin swabs were analyzed with aerobic culture and traditional antimicrobial susceptibility testing (AST) and compared with MGX profiling. Veterinary laboratory diagnostic (VDL) culture and AST identified Staphylococcus aureus, S. pseudintermedius, S. schleiferi, methicillin resistant (MR) S. schleiferi (MRSS), MR S. pseudintermedius (MRSP) and Pseudomonas aeruginosa from skin swabs. MGX data described the identical bacterial pathogens recovered by aerobic culture and methicillin resistance genes mecA, mecI, mecR1 in samples for which AST confirmed MRSP and MRSS. MGX data also identified mec genes in samples without culture-based confirmation of MR phenotypes. MGX data also described multi-domain composition of microbiomes of infected skin including bacteria, fungi, viruses, phages, AMR, plasmids, and metabolic features associated with skin infections. ConclusionsMGX data identified the identical pathogens and inferred AMR phenotypes as culture-based diagnostic testing, and additionally characterizedo multi-domain microbiota, mobile AMR elements, and metabolic features. Efforts to accelerate cures by precision medical responses depend on accelerated precision diagnostics. Challenges remain for the implementation of MGX data into veterinary diagnostic laboratory investigation and response. We demonstrate with a small case study, that MGX data can be used to complement current state of the art VDL results and potentially advance a judicious veterinary medical response regarding antibiotic administration for companion animal skin infections. In the future, simultaneous description of the polymicrobial ecology of skin infections (bacterial, viruses, phages, fungi, and even functional metabolomic features) provided by MGX data can advance epidemiology, develop new treatment strategies, accelerate diagnostics and provide data for artificial intelligence (AI) models focused on advancing veterinary diagnostics and medical treatments.

microbiology↗

bioRxiv2025

Human wastewater contamination drives the emergence of novel multidrug resistant bacteria in the Galapagos marine ecosystem.

Since the publication of Charles Darwins On the Origin of Species in 1859, the Galapagos archipelago has become emblematic of natural selection and evolution. While the lens of evolution in the Galapagos has traditionally focused on iconic megafauna, including finches, marine iguanas, and giant tortoises, the marine environment is also home to diverse microbial ecosystems that are constantly evolving under selective pressure from environmental factors such as human activity. We focused on the second most populated island within the archipelago -- San Cristobal -- an island that has experienced rapid urbanization and intense international tourism pressure. Using a lab-free approach, we spatiotemporally mapped wastewater contamination around San Cristobal. On-site metagenomic sequencing revealed a stark shift in genera and a higher count of antimicrobial resistance genes at wastewater-associated sites. Over 40% of lactose-fermenting Enterobacteriaceae isolates collected from sewage and wastewater outfall exhibited multidrug resistance (MDR). Long-read sequencing and de novo assembly of bacterial genomes and plasmids from MDR Escherichia coli revealed frequent and rapid reassortment of antimicrobial resistance genes on plasmids, generating unique antimicrobial resistance profiles. This study not only provides a framework for conducting antimicrobial resistance research in low-resource settings but also underscores the impact of wastewater contamination on the environmental AMR landscape and highlights potential threats to human and animal health.

microbiology↗

bioRxiv2024

Semi-automated Production of Cell-free Biosensors

Cell-free synthetic biology biosensors have potential as effective in vitro diagnostic technologies for the detection of chemical compounds such as toxins and human health biomarkers. They have several advantages over conventional laboratory-based diagnostic approaches, including being able to be assembled, freeze-dried, distributed, and then used at the point-of-need. This makes them an attractive platform for cheap and rapid chemical detection across the globe. Though promising, a major challenge is scaling up biosensor manufacturing to meet the needs of their multiple uses. Currently, cell-free biosensor assembly during lab-scale development is mostly performed manually by the operator, leading to quality control and performance variability issues. Here we explore the use of liquid handling robotics to manufacture cell-free biosensor reactions. We compare both manual and semi-automated reaction assembly approaches using the Opentrons OT-2 liquid handling platform on two different cell-free gene expression assay systems that constitutively produce colorimetric (LacZ) or fluorescent (GFP) signals. We test the designed protocol by constructing an entire 384-well plate of fluoride sensing cell-free biosensors and demonstrate that they perform closely to expected detection outcomes.

synthetic biology↗

bioRxiv2022

Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have spilled over from humans to companion and wild animals since the inception of the global COVID-19 pandemic. However, whole genome sequencing data of the viral genomes that infect non-human animal species has been scant. Here, we detected and sequenced a SARS-CoV-2 delta variant (AY.3) in fecal samples from an 11-year-old domestic house cat previously exposed to an owner who tested positive for SARS-CoV-2. Molecular testing of two fecal samples collected 7 days apart yielded relatively high levels of viral RNA. Sequencing of the feline-derived viral genomes showed the two to be identical, and differing by between 4 and 14 single nucleotide polymorphisms in pairwise comparisons to human-derived lineage AY.3 sequences collected in the same geographic area and time period. However, several mutations unique to the feline samples reveal their divergence from this cohort on phylogenetic analysis. These results demonstrate continued spillover infections of emerging SARS-CoV-2 variants that threaten human and animal health, as well as highlight the importance of collecting fecal samples when testing for SARS-CoV-2 in animals. To the authors knowledge, this is the first published case of a SARS-CoV-2 delta variant in a domestic cat in the United States.

microbiology↗

bioRxiv2021

A Method for Cost-Effective and Rapid Characterization of Genetic Parts

Characterizing and cataloging genetic parts are critical to the design of useful genetic circuits. Having well-characterized parts allows for the fine-tuning of genetic circuits, such that their function results in predictable outcomes. With the growth of synthetic biology as a field, there has been an explosion of genetic circuits that have been implemented in microbes to execute functions pertaining to sensing, metabolic alteration, and cellular computing. Here, we show a cost-effective and rapid method for characterizing genetic parts. Our method utilizes cell-free lysate, prepared in-house, as a medium to evaluate parts via the expression of a reporter protein. Template DNA is prepared by PCR-amplification using inexpensive primers to add variant parts to the reporter gene, and the template is added to the reaction as linear DNA without cloning. Parts that can be added in this way include promoters, operators, ribosome binding sites, insulators, and terminators. This approach, combined with the incorporation of an acoustic liquid handler and 384-well plates, allows the user to carry out high-throughput evaluations of genetic parts in a single day. By comparison, cell-based screening approaches require time-consuming cloning and have longer testing times due to overnight culture and culture density normalization steps. Further, working in cell-free lysate allows the user to exact tighter control over the expression conditions through the addition of exogenous components, or by titrating DNA concentrations rather than relying on limited plasmid copy numbers. Because this method retains a cell-like environment, the function of the genetic part will typically mimic its function in whole cells. SUMMARYWell-characterized genetic parts are necessary for the design of novel genetic circuits. Here we describe a cost-effective, high-throughput method for rapidly characterizing genetic parts. Our method reduces cost and time by combining cell-free lysates, linear DNA to avoid cloning, and acoustic liquid handling to increase throughput and reduce reaction volumes.

synthetic biology↗