Biomedical subjects

Kara L Nelson

Publications and source records attributed to Kara L Nelson.

7 recordsLinked to original sources

PubMed2026

Genomic wastewater surveillance of human and animal influenza A viruses in California during the 2024-2025 flu season.

BACKGROUND: Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. METHODS: We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. FINDINGS: Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples. INTERPRETATION: When IAV concentrations were dominated by seasonal human subtypes rather than H5N1, subtype patterns aligned between wastewater and clinical data. While sequencing IAV in wastewater was unable to distinguish if H5N1 detections were due to human or animal infections, it was able to provide clade-level information about H5N1 found in wastewater that could be useful in the future. Wastewater genomic surveillance can complement clinical surveillance, increasing ability to detect all circulating IAV subtypes and enhancing public health preparedness from a One Health perspective.

Journal Article↗

PubMed2025

Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater.

Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmarked four targeted enrichment methods suited for whole-genome sequencing including custom and off-the-shelf amplicon and probe-based methods. Our custom HA tiled-amplicon panel was sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes. However, its reliance on conserved and intact primer-binding sites limited primer design to fewer subtypes. A previously published universal amplicon method targeted all IAV subtypes, but it performed poorly in wastewater due to its reliance on intact genome segments. Probe-capture methods were resilient to RNA degradation and mismatches, potentially enabling broader surveillance and detection of emerging strains. However, probes were costly, labor-intensive, and less sensitive than tiled-amplicon. When testing compatibility of sequencing methods with upstream virus concentration and extraction methods, ultrafiltration-based virus concentration outperformed large-volume direct extraction with all four sequencing methods. This set of benchmarking comparisons and custom panels provides needed information for the translation of IAV genomic sequencing into a routine component of wastewater surveillance.

Journal Article↗

PubMed2006

A real-time PCR method for quantifying viable ascaris eggs using the first internally transcribed spacer region of ribosomal DNA.

Worldwide, 1.4 billion people are infected with the intestinal worm Ascaris lumbricoides. As a result, Ascaris eggs are commonly found in wastewater and sludges. The current microscopy method for detecting viable Ascaris eggs is time- and labor-intensive. The goal of this study was to develop a real-time quantitative PCR (qPCR) method to determine the levels of total and viable Ascaris eggs in laboratory solutions using the first internally transcribed spacer (ITS-1) region of ribosomal DNA (rDNA) and rRNA. ITS-1 rDNA levels were proportional to Ascaris egg cell numbers, increasing as eggs developed from single cells to mature larvae and ultimately reaching a constant level per egg. Treatments causing >99% inactivation (high heat, moderate heat, ammonia, and UV) eliminated this increase in ITS-1 rDNA levels and caused decreases that were dependent on the treatment type. By taking advantage of this difference in ITS-1 rDNA level between viable, larvated eggs and inactivated, single-celled eggs, qPCR results were used to develop inactivation profiles for the different treatments. No statistical difference from the standard microscopy method was found in 75% of the samples (12 of 16). ITS-1 rRNA was detected only in samples containing viable eggs, but the levels were more variable than rDNA levels and ITS-1 rRNA could not be used for quantification. The detection limit of the rDNA-based method was approximately one larvated egg or 90 single-celled eggs; the detection limit for the rRNA-based method was several orders of magnitude higher. The rDNA qPCR method is promising for both research and regulatory applications.

Animals↗

PubMed2006

Inactivation of single-celled Ascaris suum eggs by low-pressure UV radiation.

Intact and decorticated single-celled Ascaris suum eggs were exposed to UV radiation from low-pressure, germicidal lamps at fluences (doses) ranging from 0 to 8,000 J/m2 for intact eggs and from 0 to 500 J/m2 for decorticated eggs. With a UV fluence of 500 J/m2, 0.44-+/-0.20-log inactivation (mean+/-95% confidence interval) (63.7%) of intact eggs was observed, while a fluence of 4,000 J/m2 resulted in 2.23-+/-0.49-log inactivation (99.4%). (The maximum quantifiable inactivation was 2.5 log units.) Thus, according to the methods used here, Ascaris eggs are the most UV-resistant water-related pathogen identified to date. For the range of fluences recommended for disinfecting drinking water and wastewater (200 to 2,000 J/m2), from 0- to 1.5-log inactivation can be expected, although at typical fluences (less than 1,000 J/m2), the inactivation may be less than 1 log. When the eggs were decorticated (the outer egg shell layers were removed with sodium hypochlorite, leaving only the lipoprotein ascaroside layer) before exposure to UV, 1.80-+/-0.32-log reduction (98.4%) was achieved with a fluence of 500 J/m2, suggesting that the outer eggshell layers protected A. suum eggs from inactivation by UV radiation. This protection may have been due to UV absorption by proteins in the outer layers of the 3- to 4-microm-thick eggshell. Stirring alone (without UV exposure) also inactivated some of the Ascaris eggs (approximately 20% after 75 min), which complicated determination of the inactivation caused by UV radiation alone.

Animals↗

PubMed2005

Inactivation of Ascaris suum eggs by ammonia.

Uncharged ammonia is known to cause inactivation of a number of wastewater pathogens, but its effect on Ascaris eggs has never been isolated or quantified. The objectives of this research were to determine the conditions under which ammonia inactivates eggs of the swine Ascaris species, Ascaris suum, and to quantify the impact of ammonia on the U.S. EPA's requirements for alkaline treatment to produce Class A sludge. Eggs were incubated in controlled, laboratory solutions such that the effects of ammonia concentration and speciation, pH, and temperature could be separated. With a 24-h incubation, the inactivation at all pH levels (range 7-11) was not statistically different in the absence of ammonia. The presence of ammonia (0-1000 ppm as N) significantly increased Ascaris egg inactivation at pH 9 and 11, and the ovicidal effect was directly related to the concentration of the uncharged NH3 species. Increasing temperatures (32-52 degrees C) caused increased inactivation at all pH levels and ammonia concentrations. The current EPA treatment requirements to produce Class A biosolids by alkaline treatment have temperature, pH, and time requirements, but do not account for the effectof differences in ammonia concentration on inactivation. To illustrate the potential savings in temperature and pH that could be achieved when accounting for ammonia inactivation, the combinations of ammonia concentration, temperature, and pH neededto achieve 99% inactivation after 72 h were determined. The presence of ammonia at concentrations encountered in sludges and feces (up to 8000 ppm as N) allowed for 99% egg inactivation to be achieved at temperatures up to 14 degrees C lower than ammonia-free controls. Thus, environmentally relevant concentrations of ammonia may significantly increase the rate of Ascaris egg inactivation during alkaline stabilization.

Ammonia↗

PubMed2004

Sludge accumulation, characteristics, and pathogen inactivation in four primary waste stabilization ponds in central Mexico.

To support the development of safe and feasible sludge management strategies, the accumulation rates of sludge and its characteristics were studied in four primary wastewater stabilization ponds (WSPs) in central Mexico (three facultative and one anaerobic). The accumulation rates and distribution of sludge were determined by measuring the thickness of the sludge layer at 8-40 locations throughout each pond. The average, per capita sludge accumulation rates ranged from 0.021 to 0.036m(3)/person/yr. In the anaerobic pond the sludge distribution was uniform throughout the pond, whereas in the three facultative ponds most of the sludge accumulated directly in front of the inlet. To measure the horizontal and vertical variation in the sludge characteristics, sludge cores were collected from 3 to 7 locations in three of the ponds. Each core was divided into 4 sub-samples in which various physical, chemical, and microbiological parameters were measured. In addition, the inactivation of several pathogen indicator organisms was studied in a batch of sludge for 7 months. Based on the microbiological results, it is concluded that reasonable estimates of the inactivation of fecal coliform bacteria, fecal enterococci, F+ coliphage, somatic coliphage, and Ascaris eggs in WSP sludge in central Mexico can be made using first-order rate constants of 0.1, 0.1, 0.01, 0.001, and 0.001d(-1), respectively. From the observed changes in the concentrations of total solids and the volatile to fixed solids ratio, empirical equations were developed to describe anaerobic degradation and compression, which are the two most important processes affecting the volume of sludge after its deposition.

Animals↗

PubMedDate not supplied

Determination of the inactivation rate of Ascaris eggs in wastewater stabilization pond sludge using dialysis chambers and sludge cores.

The inactivation rate of Ascaris eggs was studied in the sludge layer of a primary, facultative wastewater stabilization pond located in Mexico City. Two independent methods, sludge cores and dialysis chambers, were used, to determine the inactivation rates through which a comprehensive picture of the inactivation was gained. The dialysis chambers provided a detailed picture of the initial inactivation (14 months) at one location in the pond, whereas the sludge cores provided less precise information about the inactivation rate at several locations and over the entire lifetime of the pond (10 years). The inactivation curve was characterized by an initial lag phase, a period of roughly first-order inactivation, and a tailing region. During the first year, 50 to 60% of the eggs were inactivated, after which the rate decreased. Although the observed, initial first-order rate constant was greater than 0.002 d(-1), the average, long-term rate constant was closer to 0.001 d(-1).

Animals↗