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Bibby, K.

Publications and source records attributed to Bibby, K..

8 recordsLinked to original sources

Drainage water management reduces nutrient, Escherichia coli, and antibiotic resistance gene export

Subsurface tile drainage rapidly transports nutrients and biological contaminants to surface waters, yet multi-year evaluations of drainage water management (DWM) effects on nutrients, Escherichia coli, and antibiotic resistance genes (ARGs) remain limited. A paired-field design with high-frequency soil moisture monitoring was used to quantify water yield, dissolved nitrogen, phosphorus, and Escherichia coli (E. coli) over seven and eight water years, and ARGs (tetM, tetW, ermB, sul1) over two years in southern Michigan. Soil moisture at tile depth (~75 cm) was higher under controlled drainage, confirming that DWM increases field water-holding capacity. Compared to the free drainage field, DWM reduced cumulative tile discharge by 43% and annual nutrient yields by 46-83% for nitrate and 12-82% for soluble reactive phosphorus, but effects on ammonium were variable. Average daily nutrient yields declined by ~50% over the study period, driven primarily by managed periods. Nutrient concentrations did not differ between treatments, indicating that yield reductions resulted from decreased water loss. Mean daily E. coli yields declined by 71% over the study period, and concentrations were 46% lower under controlled drainage. Controlled drainage reduced tetM and sul1 ARG concentrations and yields during managed periods and throughout the study; however, sensitivity analyses showed that these effects were strongly influenced by a high-precipitation event. After excluding the event, differences in ARG concentrations were no longer detected, although ARG yields remained 43% lower during managed periods. These findings highlight the potential for DWM to mitigate nutrient, microbial, and antibiotic resistance transport from agricultural drainage systems.

ecology↗

Environmental stability of HPAIV H5N1 in raw milk, wastewater and on surfaces

H5N1 influenza outbreaks in dairy cows necessitate studying potential transmission routes among livestock and to humans. We measured the stability of infectious H5N1 influenza virus in raw milk, wastewater, and on contaminated surfaces. We found relatively slow decay in milk, indicating that contaminated milk and fomites pose plausible transmission risks.

microbiology↗

Heat Inactivation of Aqueous Viable Norovirus and MS2 Bacteriophage

Human norovirus is a leading cause of acute gastroenteritis often associated with contaminated food or water exposure. Many studies have used morphologically similar viruses, such as MS2 bacteriophage, and molecular detection methods to study the environmental fate and inactivation characteristics, given the historical challenges to culture human norovirus. In this study, we used human intestinal enteroids (HIEs) to analyze the heat inactivation kinetics of viable human norovirus compared to the surrogate MS2 bacteriophage. Norovirus decay rates were 0.22 min-1, 0.68 min-1, and 1.11 min-1 for 50{degrees}C, 60{degrees}C, and 70{degrees}C, respectively, and MS2 bacteriophage decay rates were 0.0065 min-1, 0.045 min-1, and 0.16 min-1 for 50{degrees}C, 60{degrees}C, and 70{degrees}C, respectively. Norovirus and MS2 bacteriophage had significantly different decay rates at all tested temperatures (p = 0.002 - 0.007). No decrease of RNA titers as measured by realtime RT-PCR for both human norovirus and MS2 bacteriophage over time was observed, indicating molecular methods do not accurately depict viable human norovirus after heat inactivation. Overall, our data demonstrate that MS2 bacteriophage is a conservative surrogate to measure heat inactivation and potentially overestimates the infectious risk of norovirus. IMPORTANCENorovirus is the leading cause of epidemic and endemic acute gastroenteritis worldwide. Treatments to inactivate norovirus are critical to reducing the risk associated with contaminated food and water. The recent developments to replicate human norovirus in human intestinal enteroids (HIE) enables the evaluation of heat inactivation kinetics of viable norovirus. Historically, cultivable surrogate viruses, such as bacteriophage MS2, have been used to measure the environmental fate of human norovirus. Our findings indicate that compared to human norovirus, MS2 bacteriophage is a conservative surrogate to measure the effect of heat inactivation. Furthermore, this study corroborates that measuring viral RNA titers, as evaluated by PCR methods, does not correlate with persistence of viable norovirus.

microbiology↗

Environmental Persistence and Disinfection of Lassa Virus

Lassa Fever, caused by Lassa virus (LASV), is endemic to West Africa, where approximately 300,000 illnesses and 5,000 deaths occur annually. LASV is primarily spread by infected multimammate rats via urine and fomites, highlighting the importance of understanding the environmental fate of LASV. This study evaluated the persistence of LASV strains on surfaces in aqueous solutions and with sodium hypochlorite disinfection. LASV strains (Josiah and Sauerwald) were more stable in DI water (k = 0.23 and 0.34 days-1) than primary influent wastewater (k = 1.3 and 1.9 days-1). The decay rates of LASV on HDPE (k = 4.3 and 2.3 days-1) and Stainless Steel (k = 5.3 and 2.7 days-1) were not significantly different for either strain. Sodium hypochlorite was highly effective at inactivating both strains of LASV. This work presents data for the environmental persistence of LASV to inform future risk assessment and management efforts.

microbiology↗

Stability of mpox (monkeypox) virus in bodily fluids and wastewater

ImportanceSince May 2022, human monkeypox (mpox) infections have spread rapidly outside endemic countries. On July 23, 2023, WHO declared a Public Health Emergency of international Concern because of the unprecedented global spread of mpox. Whereas there is an incomplete understanding of transmission routes, the spread of monkeypox virus (MPXV) through sexual contact networks of men who have sex with men (MSM) highlights the potential of transmission during sexual activity, either via bodily fluids or via direct contact. This research assesses the potential for MPXV to remain infectious in the environment on surfaces and in fluids under different environmental conditions. ObjectiveTo investigate the stability of MPXV on various surfaces, at different environmental conditions and in different bodily fluids (human blood, semen, serum, saliva, urine, and feces), and to assess decontamination of MPXV-contaminated wastewater via chlorination. Design, Setting, and ExposuresAll experiments involving viable MPXV were performed at the Rocky Mountains Laboratory under high containment conditions using MPXV strain hMPXV/USA/MA001. Infectious MPXV was quantified via plaque assay. Environmental decay rates were estimated using a Bayesian statistical model, with a Poisson likelihood for plaque counts. ResultsMPXV showed surface dependent stability, with faster decay at higher temperatures. Decay rates varied considerably depending on the medium in which virus was suspended, both overall MPXV displayed considerable environmental stability in bodily fluids and in particular proteinaceous fluids, such as blood and semen, lead to greater persistence. Wastewater chlorination was an effective decontamination technique. Conclusions and RelevanceMPXV retains its infectivity in the environment when it is deposited in blood, semen, and serum; environmental decay is more rapid in less proteinaceous fluids, particularly once residual liquid has evaporated. The observed persistence of MPXV implies environmental contamination in healthcare setting, could serve as vehicles of transmission and dissemination in these environments. Chlorination was effective in decontamination of wastewater. Key findings and public health implications; these results suggest that MPXV can have prolonged stability in the environment and are therefore directly relevant for hospital hygiene practices to prevent nosocomial transmission.

microbiology↗

Viability of MS2 and Phi6 Bacteriophages on Carpet and Dust

Respiratory viral illnesses are commonly spread in the indoor environment through multiple transmission routes, including droplets, aerosols, and direct/indirect contact. Indoors, resuspension of dust from flooring is a major source of human exposure. However, it is critical to determine viral persistence on dust and flooring to better characterize human exposure. The goal of this work is to determine viral viability on two carpet types (cut and looped) and house dust over time and after four different cleaning methods. MS2 and Phi6 bacteriophages were used to represent non-enveloped and enveloped viruses, respectively. These viral surrogates were placed in an artificial saliva solution and nebulized onto carpet or dust. Viability was measured at various time points (0, 1, 2, 3, 4, 24, and 48 hours) and after cleaning (vacuuming, hot water extraction with stain remover, steam, and a disinfection spray). Viability decay was modeled as first-order. MS2 bacteriophages showed slower viability decay rates in dust (-0.11 hr-1), cut carpet (-0.20 hr-1), and looped carpet (-0.09 hr-1) compared to Phi6 (-3.36 hr-1, -1.57 hr-1, and - 0.20 hr-1 respectively). The difference between phages was statistically significant in dust and cut carpet (p<0.05). Viral RNA demonstrated minimal degradation that in most cases was not statistically different from zero over the 48 hours measured (p>0.05). Viable viral concentrations were reduced to below the detection limit for steam and disinfection for both MS2 and Phi6 (p<0.05), while vacuuming and hot water extraction with stain remover showed no significant changes in concentration from uncleaned carpet (p>0.05). This study used viral surrogates and did not model risk of viral transmission via dust. Overall, these results demonstrate that MS2 and Phi6 bacteriophages can remain viable in carpet and dust for several hours to days, and cleaning techniques with heat and disinfectants may be more effective than standard vacuuming for viral removal. Future work should model risk from exposure via dust and flooring for various viruses such as influenza, SARS-CoV-2, and RSV. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/444479v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1cc0ad9org.highwire.dtl.DTLVardef@dc440corg.highwire.dtl.DTLVardef@f787dcorg.highwire.dtl.DTLVardef@f8bda3_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the worlds countries, and showed that its phylogeography is locally clustered within countries, cities, and individuals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.

microbiology↗

Evaluation of Oxford Nanopore MinION Sequencing for 16S rRNA Microbiome Characterization

In this manuscript we evaluate the potential for microbiome characterization by sequencing of near-full length 16S rRNA gene region fragments using the Oxford Nanopore MinION (hereafter Nanopore) sequencing platform. We analyzed pure-culture E. coli and P. fluorescens, as well as a low-diversity mixed community sample from hydraulic fracturing produced water. Both closed and open reference operational taxonomic unit (OTU) picking failed, necessitating the direct use of sequences without OTU picking. The Ribosomal Database Project classifier against the Green Genes database was found to be the optimal annotation approach, with average pure-culture annotation accuracies of 93.8% and 82.0% at the phyla and genus levels, respectively. Comparative analysis of an environmental sample using Nanopore and Illumina MiSeq sequencing identified high taxonomic similarity when using a weighted metric (Bray-Curtis), and significantly reduced similarity when using an unweighted metric (Jaccard). These results highlight the great potential of Nanopore sequencing to analyze broad microbial community trends, and the challenge of applying Nanopore sequencing to discern rare taxa in mixed microbial communities. Finally, we observed that between-run carryover following washes on the same flowcell accounted for >10% of sequence reads, necessitating future development to either prevent carryover or filter sequences of interest (e.g. barcoding).

microbiology↗