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Chen X, Zhang C, Guo J, Huang X, Lv R, Quan X. Thermal and Chemical Inactivation of Bacillus Phage BM-P1. J Food Prot 2024; 87:100223. [PMID: 38242288 DOI: 10.1016/j.jfp.2024.100223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Bacillus spp. are often used as probiotics; however, they can be infected by phages, leading to significant economic losses. Biocidal and thermal treatments are considered rapid and effective methods for controlling microbial contamination. To prevent viral contamination in industrial dairy production, the impact of temperature and biocides on the viability of Bacillus methylotrophic phage BM-P1 was assessed. The results demonstrated that reconstituted skim milk (RSM) as a medium showed the most effective protective effect on phage BM-P1. Treatment at 90°C for 5 min or 72°C for 10 min inactivated it to nondetectable levels from the initial titer of 7.19 ± 0.11 log, regardless of the culture medium. Sodium hypochlorite exhibited the best inactivating effect, which could reduce the phage titer below the detection level in 4 min at 50 ppm. Additionally, treatment with 75% ethanol for 20 min or 50% isopropanol for 30 min could achieve inactivation to nondetectable levels. The inactivating effect of peracetic acid was limited; even when treated at the highest concentration (0.45%) for 60 min, only a 2.47 ± 0.17 log reduction was observed. This study may provide some theoretical basis and data support for establishing measures against Bacillus spp. phages.
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Affiliation(s)
- Xia Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China.
| | - Can Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Jing Guo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Xuecheng Huang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Ruirui Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
| | - Xingyu Quan
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, 010018, PR China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, 010018, PR China; Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, 010018, PR China
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Harrison K, Snead D, Kilts A, Ammerman ML, Wigginton KR. The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13757-13766. [PMID: 37656816 PMCID: PMC10516120 DOI: 10.1021/acs.est.3c03814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
Virus concentrations measured in municipal wastewater help inform both the water treatment necessary to protect human health and wastewater-based epidemiology. Wastewater measurements are typically PCR-based, and interpreting gene copy concentrations requires an understanding of the form and stability of the nucleic acids. Here, we study the persistence of model virus genomes in wastewater, the protective effects provided by the virus capsids, and the relative decay rates of the genome and infectious viruses. In benchtop batch experiments in wastewater influent at 25 °C, extraviral (+)ssRNA and dsDNA amplicons degraded by 90% within 15-19 min and 1.6-1.9 h, respectively. When encapsidated, the T90 for MS2 (+)ssRNA increased by 424× and the T90 for T4 dsDNA increased by 52×. The (+)ssRNA decay rates were similar for a range of amplicon sizes. For our model phages MS2 and T4, the nucleic acid signal in untreated wastewater disappeared shortly after the viruses lost infectivity. Combined, these results suggest that most viral genome copies measured in wastewater are encapsidated, that measured concentrations are independent of assay amplicon sizes, and that the virus genome decay rates of nonenveloped (i.e., naked) viruses are similar to inactivation rates. These findings are valuable for the interpretation of wastewater virus measurements.
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Affiliation(s)
- Katherine
R. Harrison
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Delaney Snead
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna Kilts
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Michelle L. Ammerman
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Krista R. Wigginton
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
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Zhu K, Hill C, Muirhead A, Basu M, Brown J, Brinton MA, Hayat MJ, Venegas-Vargas C, Reis MG, Casanovas-Massana A, Meschke JS, Ko AI, Costa F, Stauber CE. Zika virus RNA persistence and recovery in water and wastewater: An approach for Zika virus surveillance in resource-constrained settings. WATER RESEARCH 2023; 241:120116. [PMID: 37270953 PMCID: PMC10330535 DOI: 10.1016/j.watres.2023.120116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
During the 2015-2016 Zika virus (ZIKV) epidemic in the Americas, serological cross-reactivity with other flaviviruses and relatively high costs of nucleic acid testing in the region hindered the capacity for widespread diagnostic testing. In such cases where individual testing is not feasible, wastewater monitoring approaches may offer a means of community-level public health surveillance. To inform such approaches, we characterized the persistence and recovery of ZIKV RNA in experiments where we spiked cultured ZIKV into surface water, wastewater, and a combination of both to examine the potential for detection in open sewers serving communities most affected by the ZIKV outbreak, such as those in Salvador, Bahia, Brazil. We used reverse transcription droplet digital PCR to quantify ZIKV RNA. In our persistence experiments, we found that the persistence of ZIKV RNA decreased with increasing temperature, significantly decreased in surface water versus wastewater, and significantly decreased when the initial concentration of virus was lowered by one order of magnitude. In our recovery experiments, we found higher percent recovery of ZIKV RNA in pellets versus supernatants from the same sample, higher recoveries in pellets using skimmed milk flocculation, lower recoveries of ZIKV RNA in surface water versus wastewater, and lower recoveries from a freeze thaw. We also analyzed samples collected from Salvador, Brazil during the ZIKV outbreak (2015-2016) that consisted of archived samples obtained from open sewers or environmental waters thought to be contaminated by sewage. Although we did not detect any ZIKV RNA in the archived Brazil samples, results from these persistence and recovery experiments serve to inform future wastewater monitoring efforts in open sewers, an understudied and important application of wastewater monitoring.
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Affiliation(s)
- Kevin Zhu
- Department of Civil and Environmental Engineering, College of Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cailee Hill
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA
| | - Aaron Muirhead
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA
| | - Mausumi Basu
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 303034, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margo A Brinton
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 303034, USA
| | - Matthew J Hayat
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA
| | - Cristina Venegas-Vargas
- Department of Large Animal Clinical Sciences, College Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Mitermayer G Reis
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Salvador Bahia, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA
| | - J Scott Meschke
- Department of Environmental and Occupational Health, School of Public Health, University of Washington, Seattle, WA, USA
| | - Albert I Ko
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Salvador Bahia, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA
| | - Federico Costa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Salvador Bahia, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA; Institute of Collective Health, Federal University of Bahia, Canela, Salvador 40110-040, Brazil
| | - Christine E Stauber
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA.
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Sovic MG, Savona F, Bohrerova Z, Faith SA. MixviR: an R Package for Exploring Variation Associated with Genomic Sequence Data from Environmental SARS-CoV-2 and Other Mixed Microbial Samples. Appl Environ Microbiol 2022; 88:e0087422. [PMID: 36286480 PMCID: PMC9680627 DOI: 10.1128/aem.00874-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/19/2022] [Indexed: 11/29/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/coronavirus disease 2019 (COVID-19) pandemic has highlighted an important role for efficient surveillance of microbial pathogens. High-throughput sequencing technologies provide valuable surveillance tools, offering opportunities to conduct high-resolution monitoring from diverse sample types, including from environmental sources. However, given their large size and potential to contain mixtures of lineages within samples, such genomic data sets can present challenges for analyzing the data and communicating results with diverse stakeholders. Here, we report MixviR, an R package for exploring, analyzing, and visualizing genomic data from potentially mixed samples of a target microbial group. MixviR characterizes variation at both the nucleotide and amino acid levels and offers the RShiny interactive dashboard for exploring data. We demonstrate MixviR's utility with validation studies using mixtures of known lineages from both SARS-CoV-2 and Mycobacterium tuberculosis and with a case study analyzing lineages of SARS-CoV-2 in wastewater samples over time at a sampling location in Ohio, USA. IMPORTANCE High-throughput sequencing technologies hold great potential for contributing to genomic-based surveillance of microbial diversity from environmental samples. However, the size of the data sets, along with the potential for environmental samples to contain multiple evolutionary lineages of interest, present challenges around analyzing and effectively communicating inferences from these data sets. The software described here provides a novel and valuable tool for exploring such data. Though originally designed and used for monitoring SARS-CoV-2 lineages in wastewater, it can also be applied to analyses of genomic diversity in other microbial groups.
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Affiliation(s)
- Michael G. Sovic
- Center For Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Francesca Savona
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zuzana Bohrerova
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
- Ohio Water Resources Center, The Ohio State University, Columbus, Ohio, USA
| | - Seth A. Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
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Shaffer M, Huynh K, Costantini V, Bibby K, Vinjé J. Viable Norovirus Persistence in Water Microcosms. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2022; 9:851-855. [PMID: 37179819 PMCID: PMC10174215 DOI: 10.1021/acs.estlett.2c00553] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Human noroviruses are one of the leading causes of acute gastroenteritis worldwide. Based on quantitative microbial risk assessments, norovirus contributes the greatest infectious risk of any pathogen from exposure to sewage-contaminated water; however, these estimates have been based upon molecular (i.e., RNA-based) data as human norovirus has remained largely unculturable in the laboratory. Current approaches to assess the environmental fate of noroviruses rely on the use of culturable surrogate viruses and molecular methods. Human intestinal enteroids (HIEs) are an emerging cell culture system capable of amplifying viable norovirus. Here, we applied the HIE assay to assess both viable norovirus and norovirus RNA persistence in surface, tap, and deionized water microcosms. Viable norovirus decreased to below the detection limit in tap and deionized water microcosms and was measured in a single replicate in the surface water microcosm at study conclusion (28 days). Conversely, the norovirus RNA signal remained constant over the duration of the study, even when viable norovirus was below the limit of detection. Our findings demonstrate the disconnect between current environmental norovirus detection via molecular methods and viability as assessed through the HIE assay. These results imply that molecular norovirus monitoring is not inherently representative of infectious norovirus.
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Affiliation(s)
- Marlee Shaffer
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kimberly Huynh
- Division of Viral Diseases, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Verónica Costantini
- Division of Viral Diseases, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jan Vinjé
- Division of Viral Diseases, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
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