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Dantas CWD, Martins DT, Nogueira WG, Alegria OVC, Ramos RTJ. Tools and methodology to in silico phage discovery in freshwater environments. Front Microbiol 2024; 15:1390726. [PMID: 38881659 PMCID: PMC11176557 DOI: 10.3389/fmicb.2024.1390726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms. Current water treatment methods cannot keep pace with bacterial evolution, which increasingly exhibits a profile of multidrug resistance to antibiotics. Furthermore, using more powerful disinfectants may affect the balance of aquatic ecosystems. Therefore, there is a need to explore sustainable ways to control the spreading of pathogenic bacteria. Bacteriophages can infect bacteria and archaea, hijacking their host machinery to favor their replication. They are widely abundant globally and provide a biological alternative to bacterial treatment with antibiotics. In contrast to common disinfectants and antibiotics, bacteriophages are highly specific, minimizing adverse effects on aquatic microbial communities and offering a lower cost-benefit ratio in production compared to antibiotics. However, due to the difficulty involving cultivating and identifying environmental bacteriophages, alternative approaches using NGS metagenomics in combination with some bioinformatic tools can help identify new bacteriophages that can be useful as an alternative treatment against resistant bacteria. In this review, we discuss advances in exploring the virome of freshwater, as well as current applications of bacteriophages in freshwater treatment, along with current challenges and future perspectives.
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Affiliation(s)
- Carlos Willian Dias Dantas
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - David Tavares Martins
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Oscar Victor Cardenas Alegria
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Simulation and Computational Biology - SIMBIC, High Performance Computing Center - CCAD, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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Suh SH, Lee JS, Kim SH, Vinjé J, Kim SH, Park GW. Evaluation of crAssphages as a potential marker of human viral contamination in environmental water and fresh leafy greens. Front Microbiol 2024; 15:1374568. [PMID: 38618485 PMCID: PMC11010641 DOI: 10.3389/fmicb.2024.1374568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/04/2024] [Indexed: 04/16/2024] Open
Abstract
CrAssphages are human gut bacteriophages with potential use as an indicator of human fecal contamination in water and other environmental systems. We determined the prevalence and abundance of crAssphages in water, food, and fecal samples and compared these estimates with the prevalence of norovirus. Samples were tested using two crAssphage-specific qPCR assays (CPQ056 and TN201-203) and for norovirus using TaqMan realtime RT-PCR. CrAssphage was detected in 40% of human fecal specimens, 61% of irrigation water samples, 58.5% of stream water samples, and 68.5% of fresh leafy greens samples. Interestingly, across all sample categories, crAssphage concentrations were 2-3 log10 higher than norovirus concentrations. The correlation of detection of crAssphage and norovirus was significant for the irrigation water samples (r = 0.74, p = 7.4e-06). Sequences obtained from crAssphage positive samples from human fecal and stream water samples phylogenetically clustered with genotype I crAssphages, whereas sequences derived from irrigation water samples clustered differently from other genotypes. Our data show that crAssphages were prevalent in norovirus-positive water samples and in fresh leafy green samples, there was a strong correlation between the presence of crAssphage and norovirus. CrAssphage genomic copies were consistently higher than norovirus copies in all sample types. Overall, our findings suggest that crAssphages could be used as reliable indicators to monitor fecal-borne virus contamination within the food safety chain.
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Affiliation(s)
- Soo Hwan Suh
- Division of Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si, Republic of Korea
| | - Jeong Su Lee
- Division of Emerging Virus Vector Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si, Republic of Korea
| | - Seung Hwan Kim
- Division of Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si, Republic of Korea
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Soon Han Kim
- Division of Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si, Republic of Korea
| | - Geun Woo Park
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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Lee SY, Yang J, Lee JH. Improvement of crAssphage detection/quantification method and its extensive application for food safety. Front Microbiol 2023; 14:1185788. [PMID: 37256047 PMCID: PMC10225732 DOI: 10.3389/fmicb.2023.1185788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/24/2023] [Indexed: 06/01/2023] Open
Abstract
Water-borne diseases are usually caused by the fecal-oral transmission of human fecal pathogens. Traditionally, coliforms and enterococci are widely used as indicator bacteria, but they do not allow to differentiate between human and animal fecal contamination. Owing to its presence only in the human gut environment, crAssphage has been suggested as an alternative indicator of human fecal contamination to overcome the above challenges. In this study, 139 human and 89 animal fecal samples (e.g., chicken, cow, dog, pig, pigeon, and mouse) were collected. For the rapid detection of human crAssphage in fecal samples, quantitative real-time PCR (qPCR) was performed using five different oligonucleotide primer/probe combinations. These included three previously reported oligonucleotide primer/probe combinations (RQ, CPQ056, and CrAssBP) and two newly developed combinations (ORF00018-targeting CrAssPFL1 and ORF00044-targeting CrAssPFL2). The detection rate (crAssphage-positive rate) in human fecal samples were 23.0, 30.2, 28.8, 20.1, and 30.9%, respectively, suggesting CrAssPFL2 showed the highest detection rate. Furthermore, the lowest copy numbers (436.16 copy numbers) could be detected using the CrAssPFL2 combination. Interestingly, no difference in crAssphage detection rates was found between healthy people and intestinal inflammatory patients. As expected, no crAssphage was detected in any animal fecal samples, indicating its human specificity. Furthermore, qPCR analysis of sewage samples collected from five different sewage treatment plants revealed that they were all contaminated with 105.71 copy numbers/mL of crAssphage on average. The simulation test of crAssphage-contaminated food samples also confirmed that the detection limit was from 107.55 copy numbers of crAssphage in foods. Therefore, the newly developed and optimized qPCR would be useful for the sensitive detection of crAssphage while identifying the source of human fecal contamination.
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Affiliation(s)
- So-Young Lee
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, Republic of Korea
| | - Jihye Yang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ju-Hoon Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
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CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water. mSystems 2023; 8:e0128222. [PMID: 36744944 PMCID: PMC9948693 DOI: 10.1128/msystems.01282-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota, and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. IMPORTANCE Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.
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Nam SJ, Kim DW, Lee SH, Koo OK. Assessment of Microbial Source Tracking Marker and Fecal Indicator Bacteria on Food-Contact Surfaces in School Cafeterias. J Food Prot 2023; 86:100035. [PMID: 36916577 DOI: 10.1016/j.jfp.2022.100035] [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: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022]
Abstract
Food poisoning outbreaks in schools can affect many students, causing physical and psychological damage and time and economic loss. Fecal indicator bacteria (FIB) have been used to monitor the contamination; however, the detection is time-consuming and confirms the contamination from all warm-blooded animals. Microbial source tracking (MST) is a molecular-based detection method that is host specific. This study aimed to evaluate MSTs and FIBs for tracing contamination in the school cafeteria. The average total aerobic count was 0.89 to 3.63 log CFU/100 cm2, and the faucets in the cooking area showed a significantly high aerobic count. The stove valve, faucet, and hand-washer were the most contaminated area, with a concentration of 1.90 to 6.80 log CFU/100 cm2 from the frequent hand contact. Escherichia coli was not detected on any surfaces, and coliform was detected on five surfaces: the sink and faucet in the food preparation area, the faucet in the cooking area, the hand-washer, and the toilet seat in the restroom with 0.33 to 3.64 log CFU/100 cm2. Human-specific crAssphage appeared on a faucet in the food preparation area, while HF183 was not detected. The result indicates that the continuous monitoring of frequent hand-contact areas is recommended to maintain the hygiene condition in the school cafeteria.
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Affiliation(s)
- Su Jin Nam
- Department of Food and Nutrition, Gyeongsang National University, Jinju, Republic of Korea
| | - Dong Woo Kim
- Department of Food and Nutrition, Gyeongsang National University, Jinju, Republic of Korea
| | - Seung Hun Lee
- Department of Food and Nutrition, Gyeongsang National University, Jinju, Republic of Korea
| | - Ok Kyung Koo
- Department of Food and Nutrition, Gyeongsang National University, Jinju, Republic of Korea.
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