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Unverdi A, Erol HB, Kaskatepe B, Babacan O. Characterization of Salmonella phages isolated from poultry coops and its effect with nisin on food bio-control. Food Sci Nutr 2024; 12:2760-2771. [PMID: 38628171 PMCID: PMC11016409 DOI: 10.1002/fsn3.3956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 04/19/2024] Open
Abstract
Salmonella is a bacterium associated with food contaminated by various animals, primarily poultry. Interest and research on bacteriophages are increasing because they can be used as an alternative against increasing antibiotic resistance. In our study, eight Salmonella-specific lytic bacteriophages were isolated from chicken feces. Two of the isolated phages (AUFM_Sc1 and AUFM_Sc3) were chosen for their characterization due to their broader host range. Based on morphological and genomic analysis, AUFM_Sc1 was identified to be close to similar Enterobacteria spp. CC31 (Myoviridae) and AUFM_Sc3 was identified to be close to Salmonella phage vB_Sen_I1 (Demerecviridae (formerly Siphoviridae)). Although these phages have shown promise for use in phage therapy applications for chickens, further studies are needed on their suitability. When a cocktail of these phages (AUFM_Sc1 + AUFM_Sc3) and nisin combination was applied on chicken breast meat, it was determined that it was effective against Salmonella contamination and while a good inhibitory effect was observed on the food, especially during the first 48 h, the effect decreased later, but the bacterial concentration was still low compared to the control group. Therefore, it is considered that the combination of AUFM_Sc1 + AUFM_Sc3 + nisin can be used as a food preservative against Salmonella.
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Affiliation(s)
- Aysegul Unverdi
- Department of Pharmaceutical MicrobiologyAnkara University Faculty of PharmacyAnkaraTurkey
- Graduate School of Health ScienceAnkara UniversityAnkaraTurkey
| | - Hilal Basak Erol
- Department of Pharmaceutical MicrobiologyAnkara University Faculty of PharmacyAnkaraTurkey
| | - Banu Kaskatepe
- Department of Pharmaceutical MicrobiologyAnkara University Faculty of PharmacyAnkaraTurkey
| | - Orkun Babacan
- Department of Veterinary Science, Kepsut Vocational SchoolBalıkesir UniversityKepsut, BalıkesirTurkey
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Gunathilake KMD, Makumi A, Loignon S, Tremblay D, Labrie S, Svitek N, Moineau S. Diversity of Salmonella enterica phages isolated from chicken farms in Kenya. Microbiol Spectr 2024; 12:e0272923. [PMID: 38078723 PMCID: PMC10783031 DOI: 10.1128/spectrum.02729-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Non-typhoidal Salmonella enterica infections are one of the leading causes of diarrhoeal diseases that spread to humans from animal sources such as poultry. Hence, keeping poultry farms free of Salmonella is essential for consumer safety and for a better yield of animal products. However, the emergence of antibiotic resistance due to over usage has sped up the search for alternative biocontrol methods such as the use of bacteriophages. Isolation and characterization of novel bacteriophages are key to adapt phage-based biocontrol applications. Here, we isolated and characterized Salmonella phages from samples collected at chicken farms and slaughterhouses in Kenya. The genomic characterization of these phage isolates revealed that they belong to four ICTV (International Committee on Taxonomy of Viruses) phage genera. All these phages are lytic and possibly suitable for biocontrol applications because no lysogenic genes or virulence factors were found in their genomes. Hence, we recommend further studies on these phages for their applications in Salmonella biocontrol.
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Affiliation(s)
- K. M. Damitha Gunathilake
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec city, Quebec, Canada
| | - Angela Makumi
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Stéphanie Loignon
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec city, Quebec, Canada
| | - Denise Tremblay
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec city, Quebec, Canada
| | | | - Nicholas Svitek
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec city, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec city, Quebec, Canada
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Inbaraj S, Agrawal RK, Thomas P, Chaudhuri P, Chaturvedi VK. Isolation and characterization of vB_SenS_Ib_psk2 bacteriophage against drug-resistant Salmonella enterica serovar Kentucky. Folia Microbiol (Praha) 2023; 68:771-779. [PMID: 37074624 DOI: 10.1007/s12223-023-01052-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
Abstract
Salmonella enterica serovar Kentucky is one of the food-borne zoonotic pathogens which is isolated in high frequency from poultry meat in the recent decades and is known for its multidrug resistance. The current study was aimed to isolate and characterize a bacteriophage against S. enterica serovar Kentucky isolate, 5925, which showed resistance to at least seven antibiotics and to study its efficiency to decontaminate S. Kentucky from chicken skin. The bacteriophage against S. enterica serovar Kentucky was isolated and was named vB_SenS_Ib_psk2 representing the place, source, and host. Electron microscopy revealed that the phage possesses isometric head and contractile tail, indicative of Siphoviridae family. Molecular detection of major capsid protein E gene yielded 511 bp, and NCBI blast analysis revealed that the phage belonged to the genus chivirus. The optimum temperature and pH for phage survival and multiplication were found to be - 20 to 42 °C and 6-10, respectively. One-step growth curve experiment of vB_SenS_Ib_psk2 revealed a latent period of 20 min and burst size of 253 phages/bacterial cell. The host susceptibility studies revealed that 83% of MDR isolates of S. enterica were susceptible to vB_SenS_Ib_psk2. Artificial spiking studies on chicken skin revealed that high multiplicity of infection (MOI) of phages of 106 pfu/mL is required for significant reduction (p ≤ 0.01) of bacterial concentration (0.14 ± 0.04) after 24-h incubation at 8 °C compared to group 1 (2.55 ± 0.89 cfu/mL).
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Affiliation(s)
- Sophia Inbaraj
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
- ICAR-NRC Meat, Hyderabad, Telangana, 500092, India.
| | - Ravi Kant Agrawal
- Food Microbiology Lab, Livestock Products Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
| | - Pallab Chaudhuri
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Uttar Pradesh, Bengaluru, Karnataka, 560024, India
| | - V K Chaturvedi
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India
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Liu Y, Zhao Y, Qian C, Huang Z, Feng L, Chen L, Yao Z, Xu C, Ye J, Zhou T. Study of Combined Effect of Bacteriophage vB3530 and Chlorhexidine on the Inactivation of Pseudomonas aeruginosa. BMC Microbiol 2023; 23:256. [PMID: 37704976 PMCID: PMC10498570 DOI: 10.1186/s12866-023-02976-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Chlorhexidine (CHG) is a disinfectant commonly used in hospitals. However, it has been reported that the excessive use of CHG can cause resistance in bacteria to this agent and even to other clinical antibiotics. Therefore, new methods are needed to alleviate the development of CHG tolerance and reduce its dosage. This study aimed to explore the synergistic effects of CHG in combination with bacteriophage against CHG-tolerant Pseudomonas aeruginosa (P. aeruginosa) and provide ideas for optimizing disinfection strategies in clinical environments as well as for the efficient use of disinfectants. METHODS The CHG-tolerant P. aeruginosa strains were isolated from the First Affiliated Hospital of Wenzhou Medical University in China. The bacteriophage vB3530 was isolated from the sewage inlet of the hospital, and its genome was sequenced. Time-killing curve was used to determine the antibacterial effects of vB3530 and chlorohexidine gluconate (CHG). The phage sensitivity to 16 CHG-tolerant P. aeruginosa strains and PAO1 strain was detected using plaque assay. The emergence rate of resistant bacterial strains was detected to determine the development of phage-resistant and CHG-tolerant strains. Finally, the disinfection effects of the disinfectant and phage combination on the surface of the medical devices were preliminarily evaluated. RESULTS The results showed that (1) CHG combined with bacteriophage vB3530 significantly inhibited the growth of CHG-resistant P. aeruginosa and reduced the bacterial colony forming units (CFUs) after 24 h. (2) The combination of CHG and bacteriophage inhibited the emergence of phage-resistant and CHG-tolerant strains. (3) The combination of CHG and bacteriophage significantly reduced the bacterial load on the surface of medical devices. CONCLUSIONS In this study, the combination of bacteriophage vB3530 and CHG presented a combined inactivation effect to CHG-tolerant P. aeruginosa and reduced the emergence of strains resistant to CHG and phage. This study demonstrated the potential of bacteriophage as adjuvants to traditional disinfectants. The use of bacteriophage in combination with commercial disinfectants might be a promising method for controlling the spread of bacteria in hospitals.
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Affiliation(s)
- Yan Liu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yining Zhao
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Changrui Qian
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325000, Zhejiang Province, China
| | - Zeyu Huang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Luozhu Feng
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lijiang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhuocheng Yao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Chunquan Xu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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Evseev P, Gutnik D, Shneider M, Miroshnikov K. Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of Duplodnaviria Viruses. Biomolecules 2023; 13:biom13010110. [PMID: 36671495 PMCID: PMC9855967 DOI: 10.3390/biom13010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm Duplodnaviria, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified Duplodnaviria families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal Duplodnaviria groups, and problems relating to the taxonomic classification of Duplodnaviria have been discussed.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Daria Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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Jiang J, Lan G, Li J, Yu J, Huang H, Sun Y, Xu C, Liu D, Gong Y, Zhao C. Characterization and genomic analysis of JC01, a novel bacteriophage infecting Cronobacter sakazakii. Arch Virol 2023; 168:1. [PMID: 36527491 PMCID: PMC9759504 DOI: 10.1007/s00705-022-05663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/24/2022] [Indexed: 12/23/2022]
Abstract
The lytic bacteriophage JC01 was isolated using a strain of Cronobacter sakazakii previously isolated from powdered infant formula (PIF). The complete genome sequence of phage JC01 was determined. The double-stranded DNA genome of phage JC01 is composed of 61,736 bp with a G + C content of 58.9%, and it contains 76 putative open reading frames (ORFs) without any tRNA genes. The predicted ORFs were classified into functional groups, including DNA manipulation, transcription, phage packaging, phage structure, host lysis, and hypothetical proteins. Based on overall nucleotide sequence comparisons, calculation of phage intergenomic similarities, and phylogenetic analysis, JC01 appears to be a novel bacteriophage infecting C. sakazakii.
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Affiliation(s)
- Jie Jiang
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Guanda Lan
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Jinghua Li
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Jun Yu
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Honglan Huang
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Yanbo Sun
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Cuiting Xu
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Dandan Liu
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
| | - Yunwei Gong
- Changchun Center for Diseases Control and Prevention, Changchun, People’s Republic of China
| | - Chunyan Zhao
- grid.64924.3d0000 0004 1760 5735Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 130021 Changchun, Jilin People’s Republic of China
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Teklemariam AD, Alharbi MG, Al-Hindi RR, Alotibi I, Aljaddawi AA, Azhari SA, Esmael A. Isolation and Characterization of Chi-like Salmonella Bacteriophages Infecting Two Salmonella enterica Serovars, Typhimurium and Enteritidis. Pathogens 2022; 11. [PMID: 36558814 DOI: 10.3390/pathogens11121480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/01/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Salmonella enterica Serovar Typhimurium and Salmonella enterica Serovar Enteritidis are well-known pathogens that cause foodborne diseases in humans. The emergence of antibiotic-resistant Salmonella serovars has caused serious public health problems worldwide. In this study, two lysogenic phages, STP11 and SEP13, were isolated from a wastewater treatment plant in Jeddah, KSA. Transmission electron microscopic images revealed that both phages are new members of the genus “Chivirus” within the family Siphoviridae. Both STP11 and SEP13 had a lysis time of 90 min with burst sizes of 176 and 170 PFU/cell, respectively. The two phages were thermostable (0 °C ≤ temperature < 70 °C) and pH tolerant at 3 ≤ pH < 11. STP11 showed lytic activity for approximately 42.8% (n = 6), while SEP13 showed against 35.7% (n = 5) of the tested bacterial strains. STP11 and STP13 have linear dsDNA genomes consisting of 58,890 bp and 58,893 bp nucleotide sequences with G + C contents of 57% and 56.5%, respectively. Bioinformatics analysis revealed that the genomes of phages STP11 and SEP13 contained 70 and 71 ORFs, respectively. No gene encoding tRNA was detected in their genome. Of the 70 putative ORFs of phage STP11, 27 (38.6%) were assigned to functional genes and 43 (61.4%) were annotated as hypothetical proteins. Similarly, 29 (40.8%) of the 71 putative ORFs of phage SEP13 were annotated as functional genes, whereas the remaining 42 (59.2%) were assigned as nonfunctional proteins. Phylogenetic analysis of the whole genome sequence demonstrated that the isolated phages are closely related to Chi-like Salmonella viruses.
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Sukjoi C, Buddhasiri S, Tantibhadrasapa A, Kaewsakhorn T, Phothaworn P, Nale JY, Lopez-Garcia AV, AbuOun M, Anjum MF, Malik DJ, Galyov EE, Clokie MRJ, Korbsrisate S, Thiennimitr P. Therapeutic effects of oral administration of lytic Salmonella phages in a mouse model of non-typhoidal salmonellosis. Front Microbiol 2022; 13:955136. [DOI: 10.3389/fmicb.2022.955136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Acute non-typhoidal salmonellosis (NTS) caused by a Gram-negative bacterium Salmonella enterica serovar Typhimurium (S. Tm) is one of the most common bacterial foodborne diseases worldwide. Bacteriophages (phages) can specifically target and lyse their host bacteria, including the multidrug-resistant strains, without collateral damage to other bacteria in the community. However, the therapeutic use of Salmonella phages in vivo is still poorly investigated. Salmonella phages ST-W77 and SE-W109 have previously been shown by our group to be useful for biocontrol properties. Here, we tested whether phages ST-W77 and SE-W109 can reduce Salmonella invasion into cultured human cells and confer a therapeutic benefit for acute NTS in a mammalian host. Human colonocytes, T84 cells, were treated with phages ST-W77, SE-W109, and its combination for 5 min before S. Tm infection. Gentamicin protection assays demonstrated that ST-W77 and SE-W109 significantly reduced S. Tm invasion and inflammatory response in human colonocytes. Next, streptomycin-pretreated mice were orally infected with S. Tm (108 CFU/mouse) and treated with a single or a combination of ST-W77 and SE-W109 (1010 PFU/mouse for 4 days) by oral feeding. Our data showed that phage-treated mice had lower S. Tm numbers and tissue inflammation compared to the untreated mice. Our study also revealed that ST-W77 and SE-W109 persist in the mouse gut lumen, but not in systemic sites. Together, these data suggested that Salmonella phages ST-W77 and SE-W109 could be further developed as an alternative approach for treating an acute NTS in mammalian hosts.
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Pelyuntha W, Sanguankiat A, Kovitvadhi A, Vongkamjan K. Broad lytic spectrum of novel Salmonella phages on ciprofloxacin-resistant Salmonella contaminated in the broiler production chain. Vet World 2022; 15:2039-2045. [PMID: 36313854 PMCID: PMC9615508 DOI: 10.14202/vetworld.2022.2039-2045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Ciprofloxacin (CIP) is recommended for salmonellosis treatment as the drug of choice; however, overuse of this drug can cause drug resistance issues and failure to treat diseases. Phage therapy is an alternative approach for combatting CIP-resistant infection. This study aimed to estimate the prevalence of CIP-resistant Salmonella isolated from the broiler production chain and evaluated the lytic ability of novel Salmonella phages isolated from water samples. Materials and Methods: Samples were obtained from the broiler production chain and used for Salmonella isolation. serovar and CIP resistance of each isolate were characterized through latex agglutination and agar disk diffusion test, respectively. Water samples from different sources were acquired for phage isolation. The lytic activity of novel-isolated phages was also examined. Results: In this study, 51 Salmonella isolates were recovered from the broiler production chain (two commercial farms, one free-range farm, two slaughterhouses, and three stalls from the wet market). Kentucky was the major serovar characterized (16), followed by Typhimurium (9), Agona (5), Corvalis (5), Schwarzengrund (5), Singapore (3), Weltevreden (3), Mbandaka (2), Give (2), and Albany (1). The serovars that exhibited CIP resistance were 14/16 isolates of serovar Kentucky (87.5%) and one isolate of serovar Give (50%), whereas eight other serovars were susceptible to this drug. Overall, the prevalence of CIP-resistant Salmonella recovered from the sources included in this study was 29.4%. This study identified 11 Salmonella phages isolated from wastewater samples derived from broiler farms, wastewater treatment stations, and natural reservoirs. Our phages showed the total percentage of lysis ability ranging from 33.3% to 93.3% against CIP-resistant isolates. However, only one bacterial isolate, namely 210SL, recovered from the food contact surface of a wet market stall and was resistant to all phages. Conclusion: Diverse serovars of Salmonella were recovered in the broiler production chain in this study, while the isolates presenting CIP-resistant Salmonella were as high as 29.4%. Overall, Salmonella phages showed high lysis ability against these CIP-resistant Salmonella isolates, suggesting the potential application of phage-based treatments or biocontrol in the broiler production chain.
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Affiliation(s)
- Wattana Pelyuntha
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Arsooth Sanguankiat
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
| | - Attawit Kovitvadhi
- Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Kitiya Vongkamjan
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
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Gendre J, Ansaldi M, Olivenza DR, Denis Y, Casadesús J, Ginet N. Genetic Mining of Newly Isolated Salmophages for Phage Therapy. Int J Mol Sci 2022; 23:8917. [PMID: 36012174 PMCID: PMC9409062 DOI: 10.3390/ijms23168917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica, a Gram-negative zoonotic bacterium, is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. The main reservoirs are found in poultry farms, but they are also found in wild birds. The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections. Here, we aimed to decipher and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy. We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR. We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database. Finally, we searched for useful functions for phage therapy, such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRISPR proteins. We, thus, were able to genetically characterize nine virulent phages and one temperate phage and identify putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.
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Casjens SR, Davidson AR, Grose JH. The small genome, virulent, non-contractile tailed bacteriophages that infect Enterobacteriales hosts. Virology 2022; 573:151-166. [DOI: 10.1016/j.virol.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
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Esteves NC, Scharf BE. Flagellotropic Bacteriophages: Opportunities and Challenges for Antimicrobial Applications. Int J Mol Sci 2022; 23:7084. [PMID: 35806089 PMCID: PMC9266447 DOI: 10.3390/ijms23137084] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 12/22/2022] Open
Abstract
Bacteriophages (phages) are the most abundant biological entities in the biosphere. As viruses that solely infect bacteria, phages have myriad healthcare and agricultural applications including phage therapy and antibacterial treatments in the foodservice industry. Phage therapy has been explored since the turn of the twentieth century but was no longer prioritized following the invention of antibiotics. As we approach a post-antibiotic society, phage therapy research has experienced a significant resurgence for the use of phages against antibiotic-resistant bacteria, a growing concern in modern medicine. Phages are extraordinarily diverse, as are their host receptor targets. Flagellotropic (flagellum-dependent) phages begin their infection cycle by attaching to the flagellum of their motile host, although the later stages of the infection process of most of these phages remain elusive. Flagella are helical appendages required for swimming and swarming motility and are also of great importance for virulence in many pathogenic bacteria of clinical relevance. Not only is bacterial motility itself frequently important for virulence, as it allows pathogenic bacteria to move toward their host and find nutrients more effectively, but flagella can also serve additional functions including mediating bacterial adhesion to surfaces. Flagella are also a potent antigen recognized by the human immune system. Phages utilizing the flagellum for infections are of particular interest due to the unique evolutionary tradeoff they force upon their hosts: by downregulating or abolishing motility to escape infection by a flagellotropic phage, a pathogenic bacterium would also likely attenuate its virulence. This factor may lead to flagellotropic phages becoming especially potent antibacterial agents. This review outlines past, present, and future research of flagellotropic phages, including their molecular mechanisms of infection and potential future applications.
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13
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Cobbley HK, Evans SI, Brown HMF, Eberhard B, Eberhard N, Kim M, Moe HM, Schaeffer D, Sharma R, Thompson DW, Casjens SR, Grose JH. Complete Genome Sequences of Six Chi-Like Bacteriophages That Infect Proteus and Klebsiella. Microbiol Resour Announc 2022; 11:e0121521. [PMID: 35297681 PMCID: PMC9022528 DOI: 10.1128/mra.01215-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Proteus mirabilis and Klebsiella aerogenes are Gram-negative opportunistic pathogens that are responsible for nosocomial and health care-associated infections, including urinary tract infections. Here, the full genome sequences of six Chi-like Proteus (DanisaurMW, DoubleBarrel, Inception, Jing313, and NotEvenPhaged) or Klebsiella (Phraden) bacteriophages are announced, contributing to the understanding of Chi-like phages.
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Affiliation(s)
- Hunter K Cobbley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Seth I Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hannah M F Brown
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Braden Eberhard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Nathaniel Eberhard
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Minji Kim
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Haley Mickelsen Moe
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel Schaeffer
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Daniel W Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
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14
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Ye J, Guo J, Li T, Tian J, Yu M, Wang X, Majeed U, Song W, Xiao J, Luo Y, Yue T. Phage-based technologies for highly sensitive luminescent detection of foodborne pathogens and microbial toxins: A review. Compr Rev Food Sci Food Saf 2022; 21:1843-1867. [PMID: 35142431 DOI: 10.1111/1541-4337.12908] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023]
Abstract
Foodborne pathogens and microbial toxins are the main causes of foodborne illness. However, trace pathogens and toxins in foods are difficult to detect. Thus, techniques for their rapid and sensitive identification and quantification are urgently needed. Phages can specifically recognize and adhere to certain species of microbes or toxins due to molecular complementation between capsid proteins of phages and receptors on the host cell wall or toxins, and thus they have been successfully developed into a detection platform for pathogens and toxins. This review presents an update on phage-based luminescent detection technologies as well as their working principles and characteristics. Based on phage display techniques of temperate phages, reporter gene detection assays have been designed to sensitively detect trace pathogens by luminous intensity. By the host-specific lytic effects of virulent phages, enzyme-catalyzed chemiluminescent detection technologies for pathogens have been exploited. Notably, these phage-based luminescent detection technologies can discriminate viable versus dead microbes. Further, highly selective and sensitive immune-based assays have been developed to detect trace toxins qualitatively and quantitatively via antibody analogs displayed by phages, such as phage-ELISA (enzyme-linked immunosorbent assay) and phage-IPCR (immuno-polymerase chain reaction). This literature research may lead to novel and innocuous phage-based rapid detection technologies to ensure food safety.
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Affiliation(s)
- Jianming Ye
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jiaqing Guo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Tairan Li
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jiaxin Tian
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Mengxi Yu
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiaochen Wang
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Usman Majeed
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Wei Song
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain
| | - Yane Luo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China.,Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an, Shaanxi, China.,Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, China
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China.,Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an, Shaanxi, China.,Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, China
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15
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Carascal MB, dela Cruz-Papa DM, Remenyi R, Cruz MCB, Destura RV. Phage Revolution Against Multidrug-Resistant Clinical Pathogens in Southeast Asia. Front Microbiol 2022; 13:820572. [PMID: 35154059 PMCID: PMC8830912 DOI: 10.3389/fmicb.2022.820572] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Southeast Asia (SEA) can be considered a hotspot of antimicrobial resistance (AMR) worldwide. As recent surveillance efforts in the region reported the emergence of multidrug-resistant (MDR) pathogens, the pursuit of therapeutic alternatives against AMR becomes a matter of utmost importance. Phage therapy, or the use of bacterial viruses called bacteriophages to kill bacterial pathogens, is among the standout therapeutic prospects. This narrative review highlights the current understanding of phages and strategies for a phage revolution in SEA. We define phage revolution as the radical use of phage therapy in infectious disease treatment against MDR infections, considering the scientific and regulatory standpoints of the region. We present a three-phase strategy to encourage a phage revolution in the SEA clinical setting, which involves: (1) enhancing phage discovery and characterization efforts, (2) creating and implementing laboratory protocols and clinical guidelines for the evaluation of phage activity, and (3) adapting regulatory standards for therapeutic phage formulations. We hope that this review will open avenues for scientific and policy-based discussions on phage therapy in SEA and eventually lead the way to its fullest potential in countering the threat of MDR pathogens in the region and worldwide.
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Affiliation(s)
- Mark B. Carascal
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Donna May dela Cruz-Papa
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
- Research Center for Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Roland Remenyi
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
| | - Mely Cherrylynne B. Cruz
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
| | - Raul V. Destura
- Clinical and Translational Research Institute, The Medical City, Pasig, Philippines
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines
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16
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Zinke M, Schröder GF, Lange A. Major tail proteins of bacteriophages of the order Caudovirales. J Biol Chem 2021; 298:101472. [PMID: 34890646 DOI: 10.1016/j.jbc.2021.101472] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/18/2022] Open
Abstract
Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form or when packed within a crystal lattice. These hollow elongated protein structures, present in most bacteriophages of the order Caudovirales, connect the DNA-containing capsid with a receptor function at the distal end of the tail and consist of helical and polymerized major tail proteins. However, the resolution of cryo-EM data for these systems differs enormously between different tail tube types, partly inhibiting the building of high-fidelity models and barring a combination with further structural biology methods. Here, we review the structural biology efforts within this field and highlight the role of integrative structural biology approaches that have proved successful for some of these systems. Finally, we summarize the structural elements of major tail proteins and conceptualize how different amounts of tail tube flexibility confer heterogeneity within cryo-EM maps and, thus, limit high-resolution reconstructions.
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17
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Shakeri G, Hammerl JA, Jamshidi A, Ghazvini K, Rohde M, Szabo I, Kehrenberg C, Plötz M, Kittler S. The lytic siphophage vB_StyS-LmqsSP1 reduces Salmonella Typhimurium isolates on chicken skin. Appl Environ Microbiol 2021;:AEM0142421. [PMID: 34586906 DOI: 10.1128/AEM.01424-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Phage-based biocontrol of bacteria is considered as a natural approach to combat food-borne pathogens. Salmonella spp. are notifiable and highly prevalent pathogens that cause foodborne diseases globally. In this study, six bacteriophages were isolated and further characterized that infect food-derived Salmonella isolates from different meat sources. The siphovirus VB_StyS-LmqsSP1, which was isolated from a cow´s nasal swab, was further subjected to in-depth characterization. Phage-host interaction investigations in liquid medium showed that vB_StyS-LmqsSP1 can suppress the growth of Salmonella spp. isolates at 37°C for ten hours and reduce the bacterial titer at 4°C significantly. A reduction of 1.4 to 3 log units was observed in investigations with two food-derived Salmonella isolates and one reference strain under cooling conditions using MOIs of 104 and 105. Phage application on chicken skin resulted in a reduction of about 2 log units in the tested Salmonella isolates from the first three hours throughout a one-week experiment at cooling temperature and an MOI of 105. The one-step growth curve analysis using vB_StyS-LmqsSP1 demonstrated a 60-min latent period and a burst size of 50-61 PFU/infected cell for all tested hosts. Furthermore, the genome of the phage was determined to be free from genes causing undesired effects. Based on the phenotypic and genotypic properties, LmqsSP1 was assigned as a promising candidate for biocontrol of Salmonella Typhimurium in food. Importance: Salmonella enterica is one of the major global causes of foodborne enteritis in humans. The use of chemical sanitizers for reducing bacterial pathogens in the food chain can result in the spread of bacterial resistance. Targeted and clean label intervention strategies can reduce Salmonella contamination in food. The significance of our research demonstrates the suitability of a bacteriophage (vB_StyS-LmqsSP1) for biocontrol of Salmonella enterica serovar Typhimurium on poultry due to its lytic efficacy under conditions prevailing in food production environments.
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18
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Pelyuntha W, Ngasaman R, Yingkajorn M, Chukiatsiri K, Benjakul S, Vongkamjan K. Isolation and Characterization of Potential Salmonella Phages Targeting Multidrug-Resistant and Major Serovars of Salmonella Derived From Broiler Production Chain in Thailand. Front Microbiol 2021; 12:662461. [PMID: 34122377 PMCID: PMC8195598 DOI: 10.3389/fmicb.2021.662461] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/09/2021] [Indexed: 12/02/2022] Open
Abstract
Salmonella is a major foodborne pathogen that causes foodborne disease in humans through consumption of contaminated foods, especially those of animal origin. Multiple Salmonella strains are antibiotic-resistant due to the common use of antibiotics in farm animals, including broiler farms. In this study, an alternative strategy using phage-based treatment was evaluated against Salmonella isolated from the broiler production. The prevalence of Salmonella spp. showed up to 46.2 and 44.4% in bedding samples from the broiler farms located in eastern and southern Thailand, respectively. Overall, 21 samples (36.2%) were positive for Salmonella and eight serovars were recovered from cloacal swabs, bedding materials (rice husk), and boot swabs collected from five farms. Up to 20 Salmonella phages were isolated from seven water samples from wastewater treatment ponds, a river, and a natural reservoir in Songkhla province. Isolated phages were investigated, as well as their lysis ability on eight target Salmonella serovars derived from broiler farms, five foodborne outbreak-related serovars, and 10 multidrug-resistant (MDR) serovars. All phages showed a strong lytic ability against five serovars of Salmonella derived from broiler farms including Kentucky, Saintpaul, Schwarzengrund, Corvalis, and Typhimurium; three foodborne outbreak serovars including Enteritidis, Typhimurium, and Virchow; and eight MDR serovars including Agona, Albany, Give, Kentucky, Typhimurium, Schwarzengrund, Singapore, and Weltevreden. Three phages with the highest lysis potential including vB_SenS_WP109, vB_SenS_WP110, and vB_SenP_WP128 were selected for a phage cocktail preparation. Overall, a phage cocktail could reduce Salmonella counts by 2.2–2.8 log units at 6 h of treatment. Moreover, Salmonella did not develop a resistant pattern after being treated with a phage cocktail. Findings here suggest that a phage cocktail is an effective biocontrol to combat Salmonella derived from broiler production chain, other serovars linked to foodborne outbreaks, and MDR serovars.
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Affiliation(s)
- Wattana Pelyuntha
- Faculty of Agro-Industry, Prince of Songkla University, Songkhla, Thailand
| | | | - Mingkwan Yingkajorn
- Division of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Kridda Chukiatsiri
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai, Thailand
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Songkhla, Thailand
| | - Kitiya Vongkamjan
- Faculty of Agro-Industry, Prince of Songkla University, Songkhla, Thailand.,International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Songkhla, Thailand.,Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
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19
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Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M. Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. Microorganisms 2021; 9:microorganisms9050931. [PMID: 33925267 PMCID: PMC8146710 DOI: 10.3390/microorganisms9050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
- Correspondence:
| | - Alejandra Arancibia
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Leonardo Badilla
- Laboratorio de Biología Celular y Ecofisiología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Leopoldo Carvallo 270, Valparaíso 2360001, Chile; (A.A.); (L.B.)
| | - Jonathan Acosta
- Departamento de Estadística, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Gabriela Arancibia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Rodrigo Escar
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Gustavo Ferrada
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay-Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile; (G.A.); (R.E.); (G.F.); (M.S.)
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20
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Hussain W, Ullah MW, Farooq U, Aziz A, Wang S. Bacteriophage-based advanced bacterial detection: Concept, mechanisms, and applications. Biosens Bioelectron 2021; 177:112973. [DOI: 10.1016/j.bios.2021.112973] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022]
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21
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Montemayor EJ, Ploscariu NT, Sanchez JC, Parrell D, Dillard RS, Shebelut CW, Ke Z, Guerrero-Ferreira RC, Wright ER. Flagellar Structures from the Bacterium Caulobacter crescentus and Implications for Phage ϕ CbK Predation of Multiflagellin Bacteria. J Bacteriol 2021; 203:e00399-20. [PMID: 33288623 DOI: 10.1128/JB.00399-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
Caulobacter crescentus is a Gram-negative alphaproteobacterium that commonly lives in oligotrophic fresh- and saltwater environments. C. crescentus is a host to many bacteriophages, including ϕCbK and ϕCbK-like bacteriophages, which require interaction with the bacterial flagellum and pilus complexes during adsorption. It is commonly thought that the six paralogs of the flagellin gene present in C. crescentus are important for bacteriophage evasion. Here, we show that deletion of specific flagellins in C. crescentus can indeed attenuate ϕCbK adsorption efficiency, although no single deletion completely ablates ϕCbK adsorption. Thus, the bacteriophage ϕCbK likely recognizes a common motif among the six known flagellins in C. crescentus with various degrees of efficiency. Interestingly, we observe that most deletion strains still generate flagellar filaments, with the exception of a strain that contains only the most divergent flagellin, FljJ, or a strain that contains only FljN and FljO. To visualize the surface residues that are likely recognized by ϕCbK, we determined two high-resolution structures of the FljK filament, with and without an amino acid substitution that induces straightening of the filament. We observe posttranslational modifications on conserved surface threonine residues of FljK that are likely O-linked glycans. The possibility of interplay between these modifications and ϕCbK adsorption is discussed. We also determined the structure of a filament composed of a heterogeneous mixture of FljK and FljL, the final resolution of which was limited to approximately 4.6 Å. Altogether, this work builds a platform for future investigations of how phage ϕCbK infects C. crescentus at the molecular level.IMPORTANCE Bacterial flagellar filaments serve as an initial attachment point for many bacteriophages to bacteria. Some bacteria harbor numerous flagellin genes and are therefore able to generate flagellar filaments with complex compositions, which is thought to be important for evasion from bacteriophages. This study characterizes the importance of the six flagellin genes in C. crescentus for infection by bacteriophage ϕCbK. We find that filaments containing the FljK flagellin are the preferred substrate for bacteriophage ϕCbK. We also present a high-resolution structure of a flagellar filament containing only the FljK flagellin, which provides a platform for future studies on determining how bacteriophage ϕCbK attaches to flagellar filaments at the molecular level.
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22
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Abstract
Phage biology has been developing for the last hundred years, and the potential of phages as tools and treatments has been known since their early discovery. However, the lack of knowledge of the molecular mechanisms coded in phage genomes hindered the development of the field. With current molecular methods, the last decade has been a resurgence of the field. The Special Issue on “Diversity and Evolution of Phage Genomes” is a great example with its 17 manuscripts published. It covers some of the latest methods to sample and characterize environmental and host associated viromes, considering experimental biases and computational developments. Furthermore, the use of molecular tools coupled with traditional methods has allowed to isolate and characterize viruses from different hosts and environments with such diversity that even a new viral class is being proposed. The viruses described cover all different phage families and lifestyles. However, is not only about diversity; the molecular evolution is studied in a set of manuscripts looking at phage-host interactions and their capacity to uncover the frequency and type of mutations behind the bacterial resistance mechanisms and viral pathogenesis, and such methods are opening new ways into identifying potential receptors and characterizing the bacterial host range.
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23
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Bai J, Lee S, Ryu S. Identification and in vitro Characterization of a Novel Phage Endolysin that Targets Gram-Negative Bacteria. Microorganisms 2020; 8:microorganisms8030447. [PMID: 32245284 PMCID: PMC7143992 DOI: 10.3390/microorganisms8030447] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 12/22/2022] Open
Abstract
Most double-stranded (ds) DNA phages utilize holin proteins to secrete endolysin for host peptidoglycan lysis. In contrast, several holin-independent endolysins with secretion sequences or signal-arrest-release (SAR) sequences are secreted via the Sec pathway. In this study, we characterized a novel lysis protein (M4Lys) encoded by the dsDNA phage BSPM4, whose lysis function is not dependent on either holin or the Sec pathway in vitro. In silico analysis of M4Lys revealed that it contains a putative virion protein domain and an unusual C-terminal transmembrane domain (TMD). Turbidity reduction assays and liquid chromatography-mass spectrometry using purified peptidoglycan showed that the virion protein domain of M4Lys has peptidoglycan lysis activity. In vitro overproduction of M4Lys in Escherichia coli revealed that M4Lys alone caused rapid cell lysis. Treatment of E. coli with a Sec inhibitor did not inhibit the lysis activity of M4Lys, indicating that the Sec pathway is not involved in M4Lys-mediated cell lysis. Truncation of the TMD eliminated the cell lysis phenomenon, while production of the TMD alone did not induce the cell lysis. All these findings demonstrate that M4Lys is a novel endolysin that has a unique mosaic structure distinct from other canonical endolysins and the TMD plays a critical role in M4Lys-mediated in vitro cell lysis.
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Affiliation(s)
- Jaewoo Bai
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea;
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Division of Applied Food System, Major in Food Science & Technology, Seoul Women’s University, Seoul 01797, Korea
| | - Sangmi Lee
- Department of Food and Nutrition, Chungbuk National University, Cheongju, Chungbuk 28644, Korea;
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea;
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
- Correspondence:
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24
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Takahashi TS, Da Cunha V, Krupovic M, Mayer C, Forterre P, Gadelle D. Expanding the type IIB DNA topoisomerase family: identification of new topoisomerase and topoisomerase-like proteins in mobile genetic elements. NAR Genom Bioinform 2019; 2:lqz021. [PMID: 33575570 PMCID: PMC7671362 DOI: 10.1093/nargab/lqz021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/12/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
The control of DNA topology by DNA topoisomerases is essential for virtually all DNA transactions in the cell. These enzymes, present in every organism, exist as several non-homologous families. We previously identified a small group of atypical type IIB topoisomerases, called Topo VIII, mainly encoded by plasmids. Here, taking advantage of the rapid expansion of sequence databases, we identified new putative Topo VIII homologs. Our analyses confirm the exclusivity of the corresponding genes to mobile genetic elements (MGE) and extend their distribution to nine different bacterial phyla and one archaeal superphylum. Notably, we discovered another subfamily of topoisomerases, dubbed ‘Mini-A’, including distant homologs of type IIB topoisomerases and encoded by extrachromosomal and integrated bacterial and archaeal viruses. Interestingly, a short, functionally uncharacterized motif at the C-terminal extremity of type IIB topoisomerases appears sufficient to discriminate between Mini-A, Topo VI and Topo VIII subfamilies. This motif could be a key element for understanding the differences between the three subfamilies. Collectively, this work leads to an updated model for the origin and evolution of the type IIB topoisomerase family and raises questions regarding the role of topoisomerases during replication of MGE in bacteria and archaea.
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Affiliation(s)
- Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Unité de Microbiologie Structurale, Institut Pasteur, CNRS, F-75015 Paris, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, 75015 Paris, France
| | - Claudine Mayer
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, F-75015 Paris, France.,Université de Paris, Paris Diderot, F-75013 Paris, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Institut Pasteur, F-75015 Paris, France
| | - Danièle Gadelle
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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25
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Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L, Song J, Schreiber F, Choudhary J, Clare S, Coulibaly F, Strugnell RA, Dougan G, Lithgow T. The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre. Mol Microbiol 2019; 112:1831-1846. [PMID: 31556164 DOI: 10.1111/mmi.14396] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 11/29/2022]
Abstract
The discovery of a Salmonella-targeting phage from the waterways of the United Kingdom provided an opportunity to address the mechanism by which Chi-like bacteriophage (phage) engages with bacterial flagellae. The long tail fibre seen on Chi-like phages has been proposed to assist the phage particle in docking to a host cell flagellum, but the identity of the protein that generates this fibre was unknown. We present the results from genome sequencing of this phage, YSD1, confirming its close relationship to the original Chi phage and suggesting candidate proteins to form the tail structure. Immunogold labelling in electron micrographs revealed that YSD1_22 forms the main shaft of the tail tube, while YSD1_25 forms the distal part contributing to the tail spike complex. The long curling tail fibre is formed by the protein YSD1_29, and treatment of phage with the antibodies that bind YSD1_29 inhibits phage infection of Salmonella. The host range for YSD1 across Salmonella serovars is broad, but not comprehensive, being limited by antigenic features of the flagellin subunits that make up the Salmonella flagellum, with which YSD1_29 engages to initiate infection.
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Affiliation(s)
- Rhys A Dunstan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Sam Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Claire Cormie
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Joshua Hardy
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Fuyi Li
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Rhys Grinter
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.,School of Biological Sciences, Monash University, Clayton, 3800, Australia
| | | | - Lu Yu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jiangning Song
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | | | - Jyoti Choudhary
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fasseli Coulibaly
- Infection and Immunity Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, 3052, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
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