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Pchelin IM, Smolensky AV, Azarov DV, Goncharov AE. Lytic Spectra of Tailed Bacteriophages: A Systematic Review and Meta-Analysis. Viruses 2024; 16:1879. [PMID: 39772189 PMCID: PMC11680127 DOI: 10.3390/v16121879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 11/25/2024] [Accepted: 12/02/2024] [Indexed: 01/11/2025] Open
Abstract
As natural predators of bacteria, tailed bacteriophages can be used in biocontrol applications, including antimicrobial therapy. Also, phage lysis is a detrimental factor in technological processes based on bacterial growth and metabolism. The spectrum of bacteria bacteriophages interact with is known as the host range. Phage science produced a vast amount of host range data. However, there has been no attempt to analyse these data from the viewpoint of modern phage and bacterial taxonomy. Here, we performed a meta-analysis of spotting and plaquing host range data obtained on strains of production host species. The main metric of our study was the host range value calculated as a ratio of lysed strains to the number of tested bacterial strains. We found no boundary between narrow and broad host ranges in tailed phages taken as a whole. Family-level groups of strictly lytic bacteriophages had significantly different median plaquing host range values in the range from 0.18 (Drexlerviridae) to 0.70 (Herelleviridae). In Escherichia coli phages, broad host ranges were associated with decreased efficiency of plating. Bacteriophage morphology, genome size, and the number of tRNA-coding genes in phage genomes did not correlate with host range values. From the perspective of bacterial species, median plaquing host ranges varied from 0.04 in bacteriophages infecting Acinetobacter baumannii to 0.73 in Staphylococcus aureus phages. Taken together, our results imply that taxonomy of bacteriophages and their bacterial hosts can be predictive of intraspecies host ranges.
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Affiliation(s)
- Ivan M. Pchelin
- Department of Molecular Microbiology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia; (D.V.A.); (A.E.G.)
| | - Andrei V. Smolensky
- Department of Computer Science, Neapolis University Pafos, Paphos 8042, Cyprus;
| | - Daniil V. Azarov
- Department of Molecular Microbiology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia; (D.V.A.); (A.E.G.)
| | - Artemiy E. Goncharov
- Department of Molecular Microbiology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia; (D.V.A.); (A.E.G.)
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Padmesh S, Singh A, Chopra S, Sen M, Habib S, Shrivastava D, Johri P. Isolation and characterization of novel lytic bacteriophages that infect multi drug resistant clinical strains of Escherichia coli. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:57327-57337. [PMID: 37347328 DOI: 10.1007/s11356-023-28081-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023]
Abstract
The pathogenic strains of Escherichia coli (E. coli) are frequent cause of urinary tract infections including catheter-associated, soft tissue infections and sepsis. The growing antibiotic resistance in E. coli is a major health concern. Bacteriophages are specific for their bacterial host, thus providing a novel and effective alternatives. This study focuses on isolation of bacteriophages from urban sewage treatment plants. Initially 50 different bacteriophages have been isolated against non-resistant reference E. coli strain and fifty multidrug resistant clinical isolates of extraintestinal infections. Out of which only thirty-one lytic phages which gave clear plaques were further analysed for different physico-chemical aspects such as thermal inactivation, pH, effect of organic solvents and detergents. Two bacteriophages, ASEC2201 and ASEC2202, were selected for their ability to withstand temperature fluctuation from -20 to 62 °C and a pH range from 4 to 10. They also showed good survival (40-94%) in the presence of organic solvents like ethanol, acetone, DMSO and chloroform or ability to form plaques even after the treatment with detergents like SDS, CTAB and sarkosyl. Both efficiently killed reference strain and 40-44% of multidrug resistant clinical isolates of E. coli. Later ASEC2201 and ASEC2202 were subjected to morphological characterisation through transmission electron microscopy, which revealed them to be tailed phages. The genomic analysis confirmed them to be Escherichia phages which belonged to family Drexlerviridae of Caudovirales.
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Affiliation(s)
- Sudhakar Padmesh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomti Nagar Extension, Lucknow, 226028, India
| | - Aditi Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomti Nagar Extension, Lucknow, 226028, India.
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manodeep Sen
- Department of Microbiology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, 226010, India
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepti Shrivastava
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Parul Johri
- Department of Biotechnology, Dr. Ambedkar Institute of Technology for Handicapped, Kanpur, 208024, India
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Sukwa N, Bosomprah S, Somwe P, Muyoyeta M, Mwape K, Chibesa K, Luchen CC, Silwamba S, Mulenga B, Munyinda M, Muzazu S, Chirwa M, Chibuye M, Simuyandi M, Chilengi R, Svennerholm AM. The Incidence and Risk Factors for Enterotoxigenic E. coli Diarrheal Disease in Children under Three Years Old in Lusaka, Zambia. Microorganisms 2024; 12:698. [PMID: 38674642 PMCID: PMC11051722 DOI: 10.3390/microorganisms12040698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 04/28/2024] Open
Abstract
This study aimed to estimate the incidence and risk factors for Enterotoxigenic Escherichia coli (ETEC) diarrhea. This was a prospective cohort study of children recruited in a household census. Children were enrolled if they were 36 months or below. A total of 6828 children were followed up passively for 12 months to detect episodes of ETEC diarrhea. Diarrheal stool samples were tested for ETEC using colony polymerase chain reaction (cPCR). Among the 6828 eligible children enrolled, a total of 1110 presented with at least one episode of diarrhea. The overall incidence of ETEC diarrhea was estimated as 2.47 (95% confidence interval (CI): 2.10-2.92) episodes per 100 child years. Children who were HIV-positive (adjusted Hazard ratio (aHR) = 2.14, 95% CI: 1.14 to 3.99; p = 0.017) and those whose source of drinking water was public tap/borehole/well (aHR = 2.45, 95% CI: 1.48 to 4.06; p < 0.002) were at increased risk of ETEC diarrhea. This study found that children whose mothers have at least senior secondary school education (aHR = 0.49, 95% CI: 0.29 to 0.83; p = 0.008) were at decreased risk of ETEC diarrhea. Our study emphasizes the need for integrated public health strategies focusing on water supply improvement, healthcare for persons living with HIV, and maternal education.
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Affiliation(s)
- Nsofwa Sukwa
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Samuel Bosomprah
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
- Department of Biostatistics, School of Public Health, University of Ghana, Accra P.O. Box LG13, Ghana
| | - Paul Somwe
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Monde Muyoyeta
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Kapambwe Mwape
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Kennedy Chibesa
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Charlie Chaluma Luchen
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Suwilanji Silwamba
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Bavin Mulenga
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Masiliso Munyinda
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Seke Muzazu
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Masuzyo Chirwa
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Mwelwa Chibuye
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Michelo Simuyandi
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Roma Chilengi
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka P.O. Box 34681, Zambia; (N.S.); (P.S.); (M.M.); (K.M.); (K.C.); (C.C.L.); (S.S.); (B.M.); (M.M.); (S.M.); (M.C.); (M.C.); (M.S.); (R.C.)
| | - Ann-Mari Svennerholm
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden;
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A New Kayfunavirus-like Escherichia Phage vB_EcoP-Ro45lw with Antimicrobial Potential of Shiga Toxin-Producing Escherichia coli O45 Strain. Microorganisms 2022; 11:microorganisms11010077. [PMID: 36677369 PMCID: PMC9866566 DOI: 10.3390/microorganisms11010077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Lytic bacteriophages are re-considered as a solution to resolve antibiotic-resistant rampage. Despite frequent foodborne outbreaks caused by the top six non-O157 Shiga-toxin-producing Escherichia coli (STEC), the current interventions are not sufficiently effective against each serogroup, particularly O45. Therefore, this study aimed to characterize a new short-tailed phage, vB_EcoP-Ro45lw (or Ro45lw), as an alternative antimicrobial agent for STEC O45 strains. Phage Ro45lw belongs to the Kayfunavirus genus within the Autographiviridae family and shares no close evolutionary relationship with any reference phages. Ro45lw contains a tail structure composed of a unique tail fiber and tail tubular proteins A and B, likely to produce enzymatic activity against the target bacterial cells besides structural function. Additionally, the phage genome does not contain virulent, antibiotic-resistant, or lysogenic genes. The phage has a latent period of 15 min with an estimated burst size of 55 PFU/CFU and is stable at a wide range of pH (pH4 to pH11) and temperatures (30 °C to 60 °C). Regardless of the MOIs (MOI = 0.1, 1, and 10) used, Ro45lw has a strong antimicrobial activity against both environmental (E. coli O45:H-) and clinical (E. coli O45:H2) strains at 25 °C. These findings indicate that phage Ro45lw has antimicrobial potential in mitigating pathogenic STEC O45 strains.
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Alexyuk P, Bogoyavlenskiy A, Alexyuk M, Akanova K, Moldakhanov Y, Berezin V. Isolation and Characterization of Lytic Bacteriophages Active against Clinical Strains of E. coli and Development of a Phage Antimicrobial Cocktail. Viruses 2022; 14:v14112381. [PMID: 36366479 PMCID: PMC9697832 DOI: 10.3390/v14112381] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 01/31/2023] Open
Abstract
Pathogenic E. coli cause urinary tract, soft tissue and central nervous system infections, sepsis, etc. Lytic bacteriophages can be used to combat such infections. We investigated six lytic E. coli bacteriophages isolated from wastewater. Transmission electron microscopy and whole genome sequencing showed that the isolated bacteriophages are tailed phages of the Caudoviricetes class. One-step growth curves revealed that their latent period of reproduction is 20-30 min, and the average value of the burst size is 117-155. During co-cultivation with various E. coli strains, the phages completely suppressed bacterial host culture growth within the first 4 h at MOIs 10-7 to 10-3. The host range lysed by each bacteriophage varied from six to two bacterial strains out of nine used in the study. The cocktail formed from the isolated bacteriophages possessed the ability to completely suppress the growth of all the E. coli strains used in the study within 6 h and maintain its lytic activity for 8 months of storage. All the isolated bacteriophages may be useful in fighting pathogenic E. coli strains and in the development of phage cocktails with a long storage period and high efficiency in the treatment of bacterial infections.
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Xi M, Yao Q, Ge W, Chen Y, Cao B, Wang Z, Cui X, Sun Q. Effects of stachyose on intestinal microbiota and immunity in mice infected with enterotoxigenic Escherichia coli. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Chakraborty S, von Mentzer A, Begum YA, Manzur M, Hasan M, Ghosh AN, Hossain MA, Camilli A, Qadri F. Correction: Phenotypic and genomic analyses of bacteriophages targeting environmental and clinical CS3-expressing enterotoxigenic Escherichia coli (ETEC) strains. PLoS One 2019; 14:e0213612. [PMID: 30835765 PMCID: PMC6400374 DOI: 10.1371/journal.pone.0213612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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