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Wandro S, Oliver A, Gallagher T, Weihe C, England W, Martiny JBH, Whiteson K. Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1. Front Microbiol 2019; 9:3192. [PMID: 30766528 PMCID: PMC6365445 DOI: 10.3389/fmicb.2018.03192] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/10/2018] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are highly abundant in human microbiota where they coevolve with resident bacteria. Phage predation can drive the evolution of bacterial resistance, which can then drive reciprocal evolution in the phage to overcome that resistance. Such coevolutionary dynamics have not been extensively studied in human gut bacteria, and are of particular interest for both understanding and eventually manipulating the human gut microbiome. We performed experimental evolution of an Enterococcus faecium isolate from healthy human stool in the absence and presence of a single infecting Myoviridae bacteriophage, EfV12-phi1. Four replicates of E. faecium and phage were grown with twice daily serial transfers for 8 days. Genome sequencing revealed that E. faecium evolved resistance to phage through mutations in the yqwD2 gene involved in exopolysaccharide biogenesis and export, and the rpoC gene which encodes the RNA polymerase β’ subunit. In response to bacterial resistance, phage EfV12-phi1 evolved varying numbers of 1.8 kb tandem duplications within a putative tail fiber gene. Host range assays indicated that coevolution of this phage-host pair resulted in arms race dynamics in which bacterial resistance and phage infectivity increased over time. Tracking mutations from population sequencing of experimental coevolution can quickly illuminate phage entry points along with resistance strategies in both phage and host – critical information for using phage to manipulate microbial communities.
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Affiliation(s)
- Stephen Wandro
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Andrew Oliver
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Tara Gallagher
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Whitney England
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
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Enterococcus faecalis Countermeasures Defeat a Virulent Picovirinae Bacteriophage. Viruses 2019; 11:v11010048. [PMID: 30634666 PMCID: PMC6356687 DOI: 10.3390/v11010048] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 12/29/2018] [Accepted: 12/31/2018] [Indexed: 12/23/2022] Open
Abstract
Enterococcus faecalis is an opportunistic pathogen that has emerged as a major cause of nosocomial infections worldwide. Many clinical strains are indeed resistant to last resort antibiotics and there is consequently a reawakening of interest in exploiting virulent phages to combat them. However, little is still known about phage receptors and phage resistance mechanisms in enterococci. We made use of a prophageless derivative of the well-known clinical strain E. faecalis V583 to isolate a virulent phage belonging to the Picovirinae subfamily and to the P68 genus that we named Idefix. Interestingly, most isolates of E. faecalis tested—including V583—were resistant to this phage and we investigated more deeply into phage resistance mechanisms. We found that E. faecalis V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abiα. It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis of infected E. faecalis. The abiα gene is widespread among prophages of enterococci and other Gram-positive bacteria. Furthermore, we identified two genes involved in the synthesis of the side chains of the surface rhamnopolysaccharide that are important for Idefix adsorption. Interestingly, mutants in these genes arose at a frequency of ~10−4 resistant mutants per generation, conferring a supplemental bacterial line of defense against Idefix.
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Møller-Olsen C, Ho SFS, Shukla RD, Feher T, Sagona AP. Engineered K1F bacteriophages kill intracellular Escherichia coli K1 in human epithelial cells. Sci Rep 2018; 8:17559. [PMID: 30510202 PMCID: PMC6277420 DOI: 10.1038/s41598-018-35859-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/09/2018] [Indexed: 01/13/2023] Open
Abstract
Bacterial infections can be treated with bacteriophages that show great specificity towards their bacterial host and can be genetically modified for different applications. However, whether and how bacteriophages can kill intracellular bacteria in human cells remains elusive. Here, using CRISPR/Cas selection, we have engineered a fluorescent bacteriophage specific for E. coli K1, a nosocomial pathogen responsible for urinary tract infections, neonatal meningitis and sepsis. By confocal and live microscopy, we show that engineered bacteriophages K1F-GFP and E. coli EV36-RFP bacteria displaying the K1 capsule, enter human cells via phagocytosis. Importantly, we show that bacteriophage K1F-GFP efficiently kills intracellular E. coli EV36-RFP in T24 human urinary bladder epithelial cells. Finally, we provide evidence that bacteria and bacteriophages are degraded by LC3-associated phagocytosis and xenophagy.
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Affiliation(s)
| | - Siu Fung Stanley Ho
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
| | - Ranti Dev Shukla
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamas Feher
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
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54
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Kim S, Kim SH, Rahman M, Kim J. Characterization of a Salmonella Enteritidis bacteriophage showing broad lytic activity against Gram-negative enteric bacteria. J Microbiol 2018; 56:917-925. [PMID: 30361974 DOI: 10.1007/s12275-018-8310-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 01/03/2023]
Abstract
In this study, we sought to isolate Salmonella Enteritidis-specific lytic bacteriophages (phages), and we found a lytic phage that could lyse not only S. Enteritidis but also other Gramnegative foodborne pathogens. This lytic phage, SS3e, could lyse almost all tested Salmonella enterica serovars as well as other enteric pathogenic bacteria including Escherichia coli, Shigella sonnei, Enterobacter cloacae, and Serratia marcescens. This SS3e phage has an icosahedral head and a long tail, indicating belong to the Siphoviridae. The genome was 40,793 base pairs, containing 58 theoretically determined open reading frames (ORFs). Among the 58 ORFs, ORF49, and ORF25 showed high sequence similarity with tail spike protein and lysozyme-like protein of Salmonella phage SE2, respectively, which are critical proteins recognizing and lysing host bacteria. Unlike SE2 phage whose host restricted to Salmonella enterica serovars Enteritidis and Gallinarum, SS3e showed broader host specificity against Gram-negative enteric bacteria; thus, it could be a promising candidate for the phage utilization against various Gram-negative bacterial infection including foodborne pathogens.
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Affiliation(s)
- Shukho Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Sung-Hun Kim
- CJ CheilJedang Research Institute of Biotechnology, Suwon, 16495, Republic of Korea
| | - Marzia Rahman
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea.,Present address: Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea.
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Potential Application of Bacteriophages in Enrichment Culture for Improved Prenatal Streptococcus agalactiae Screening. Viruses 2018; 10:v10100552. [PMID: 30308933 PMCID: PMC6213948 DOI: 10.3390/v10100552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/24/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
Abstract
Vertical transmission of Streptococcus agalactiae can cause neonatal infections. A culture test in the late stage of pregnancy is used to screen for the presence of maternal S. agalactiae for intrapartum antibiotic prophylaxis. For the test, a vaginal–rectal sample is recommended to be enriched, followed by bacterial identification. In some cases, Enterococcus faecalis overgrows in the enrichment culture. Consequently, the identification test yields false-negative results. Bacteriophages (phages) can be used as antimicrobial materials. Here, we explored the feasibility of using phages to minimize false-negative results in an experimental setting. Phage mixture was prepared using three phages that specifically infect E. faecalis: phiEF24C, phiEF17H, and phiM1EF22. The mixture inhibited the growth of 86.7% (26/30) of vaginal E. faecalis strains. The simple coculture of E. faecalis and S. agalactiae was used as an experimental enrichment model. Phage mixture treatment led to suppression of E. faecalis growth and facilitation of S. agalactiae growth. In addition, testing several sets of S. agalactiae and E. faecalis strains, the treatment with phage mixture in the enrichment improved S. agalactiae detection on chromogenic agar. Our results suggest that the phage mixture can be usefully employed in the S. agalactiae culture test to increase test accuracy.
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Gelman D, Beyth S, Lerer V, Adler K, Poradosu-Cohen R, Coppenhagen-Glazer S, Hazan R. Combined bacteriophages and antibiotics as an efficient therapy against VRE Enterococcus faecalis in a mouse model. Res Microbiol 2018; 169:531-539. [PMID: 29777835 DOI: 10.1016/j.resmic.2018.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/17/2018] [Indexed: 10/16/2022]
Abstract
Clinical applications of bacteriophage therapy have been recently gathering significant attention worldwide, used mostly as rescue therapy in cases of near-fatal antibiotic failure. Thus, clinically relevant in-vivo models presenting both short- and long-term implications of phage therapy given as rescue treatment for fulminant infections are of highest importance. In this study, a cocktail consisting of two lytic bacteriophages was used to evaluate the therapeutic efficacy of phage therapy as a rescue treatment for severe septic peritonitis in a mouse model. We established that a single injection of the bacteriophage cocktail was sufficient to completely reverse a 100% mortality trend caused by Vancomycin-Resistant Enterococcus faecalis, with significant improvement in both the clinical state and laboratory test results, and without harmful effects on the microbiome. The combination of bacteriophages with a suboptimal antibiotic regimen imparts an additional beneficial effect on the treatment success.
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Affiliation(s)
- Daniel Gelman
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Hadassah Campus, P.O.B 12272, Jerusalem, 91120, Israel; The Military Track of Medicine, Faculty of Medicine, The Hebrew University - Hadassah School of Medicine, Hadassah Campus, P.O.B 12272, Jerusalem, 91120, Israel.
| | - Shaul Beyth
- Orthopedic Surgery Department, Hadassah Medical Center, Hadassah University Hospital, P.O.B 12000, Jerusalem, 91120, Israel.
| | - Vanda Lerer
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Hadassah Campus, P.O.B 12272, Jerusalem, 91120, Israel.
| | - Karen Adler
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Hadassah Campus, P.O.B 12272, Jerusalem, 91120, Israel.
| | - Ronit Poradosu-Cohen
- Department of Infectious Diseases of Sourasky Medical Center and Tel-Aviv University, Tel-Aviv, Israel.
| | - Shunit Coppenhagen-Glazer
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Hadassah Campus, P.O.B 12272, Jerusalem, 91120, Israel.
| | - Ronen Hazan
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Hadassah Campus, P.O.B 12272, Jerusalem, 91120, Israel.
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