Source: TEXAS A&M UNIVERSITY submitted to
BACTERIOPHAGE BIOLOGY AND THE CONTROL OF PATHOGENIC BACTERIA
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1000621
Grant No.
(N/A)
Project No.
TEX09555
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Sep 10, 2013
Project End Date
Jul 30, 2018
Grant Year
(N/A)
Project Director
Gill, JA, J.
Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Animal Science
Non Technical Summary
Since the 1940's, bacterial infections have been successfully controlled in humans and animals with antibiotics. Shortly after the introduction of antibiotics, strains of bacteria that were resistant to these drugs began to emerge. Today, the continued emergence of bacterial strains that are resistant to antibiotics has raised significant concern among the general medical community, some even suggesting we may be about to enter a "post-antibiotic era". Antimicrobial resistance (AMR) in bacteria poses a significant threat to the health of Americans. This problem has become greatly potentiated the fact that the pharmaceutical industry has largely abandoned the development of new antibiotics, leaving the development pipeline dry. There is a clear and present need for new antibiotic agents that are effective against AMR bacteria and that can be used in agricultural, veterinary and medical settings. Bacteriophages (typically called "phages") are viruses that infect bacteria. These viruses are the most abundant form of life on Earth, estimated to number some 1031 to 1032 organisms in total. Phages are ubiquitous, non-toxic and highly successful predators of bacteria, and are naturally present in soil, fresh water, open oceans, and associated with plants and animals as a part of their normal flora. The emergence of widespread antibiotic resistance in a variety of bacteria has sparked interest in the use of phages as antimicrobials. Phages have been shown to be effective in controlling a wide variety of pathogens in animal models, including Salmonella in poultry and swine, pathogenic E. coli in cattle and sheep, and numerous other pathogenic bacteria including Pseudomonas aeruginosa, Enterococcus faecium, Staphylococcus aureus and Klebsiella pneumoniae. This project aims to develop the use of bacteriophages as therapeutics against common foodborne pathogenic bacteria, initially focussing on Salmonella enterica carriage by beef cattle but also branching out into pathogenic E. coli (STEC, EPEC) and Staphylococcus aureus. Phages will be isolated, caharacterized, and their basic biology studied by a combination of classical genetic and modern high-throughput genomics techniques. Thier potential for controlling pathogenic bacteria in a practical setting will be evaluated. The project's ultimate goals are to increase the safety of the food supply and to develop knowledge and methods for further development of this technology.
Animal Health Component
30%
Research Effort Categories
Basic
50%
Applied
10%
Developmental
40%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
7123399110040%
7124030110140%
7123999110020%
Knowledge Area
712 - Protect Food from Contamination by Pathogenic Microorganisms, Parasites, and Naturally Occurring Toxins;

Subject Of Investigation
3999 - Animal research, general; 4030 - Viruses; 3399 - Beef cattle, general/other;

Field Of Science
1101 - Virology; 1100 - Bacteriology;
Goals / Objectives
Control of Salmonella colonizing the lymph nodes of beef cattle Collection of cattle-associated bacterial strains Collection of a characterized phage library Study of efficacy of phages in Salmonella prophylaxis Study the basic biology of therapeutic phages Determination of essential phage genes in an amenable model system Development of tools for genetic manipulation of phage
Project Methods
Bacteria and phages will be cultured and maintained by standard microbiological methods using approopriate media for the system. Phages will be isolated from the environment by direct plating of samples to bacterial lawns, direct plating of pre-concentrated samples, or enrichment of samples. Phages will be subcultured and maintained as pure stocks. Phages will be characterized for morphology using transmission electron microscopy, and for host range by plating serially diluted phage stocks to lawns of a panel of test strains. Initial focus will be given to phages of Salmonella, as this pathogen poses a current problem in beef production, but paralell efforts will include isolation of phages against pathogenic E. coli (mainly STEC), Staphylococcus aureus, and other pathogens of importance as the opportunity arises. Phage DNA will be extracted by standard methods, and sequenced by either Illumina or 454 to generate complete contigs. Phage genomes will be annotated with the aid of the Texas A&M Center for Phage Technology genomics server, which hosts a number of custom-built bioinformatics tools for phage genome annotation and comparative genomics. Phage genomes will be screened for the presence of deleterious genes (e.g., toxins or known pathogenicity factors) and gene associated with a temperate lifestyle, and phages containing such genes will be discarded. Using host range and genomic data, a cocktail of phages will be assembled that has broad activity against Salmonella for use in controlling this pathogen in beef cattle. In laboratory experiments, phages will be tested for their ability to reduce contamination of possible environmental reserviors of Salmonella such as feed, water and soil. Phages will then be evaluated for their ability to reduce Salmonella contamination in a cattle production environment. Phages will be evaluated for thier ability to reduce environmental Salmonella loads, and also the frequency of Salmonella carriage by cattle lymph nodes and carcass contamination. In order to study the biology of potentially therapeutic phages, phages representative of novel phage types that could prove to be therapeutic will be selected for study. Phages representing types for which there is relatively little biological information will be given priority. Phages will be mutagenized by radiation or chemical mutagens and plated to suppressor strains to isolate a library of suppressor mutants. Novel methods will be developed for the high-throughput parallel sequencing of phage mutants. These mutants will be used to develop systems for allelic replacement in virulent phages, techniques that should be applicable to other systems.

Progress 09/10/13 to 07/30/18

Outputs
Target Audience:Cattlemen, food safety professionals, medical professionals, microbiology professionals, graduate students, general public Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two graduate students have graduated with PhD degrees this year. Three other graduates students and one postdoc continue to work on this project. How have the results been disseminated to communities of interest?Results have been published in the peer-reviewed literature, and presented at the BIFSCO meeting. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 35 Salmonella phage genomes and 20 S. aureus phage genomes have been sequenced. Phage efficacy against Salmonella was evaluated in models of cattle hides and soil, with ~2-fold to 50-fold reductions observed. Phage were more effective on hides than in soil. A manuscript detailing work in model systems is in preparation.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Xie Y, Wahab L, Gill JJ. Development and Validation of a Microtiter Plate-Based Assay for Determination of Bacteriophage Host Range and Virulence. Viruses. 2018 Apr 12;10(4). pii: E189. doi: 10.3390/v10040189. PubMed PMID: 29649135; PubMed Central PMCID: PMC5923483.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Tolen TN, Xie Y, Hairgrove TB, Gill JJ, Taylor TM. Evaluation of Commercial Prototype Bacteriophage Intervention Designed for Reducing O157 and Non-O157 Shiga-Toxigenic Escherichia coli (STEC) on Beef Cattle Hide. Foods. 2018 Jul 16;7(7). pii: E114. doi: 10.3390/foods7070114. PubMed PMID: 30012993; PubMed Central PMCID: PMC6068917.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Cattlemen, food safety professionals, medical professionals, microbiology professionals, graduate students, general public Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The lab now mentors 5 graduate students and 1 postdoctoral researcher. Students are encouraged to attend conferences and campus seminars. How have the results been disseminated to communities of interest?Publications in the peer reviewed literature and interviews in popular press. What do you plan to do during the next reporting period to accomplish the goals?Study of ability of phage to control Salmonella on cattle hides and in soil. Continue genome sequencing of Salmonella phages. Projects studying the biology of S. aureus and E. coli phages are ongoing.

Impacts
What was accomplished under these goals? 15 Salmonella phage genomes have been sequenced. Work on phages infecting other medically important bacteria including Klebsiella pneumoniae and Acinetobacter baumannii has been initiated. Novel phage host range methods have been developed. Manuscripts detailing this work are in preparation.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Piya D, Vara L, Russell WK, Young R, Gill JJ. The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis. Mol Microbiol. 2017 Aug;105(3):399-412. doi: 10.1111/mmi.13705. Epub 2017 May 29. PubMed PMID: 28509398.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Parvataneni S, Mijalis EM, Kuty Everett GF, Rasche ES, Liu M, Gill JJ. Complete Genome Sequence of Citrobacter freundii Myophage Mijalis. Genome Announc. 2017 Aug 3;5(31). pii: e00228-17. doi: 10.1128/genomeA.00228-17. PubMed PMID: 28774966; PubMed Central PMCID: PMC5543628.


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Cattlemen, food safety professionals, microbiology professionals, graduate students, general public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Lab now employs 3 PhD students, 1 postdoctoral researcher, and 1 undergraduate student. How have the results been disseminated to communities of interest?Presentation of findings at the National Cattlemen's Beef Association Food Safety Summit in 2016; publication in J Food Prot. What do you plan to do during the next reporting period to accomplish the goals? Second publication on Salmonella phage characterization is planned. Continue work on objectives 1.2, 1.3, 2.1 and 2.2.

Impacts
What was accomplished under these goals? Control of Salmonella colonizing the lymph nodes of beef cattle Characterization of the phage library continues. 25 phage genomes have been sequenced and are under analysis. Preliminary studies of phage efficacy in an excised cattle hide model were begun. Study the basic biology of therapeutic phages NIH and NSF funding was obtained to study the biology of S. aureus phage K and to develop bioinformatic tools for analysis of phage genomes. A postdoctoral researcher was hired to work on development of genetic tools for phage K.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Xie Y, Savell JW, Arnold AN, Gehring KB, Gill JJ, Taylor MT. 2016. Prevalence and characterization of Salmonella enterica and Salmonella bacteriophages recovered from beef cattle feedlots in South Texas. Journal of Food Protection 79: 1332-40.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Yicheng Xie, Jason J. Gill. 2016. Development and Evaluation of Bacteriophage Cocktail against Salmonella Isolated from the Beef Feedlot Environment. Beef Industry Safety Summit, March 1-3, 2016, Austin, TX.


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Cattlemen, food safety professionals, microbiology professionals, graduate students, general public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Lab now employs 2 PhD students, 1 MS student, and 2 undergraduate researchers. Students presented thier research findings at national and international conference venues. How have the results been disseminated to communities of interest?Presentation of findings at the National Cattlemen's Beef Association Food Safety Summit in March 2015; presentations at a broadly-attended microbiology conference (ASM) in May 2015. What do you plan to do during the next reporting period to accomplish the goals?Submit manuscript describing objective 1.1. Continue work on objectives 1.2. and 1.3. One manuscript related to objective 1.2 expected in this project year. Postdoctoral researcher will begin work full-time on objectives 2.1 and 2.2 in Feb. 2016.

Impacts
What was accomplished under these goals? 1.1: Complete. Manuscript in preparation. 1.2: After major phage isolations in 2014, 6 additional Salmonella phages have been isolated using poultry-associated hosts. Preliminary analysis of phage genome sequences indicates the presence of Chi-like, 9NA-like, P2-like and T5-like phages in the collection. We have also identified two unusual "jumbo" ~350 kb phages in the collection. 1.3: Initial attempts at determining in vitro virulence of phages were hampered by a high mutation rate to phage resistance, resulting in high rates of bacterial survival when challeneged with individual phages. Experiemnts are now underway to determine how resistance to one phage affects sensitivity to other phages in the collection. This data will be used to formulate phage combinations that can overcome host resistance by targeting genetically independent receptors. 2.1: Departure of staff resulted in suspension of further work in this system. Enough data has been accumulated from the LL12 and LL5 stystems to prepare a small manuscript. Federal funding (NIH-NIAID) has been obtained for aims 2.1 and 2.2 of this project to continue in Staphylococcus aureus, a postdoctoral researcher has been hired and will begin work in Feb. 2016. 2.2: See above; project will resume with full-time effort in Feb. 2016.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Bull, J, Gill, JJ. The habits of highly effective phages: population dynamics as a framework for identifying therapeutic phages. Front. Microbiol., 18 November 2014, doi: 10.3389/fmicb.2014.00618
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Y. Xie, G. Everett, A. Arnold, J. W. Savell, K. B. Gehring, T. M. Taylor, J. J. Gill. Characterization of Salmonella Bacteriophages Inhabiting the Beef Feedlot Environment. ASM General Meeting, New Orleans, LA May 30-June 2, 2015
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: A. Korn, J. Grimm, J. Gill. Characterization of the Host Receptor and Receptor-binding Proteins in a Twort-like Staphylococcal Phage. ASM General Meeting, New Orleans, LA, May 30-June 2, 2015
  • Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Yicheng Xie, Ashley Arnold, Jeffrey W. Savell, Kerri B. Gehring, T. Matthew Taylor, Jason J. Gill. Prevalence and Identification of Salmonella Bacteriophages in the Beef Feedlot Environment. Beef Industry Safety Summit, Dallas, TX, March 4-6, 2015.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: Target audiences: Cattlemen, food safety professionals, microbiology professionals, graduate students, general public. Efforts: Delivered seminar at National Cattlemen's Beef Association Beef Safety Summit in March 2014 on progress of Salmonella project. Delivered a seminar at the National Institute of Allergy and Infectious Diseases on phage therapy in Sept 2014. Delivered a seminar at the Jiangsu Academy of Agricultural Sciences (Nanjing, PR China) on bovine mastitis and microbial genomics in Nov. 2013. Gave 5 popular press interviews on the subject of bacteriophages and phage tharapy. Instructed graduate seminar (ANSC 681) in fall 2013 and spring 2014. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Objectives are being conduced by two graduate students as part of their research projects. How have the results been disseminated to communities of interest? A progress update on objectives 1.1 - 1.2 was delivered to the NCBA who provided funding for this project. What do you plan to do during the next reporting period to accomplish the goals? Complete objective 1.2 and 1.3, publish results on objective 1.1. Findings will be presented at the NCBA meeting in March 2015, and a presentation at the American Society for Microbiology 2015 general meeting is anticipated. Work will continue on objectives 2.1 and 2.2, pending completion of the S. aureus amber suppressor strain.

Impacts
What was accomplished under these goals? 1.1: Collection of environmental Salmonella isolates from beef cattle feedlots is complete. A total of 38 Salmonella isolates were obtained, serotyped and tested for antibiotic resistance. The majority of the isolates are serovars Anatum and Montevideo. All strains were resistant or intermediate to streptomycin, and 4 were also resistant to sulfisoxazole. 1.2: Twenty-nine phage isolates were collected from beef feeedlot environmental samples against environmental Salmonella strains and other beef-associated isolates. These were found to comprise 14 distict phage types based on restriction analysis of whole genomic DNA. Phages possessed variable host ranges, with broadest host-range phages infecting 16 of 20 tested Salmonella strains. Genome sequencing of the phages is in progress. 1.3: Not yet commenced. 2.1: Conducted in a pilot system of E. coli phage LL12. Feasibility of the method was demonstrated. 2.2: S. aureus amber suppessor strain construction in progress. Constructs completed and awaiting transfer to S. aureus.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gill, JJ. 2014. Revised Genome Sequence of Staphylococcus aureus Bacteriophage K. Genome Announc. 2014 Jan 23;2(1). pii: e01173-13.
  • Type: Other Status: Published Year Published: 2014 Citation: Gill, JJ, Taylor, TM. Fighting microbes with microbes. National Provisioner, March 5, 2014.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Yicheng Xie, T. Matthew Taylor, Kerri B. Harris, Ashley N. Arnold, Jeffrey W. Savell, Jason J. Gill. 2013. Isolation and characterization of bacteriophages infecting beef-associated Salmonella serovars. Beef Industry Safety Summit, Dallas, TX, March 4-6 2014


Progress 09/10/13 to 09/30/13

Outputs
Target Audience: Nothing Reported Changes/Problems: Objective 2: Staphylococcus aureus and its virulent phage K have been added to this study as model organisms. S. aureus is a major human pathogen and antibiotic resistant strains have been associated with swine and cattle. We have begun experiments to produce a nonsense-supresssor strain in S. aureus for use in the procedures described in Objective 2. What opportunities for training and professional development has the project provided? Training activities: The lab now contains three graduate student and one technician. All four personnell operate under the mentorship of Jason Gill, PI. There is ample opportunity for all lab personnell to optain training in microbiology, phage biology, molecular biology and genomics as part of thier lab duties. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? IMPACT This project studies the use of bacteriophages (phages), or viruses that infect bacteria, for the control of pathogneic bacteria. Phages are ubiquitous and highly successful predators of bacteria, and are present in soil, fresh water, open oceans, and associated with plants and animals as a part of their normal flora. Phages are attractive for use in agricultural applications for several reasons: phages are specific, non-toxic and do not disrupt non-targeted beneficial bacterial flora; phages can be used to treat antibiotic-resistant bacteria that are otherwise difficult to eliminate using conventional antibiotics; there is increasing pressure to reduce the use of chemical antibiotics in agriculture, and phages may be a viable alternative in some applications. This project has one aim that specifically targets Salmonella carriage in beef cattle, and another aim that focuses on general phage biology. This is the first year of the project, during whcihch collaborations have been established and personell hired. Some preliminary phage isolations were conducted by Jaqueline Grimm and Yicheng Xie. GOALS AND OUTCOMES Control of Salmonella colonizing the lymph nodes of beef cattle Collection of cattle-associated bacterial strains A type strain, Salmonella Typhimurium LT2, has been obtained. Agreements with Dr. Tom Edrington at USDA have been executed to obtain non-cattle Salmonella field isolates that have been typed. Field samples from beef feedlots are in storage and awaiting processing for Salmonella. Collection of a characterized phage library Four phages infective against Salmonella LT2 have been obtained from environmental samples. Study of efficacy of phages in Salmonella prophylaxis This phase has not commenced, awaiting more Salmonella isolates and phages. Study the basic biology of therapeutic phages Determination of essential phage genes in an amenable model system A high-throughput screen was conducted to determine bacterial host genes required for phage function. This screen studied two novel phages, LL5 and LL12, that are able to infect pathogneic E. coli. For this work, the entire E. coli Keio collection was obtained, which is a collection of over 9,000 strains each with a single non-esential gene deleted by site-specific recombination. The phages were used to infect individual cultures of these strains, and cultures that failed to clear were presumed to confer some defect in phage replication and were studied further. Upon further study of these strains, several with bacterial outer-wall lipopolysaccharide (LPS) synthesis defects were found to be resistant to the phages, suggesting these phages use LPS as a major receptor. Several other genes, including the protein chaperones ppiB and secB, were found to have only a mild phenotype, associated with efficiency of plating (EOP) defects of less than 100-fold. Experiments to study the nature of these mutations is ongoing. Initial work commenced using a previously described Staphylococcus aureus nonsense suppressor strain, which was found to be unsuitble. Experiments are proceeding to construct a set of novel amber-suppressor strains in S. aureus for future work. Development of tools for genetic manipulation of phage Work not yet commenced.

Publications