Biology subjects

Gill, J. J.

Publications and source records attributed to Gill, J. J..

7 recordsLinked to original sources

bioRxiv2026

Genomic Characterization of 30 Lytic Klebsiella pneumoniae Bacteriophages

The spread and rise of antimicrobial resistance poses a risk to public health due to limited effective treatment options. Alternative antimicrobials that are effective against gram-negative multi-drug resistant pathogens. The increasing rate of carbapenem resistance observed in Klebsiella pneumoniae, indicates the need for alternative antimicrobial options. Bacteriophages that target Klebsiella pneumoniae are promising alternative antimicrobial option, with successful treatments being reported. Here we characterized 30 lytic bacteriophages from various environmental sources and tested their effectiveness against nine clinically relevant carbapenem-resistant K. pneumoniae isolates. These phages were characterized through genomic sequencing, bioinformatic analysis, virulence in liquid medium, and host range on different mediums. Bioinformatic analysis revealed a diverse collection of phages that span 9 ICTV recognized families and 13 genera with genome sizes ranging from 39-349 kbp. The phages were able to inhibit bacterial growth, and no virulence or antibiotic resistance genes were detected within the phage genomes. Host range testing demonstrated phages with broad host range have varying infectivity when plated on different common growth mediums. This study includes candidate phages for further potential development as potential antimicrobial agents against CR-KP, and the complexity in understanding phage-host dynamics of non-capsule phages that target against K. pneumoniae.

microbiology↗

bioRxiv2024

Bacteriophage Treatment against Carbapenem-resistant Klebsiella pneumoniae (KPC) in a Neutropenic Murine Model of Gastrointestinal Translocation and Renal Infection

BackgroundCarbapenemase producing Klebsiella pneumoniae (KPC) are globally emerging pathogens which that cause life-threatening infections. Novel treatment alternatives are urgently needed. MethodsWe therefore investigated the effectiveness of three novel bacteriophages (Spivey, Pharr and Soft) in a neutropenic murine model of KPC gastrointestinal colonization, translocation, and disseminated infection. Bacteriophage efficacy was determined by residual bacterial burden of KPC in kidneys. Parallel studies were conducted of bacteriophage pharmacokinetics and resistance.. ResultsTreatment of mice with 5x109 PFU of phage cocktail via intraperitoneal injection was effective in significantly reducing renal KPC burden by 102 CFU (p<0.01) when administered every 24 hours and 103 CFU (p<0.01) every 12 hours. Moreover, a combination of bacteriophage and ceftazidime-avibactam produced a synergistic effect, resulting in a 105 reduction in bacterial burden in caecum and kidney (p<0.001 in both tissues). Prophylactic administration of bacteriophages via oral gavage did not prevent KPC translocation to the kidneys. Bacteriophage decay determined by linear regression of the ln of mean concentrations demonstrated R2 values in plasma of 0.941, kidney 0.976, and caecum 0.918, with half-lives of 2.5h < t1/2 < 3.5 h. Furthermore, a phage-resistant mutant displayed increased sensitivity to serum killing in vitro, but did not show significant defects in renal infection in vivo. ConclusionsA combination of bacteriophages demonstrated significant efficacy alone and synergy with ceftazidime/avibactam in treatment of experimental disseminated KPC infection in neutropenic mice.

microbiology↗

bioRxiv2021

Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy

In 2016, a 68-year-old patient with a disseminated multi-drug resistant Acinetobacter baumannii infection was treated using lytic bacteriophages in one of the first modern human clinical uses of phage therapy in the United States. Due to the emergency nature of the treatment there was little time to thoroughly characterize the phages used in this intervention or the pathogen itself. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The eight phages used in the initial treatment were found to be a group of closely related T4-like myophages; the ninth phage, AbTP3{Phi}1, was found to be an unrelated Fri1-like podophage. Analysis of 19 A. baumannii isolates collected before and during phage treatment showed that resistance to the T4-like phages appeared as early as two days following the start of treatment. Three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment were sequenced to closure, and all contained a 3.9 Mb chromosome of sequence type 570 with a KL116 capsule locus and identical 8.7 kb plasmids. Phage-insensitive mutants of A. baumannii strain TP1 were generated in vitro and the majority of identified mutations were located in the bacterial capsule locus. The presence of the same mutation in both the in vitro mutants and in phage-insensitive isolates TP2 and TP3, which evolved in vivo during phage treatment, indicate that in vitro investigations can produce results that are relevant and predictive for the in vivo environment.

microbiology↗

bioRxiv2021

Preliminary Characterization of Phage-like Particles from the Male-Killing Mollicute Spiroplasma poulsonii (an Endosymbiont of Drosophila)

Bacteriophages are vastly abundant, diverse, and influential, but with few exceptions (e.g. the Proteobacteria genera Wolbachia and Hamiltonella), the role of phages in heritable bacteria-arthropod interactions, which are ubiquitous and diverse, remains largely unexplored. Despite prior studies documenting phage-like particles in the mollicute Spiroplasma associated with Drosophila flies, genomic sequences of such phage are lacking, and their effects on the Spiroplasma-Drosophila interaction have not been comprehensively characterized. We used a density step gradient to isolate phage-like particles from the male-killing bacterium Spiroplasma poulsonii (strains NSRO and MSRO-Br) harbored by Drosophila melanogaster. Isolated particles were subjected to DNA sequencing, assembly, and annotation. Several lines of evidence suggest that we recovered phage-like particles of similar features (shape, size, DNA content) to those previously reported in Drosophila-associated Spiroplasma strains. We recovered three [~]19 kb phage-like contigs (two in NSRO and one in MSRO-Br) containing 21-24 open reading frames, a read-alignment pattern consistent with circular permutation, and terminal redundancy (at least in NSRO). Although our results do not allow us to distinguish whether these phage-like contigs represent infective phage-like particles capable of transmitting their DNA to new hosts, their encoding of several typical phage genes suggests that they are at least remnants of functional phage. We also recovered two smaller non-phage-like contigs encoding a known Spiroplasma toxin (Ribosome Inactivating Protein; RIP), and an insertion element, suggesting that they are packaged into particles. Substantial homology of our particle-derived contigs was found in the genome assemblies of members of the Spiroplasma poulsonii clade.

microbiology↗

bioRxiv2021

Development and Characterization of a Weaned Pig Model of Shiga Toxin-Producing E. coli-Induced Gastrointestinal Disease

Post-weaning enteropathies in swine caused by pathogenic E. coli, such as post-weaning diarrhea (PWD) or edema disease (ED), remain a significant problem for the swine industry. Reduction in the use of antibiotics over concerns of antibiotic resistance and public health concerns, necessitate the evaluation of effective antibiotic alternatives to prevent significant loss of livestock and/or reductions in swine growth performance. For this purpose, an appropriate piglet model of enterotoxigenic E. coli enteropathy is required. In this study, we attempted to induce clinical signs of post-weaning disease in a piglet model using a one-time acute or lower daily chronic dose of a Shiga toxin-producing and enterotoxigenic E. coli strain. The induced disease state was monitored by determining fecal shedding and colonization of the challenge strain, animal growth performance, cytokine levels, fecal calprotectin, histology, fecal metabolomics, and fecal microbiome shifts. The most informative analyses were colonization and shedding of the pathogen, serum cytokines, metabolomics, and targeted metagenomics to determine dysbiosis. Histopathological changes of the gastrointestinal (GI) tract and tight junction leakage as measured by fecal calprotectin concentrations were not observed. Chronic dosing was similar to the acute regimen suggesting that a high dose of pathogen, as used in many studies, may not be necessary. The piglet disease model presented here can be used to evaluate alternative PWD treatment options. Furthermore, this relatively mild disease model presented here may be informative for modeling human chronic gastrointestinal diseases, such as inflammatory bowel disease, which otherwise require invasive procedures for study. ImportancePost-weaning diarrhea remains a significant problem in swine production and appropriate models of pathogenesis are needed to test alternative treatment options. In this study, we present an E. coli induced piglet model for post-weaning diarrhea, and also explore its translational potential as a model for human intestinal inflammation. Our study here presents two firsts to our knowledge. 1) The first simultaneous analysis of the intestinal microbiome and metabolome through fecal sampling of piglets challenged with Shiga toxin-producing E. coli. This is valuable given the limited metabolomics data from swine in various disease states. 2) A comparison of the clinical signs caused by a daily chronic vs one-time dosing regimen of E. coli. This comparison is key as infection by pathogenic E. coli in real-world settings likely occurs from chronic exposure to contaminated food, water, or environment rather than the highly concentrated dose of pathogen that is commonly given in the literature.

pathology↗

bioRxiv2021

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance StatementThe primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.

bioinformatics↗

bioRxiv2020

Comparative Genomics of Three Novel Lytic Jumbo Bacteriophages Infecting Staphylococcus aureus

The majority of previously described Staphylococcus aureus bacteriophages belong to three major groups: P68-like Podoviridae, Twort-like or K-like Myoviridae, and a more diverse group of temperate Siphoviridae. Here we present three novel S. aureus "jumbo" phages: MarsHill, Madawaska, and Machias. These phages were isolated from swine production environments in the United States and represent a novel clade of S. aureus Myoviridae that is largely unrelated to other known S. aureus phages. The average genome size for these phages is ~269 kb with each genome encoding ~263 predicted protein-coding genes. Phage genome organization and content is most similar to known jumbo phages of Bacillus, including AR9 and vB_BpuM-BpSp. All three phages possess genes encoding complete viral and non-viral RNA polymerases, multiple homing endonucleases, and a retron-like reverse transcriptase. Like AR9, all of these phages are presumed to have uracil-substituted DNA which interferes with DNA sequencing. These phages are also able to transduce host plasmids, which is significant as these phages were found circulating in swine production environments and can also infect human S. aureus isolates. Importance of workThis study describes the comparative genomics of three novel S. aureus jumbo phages: MarsHill, Madawaska, and Machias. These three S. aureus Myoviridae represent a new class of S. aureus phage that have not been described previously. These phages have presumably hypermodified DNA which inhibits sequencing by several different common platforms. Therefore, not only are these phages an exciting new type of S. aureus phage, they also represent potential genomic diversity that has been missed due to the limitations of standard sequencing techniques. The data and methods presented in this study could be useful for an audience far beyond those working in S. aureus phage biology. This work is original and has not been submitted for publication in any other journal.

genomics↗