Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Salmonella Typhimurium ST34 pandemic strain

Charity, Oliver J.; Acton, Luke; Bawn, Matt; Tassinari, Eleonora; Thilliez, Gaёtan; Chattaway, Marie Anne; Dallman, Timothy J.; Petrovska, Liljana; Kingsley, Robert A.

doi:10.1099/mgen.0.000897

Cited by 3 publications

(3 citation statements)

References 81 publications

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“…A prophage is an inherited form of a temperate bacteriophage, functioning as a dormant form of the viral genome, which is mostly integrated into the bacterial chromosome and replicates vertically with the genome of the bacterial host [ 28 , 29 ]. In bacterial cells, after infection with lysogenic phage, phenotypic changes (lysogenic conversion) are observed [ 28 , 30 ]. Lysogenic conversion may result in a resistance to related phages and in some cases, the acquisition of cargo genes affects population dynamics, including genes involved in virulence, metabolism, or antibiotic resistance genes [ 30 ].…”

Section: Resultsmentioning

confidence: 99%

“…In bacterial cells, after infection with lysogenic phage, phenotypic changes (lysogenic conversion) are observed [ 28 , 30 ]. Lysogenic conversion may result in a resistance to related phages and in some cases, the acquisition of cargo genes affects population dynamics, including genes involved in virulence, metabolism, or antibiotic resistance genes [ 30 ]. Until the lytic cycle resumes, no offspring are produced.…”

Section: Resultsmentioning

confidence: 99%

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Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

Wójcicki

Świder

Średnicka

et al. 2023

IJMS

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Due to irrational antibiotic stewardship, an increase in the incidence of multidrug resistance of bacteria has been observed recently. Therefore, the search for new therapeutic methods for pathogen infection treatment seems to be necessary. One of the possibilities is the utilization of bacteriophages (phages)—the natural enemies of bacteria. Thus, this study is aimed at the genomic and functional characterization of two newly isolated phages targeting MDR Salmonella enterica strains and their efficacy in salmonellosis biocontrol in raw carrot–apple juice. The Salmonella phage vB_Sen-IAFB3829 (Salmonella phage strain KKP 3829) and Salmonella phage vB_Sen-IAFB3830 (Salmonella phage strain KKP 3830) were isolated against S. I (6,8:l,-:1,7) strain KKP 1762 and S. Typhimurium strain KKP 3080 host strains, respectively. Based on the transmission electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the viruses were identified as members of tailed bacteriophages from the Caudoviricetes class. Genome sequencing revealed that these phages have linear double-stranded DNA and sizes of 58,992 bp (vB_Sen-IAFB3829) and 50,514 bp (vB_Sen-IAFB3830). Phages retained their activity in a wide range of temperatures (from −20 °C to 60 °C) and active acidity values (pH from 3 to 11). The exposure of phages to UV radiation significantly decreased their activity in proportion to the exposure time. The application of phages to the food matrices significantly reduced the level of Salmonella contamination compared to the control. Genome analysis showed that both phages do not encode virulence or toxin genes and can be classified as virulent bacteriophages. Virulent characteristics and no possible pathogen factors make examined phages feasible to be potential candidates for food biocontrol.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

Wójcicki

Świder

Średnicka

et al. 2023

IJMS

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“…Owen et al, in 2021, identified BstA-phage-defense proteins encoded by prophage that inhibit exogenous lytic phage infections [77]. Similarly, Charity et al, in 2022, correlated mTmII prophage genome integration in Salmonella typhimurium to cause increased fitness and drug resistance [78]. Aforementioned studies are rather a glimpse at the ongoing research to unravel phage-host interactions and resistance mechanisms.…”

Section: Mary Et Al 2023mentioning

confidence: 99%

Machine Learning Mediated Advanced Phage and Antimicrobial Therapy- A Futuristic Approach

Shanmugha Mary,

Manik Patil,

Kundu

et al. 2023

Highlights in BioScience

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The emergence of antimicrobial resistance (AMR) has overwhelmed the contemporary curatives and have turned into one of the major challenges in the biomedical sector. With increasing deaths being associated with AMR every year; early detection of pathogens and development of novel drugs and alternative therapies, have all become ad hoc in diagnosis, prognosis and patient survival. Bacteriophage therapy remains a viable strategy to counteract AMR, yet unduly restrained by phage resistance. Phage infection is a natural phenomenon and can be widely manipulated in vitro using advanced techniques including the CRISPR/Cas systems which renders phage therapy an upper hand in comparison to conventional drugs. Phage identification, host range detection, determination of phage-receptor binding efficiency, adsorption rate, phage genome analysis are crucial stages in phage selection and phage cocktail preparation and moreover pivotal in flourishing phage therapy. The ascent of translational research and omics has allowed the development of quick, reliable and precise strategies for phage-based diagnosis and treatment techniques. However, in vitro evaluation of AMR and phage factors as well as storing, processing and analyzing large laboratory data outputs are expensive, time-consuming and labor-intensive. Machine learning (ML) is a utilitarian strategy to organize, store, analyze data sets and more importantly allows prediction of certain features by recognizing patterns in the data sets. With the huge number of research been carried out around the globe and enormous data sets being published and stored in databases, ML can utilize the available data to perform and guide in developing alternative therapeutics. Several ML based tools have been developed to predict resistance in host, phage grouping for cocktail preparation, resistance and lysogenic genes detection, phage genomic evaluation and to understand phage-host interactions. ML also allows the in silico analysis of large samples (drug/phage) and reduces sample size for in vitro evaluation thereby reducing overall costs, time and labor. The present review summarizes the available ML algorithms and corresponding databases used in AMR and phage research. It also emphasizes the status quo of antimicrobial and phage resistance in the healthcare sector and analyses the role of ML in analyzing biological databases in order to predict possible phage/drug-host interaction patterns, phage susceptibility, suitability of phage strains for therapy and recommends the most efficient drug combinations and treatment strategies.

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Reversible excision of thewzylocus inSalmonellaTyphimurium may aid recovery following phage predation

Charity,

Thilliez,

Al-Khanaq

et al. 2024

Preprint

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Bacteriophage (phage) are promising novel antimicrobials but a key challenge to their effective implementation is the rapid emergence of phage resistance. An improved understanding of phage-host interactions is therefore needed. The Anderson phage typing scheme differentiates closely related strains of Salmonella enterica serovar Typhimurium (S. Typhimurium) based on sensitivity to a panel of phage preparations. Switches in phage type are indicative of changes in phage sensitivity and inform on the dynamics of phage interaction with their host bacteria. We investigated the molecular basis of switches between the relatively phage sensitive S. Typhimurium DT8 and phage resistant DT30 strains that are present in the same phylogenetic clade. DT30 strains emerged from DT8 strains predominantly by deletion of a genomic region affecting the wzy locus encoding an O-antigen polymerase. The deletion site was flanked by two perfect direct repeats designated attL and attR. During broth culture in the presence of a typing phage that used O-antigen as primary receptor the Deltawzy genotype increased in frequency compared with culture in the absence of phage and removal of attL prevented deletion of the wzy locus. Co-culture of S. Typhimurium DT8 with a strain lacking wzy resulted in reversion of the latter to wild type. We propose a model in which reversible deletion of the wzy locus enables recovery of S. Typhimurium DT8 following predation by phage that use O-antigen as their primary receptor. This was consistent with ancestral state reconstruction of DT8 and DT30 phylogeny that supported a model of reversible transition from DT8 to DT30 in natural populations.

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Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Salmonella Typhimurium ST34 pandemic strain

Cited by 3 publications

References 81 publications

Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

Newly Isolated Virulent Salmophages for Biocontrol of Multidrug-Resistant Salmonella in Ready-to-Eat Plant-Based Food

Machine Learning Mediated Advanced Phage and Antimicrobial Therapy- A Futuristic Approach

Reversible excision of thewzylocus inSalmonellaTyphimurium may aid recovery following phage predation

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