Inducible Prophage Mutant of Escherichia coli Can Lyse New Host and the Key Sites of Receptor Recognition Identification

Chen, Mianmian; Zhang, Lei; Xin, Sipei; Yao, Huochun; Chen, Lu; Zhang, Wei

doi:10.3389/fmicb.2017.00147

Cited by 19 publications

(18 citation statements)

References 43 publications

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“…Traditionally, new host-ranges can be achieved through natural evolution or through rational genetic engineering by swapping genes. However, the latter strategy requires prior knowledge of related genetic elements with the desired host-range and the capacity to engineer those elements into a functional phage, which often results in laborious ad hoc trial and error periods (Ando et al, 2015; Chen et al, 2017; Gebhart et al, 2017; Hawkins et al, 2008; Heilpern and Waldor, 2003; Lin et al, 2012; Nguyen et al, 2012; Scholl et al, 2009; Yoichi et al, 2005). Harnessing natural evolution, on the other hand, requires elaborate co-culture and selection strategies that balance the need to have the phage population grow and mutate while also providing an alternative host for phage mutants to reproduce on (Qimron et al, 2006; Ross et al, 2016; Yu et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Various approaches have been undertaken to rationally expand the host-range of phages to combat resistance (Ando et al, 2015; Chen et al, 2017; Gebhart et al, 2017; Hawkins et al, 2008; Heilpern and Waldor, 2003; Lin et al, 2012; Nguyen et al, 2012; Scholl et al, 2009; Yoichi et al, 2005; Yosef et al, 2017). However, these approaches depend on hybridization between already characterized bacteriophages with known and desired host-ranges.…”

Section: Introductionmentioning

confidence: 99%

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Engineering Phage Host-Range and Suppressing Bacterial Resistance Through Phage Tail Fiber Mutagenesis

Yehl

Lemire

Yang

et al. 2019

Preprint

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26The rapid emergence of antibiotic-resistant infections is prompting increased interest in 27 phage-based antimicrobials. However, acquisition of resistance by bacteria is a major issue in the 28 successful development of phage therapies. Through natural evolution and structural modeling, 29 we identified host-range determining regions (HRDR) in the T3 phage tail fiber protein and 30 developed a high-throughput strategy to genetically engineer these regions through site-directed 31 mutagenesis. Inspired by antibody specificity engineering, this approach generates deep functional 32 diversity (>10 7 different members), while minimizing disruptions to the overall protein structure, 33 resulting in synthetic "phagebodies". We showed that mutating HRDRs yields phagebodies with 34 altered host-ranges. Select phagebodies enable long-term suppression of bacterial growth by 35 preventing the appearance of resistance in vitro and are functional in vivo using a mouse skin 36 infection model. We anticipate this approach may facilitate the creation of next-generation 37 antimicrobials that slow resistance development and could be extended to other viral scaffolds for 38 a broad range of applications. 39 evolution, tail fiber 41 3 Highlights: 42  Vastly diverse phagebody libraries containing 10 7 different members were created. 43  Structure-informed engineering of viral tail fibers efficiently generated host-range 44 alterations. 45  Phagebodies prevented the development of bacterial resistance across long timescales in 46 vitro and are functional in vivo. 47 48 49 59 Schooley et al., 2017). In addition, phages are selective for particular bacterial strains, as opposed 60 conventional chemical antibiotics that exhibit broad-spectrum activity, which contributes to 61 antibiotic-resistance development. Phage selectivity is dependent on binding to cell surface 62 receptors in order to recognize their host and initiate infection (Silva et al., 2016). However, 63 4reliance on receptor recognition for infectivity implies that resistance against a bacteriophage can 64 occur through receptor mutations. As a result, phage-based products are usually composed of 65 multiple unrelated phages that collectively target a range of receptors, thus distributing the 66 selective pressure away from any individual phage receptor. However, these cocktails are often 67 composed of uncharacterized phages whose biology are poorly defined. Furthermore, 68 manufacturing cocktails composed of diverse phages, as well as tracking their pharmacodynamics 69 and immunogenic properties, is complex, which can limit their development as antimicrobial drugs 70 (Cooper et al., 2016). 71 Various approaches have been undertaken to rationally expand the host-range of phages to 72 combat resistance (74 2005; Yosef et al., 2017). However, these approaches depend on hybridization between already 75 characterized bacteriophages with known and desired host-ranges. Natural evolution of phages has 76 also been harnessed to alter phage host-range, but...

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Engineering Phage Host-Range and Suppressing Bacterial Resistance Through Phage Tail Fiber Mutagenesis

Yehl

Lemire

Yang

et al. 2019

Preprint

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“…E. coli strains DE017 and DE205B were used as the hosts of phages WG01 and QL01, respectively, for propagation. A total of 104 avian E. coli strains used in these experiments were isolated from the brains of ducks with clinical signs of septicemia and neurological symptoms at different times and in different areas within the eastern region of China, as previously described (36)(37)(38). The pathogenic avian E. coli strain, IMT5155, was kindly provided by Lothar H. Wieler and Christa Ewers (39).…”

Section: Methodsmentioning

confidence: 99%

Alterations in gp37 Expand the Host Range of a T4-Like Phage

Chen

Zhang

Abdelgader

et al. 2017

Appl Environ Microbiol

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The use of phages as antibacterial agents is limited by their generally narrow host range. The aim of this study was to make a T4-like phage, WG01, obtain the host range of another T4-like phage, QL01, by replacing its host determinant gene region with that of QL01. This process triggered a direct expansion of the WG01 host range. The offspring of WG01 obtained the host ranges of both QL01 and WG01, as well as the ability to infect eight additional host bacteria in comparison to the wildtype strains. WQD had the widest host range; therefore, the corresponding QD fragments could be used for constructing a homologous sequence library. Moreover, after a sequencing analysis of gene37, we identified two different mechanisms responsible for the expanded host range: 1) the first generation of WG01 formed chimeras without mutations; and 2) the second generation of WG01 mutants formed from the chimeras. The expansion of the host range indicated that regions other than the C-terminal region may indirectly change the receptor specificity by altering the supportive capacity of the binding site. Additionally, we also found that the subsequent generations acquired a novel means of expanding the host range through acquiring a wider temperature range for lysis by exchanging gene37. The method developed in this work offers a quick way to change or expand the host range of a phage. Future clinical applications for screening phages against a given clinical isolate could be achieved after acquiring more suitable homologous sequences. T4-like phages have been established as safe in numerous phage therapy applications. The primary drawbacks to the use of phages as therapeutic agents include their highly specific host range. Thus, changing or expanding the host range of T4-like phages is beneficial for selecting phages for phage therapy. In this study, the host range of one T4-like phage WG01 was expanded using genetic manipulation. The WG01 derivatives acquired a novel means of expanding their host range through acquiring a wider temperature range for lysis. A region was located that had the potential to be used as a sequence region for homologous sequence recombination.

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“…According to our data, S. Napoli serovar is characterized by the frequent identification of P88 phage, which is reported to be phylogenetically divergent from other P2-like prophages [36]. Moreover S. Napoli genomes are characterized by the absence of many prophage sequences that are commonly identified in S. enterica such as Gifsy-1 and Gifsy-2 [37].…”

Section: Discussionmentioning

confidence: 76%

Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

et al. 2020

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Background: Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars. Results: 179 S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum β-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans. Conclusions: Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.

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Inducible Prophage Mutant of Escherichia coli Can Lyse New Host and the Key Sites of Receptor Recognition Identification

Cited by 19 publications

References 43 publications

Engineering Phage Host-Range and Suppressing Bacterial Resistance Through Phage Tail Fiber Mutagenesis

Engineering Phage Host-Range and Suppressing Bacterial Resistance Through Phage Tail Fiber Mutagenesis

Alterations in gp37 Expand the Host Range of a T4-Like Phage

Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

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