Spontaneous and transient defence against bacteriophage by phase-variable glucosylation of O-antigen in Salmonella enterica serovar Typhimurium

A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide

Salmonella Typhimurium isolate D23580 represents a recently identified ST313 lineage of invasive non-typhoidal Salmonellae (iNTS). One of the differences between this lineage and other non-iNTS S. Typhimurium isolates is the presence of prophage BTP1. This prophage encodes a gtrC gene, implicated in O-antigen modification. GtrC^BTP1 is essential for maintaining O-antigen length in isolate D23580, since a gtr^BTP1 mutant yields a short O-antigen. This phenotype can be complemented by gtrC^BTP1 or very closely related gtrC genes. The short O-antigen of the gtr^BTP1 mutant was also compensated by deletion of the BTP1 phage tailspike gene in the D23580 chromosome. This tailspike protein has a putative endorhamnosidase domain and thus may mediate O-antigen cleavage. Expression of the gtrC^BTP1 gene is, in contrast to expression of many other gtr operons, not subject to phase variation and transcriptional analysis suggests that gtrC is produced under a variety of conditions. Additionally, GtrC^BTP1 expression is necessary and sufficient to provide protection against BTP1 phage infection of an otherwise susceptible strain. These data are consistent with a model in which GtrC^BTP1 mediates modification of the BTP1 phage O-antigen receptor in lysogenic D23580, and thereby prevents superinfection by itself and other phage that uses the same O-antigen co-receptor.

Variations in O-antigen biosynthesis and O-acetylation associated with altered phage sensitivity in Escherichia coli 4s

The O polysaccharide of the lipopolysaccharide (O antigen) of Gram-negative bacteria often serves as a receptor for bacteriophages that can make the phage dependent on a given O-antigen type, thus supporting the concept of the adaptive significance of the O-antigen variability in bacteria. The O-antigen layer also modulates interactions of many bacteriophages with their hosts, limiting the access of the viruses to other cell surface receptors. Here we report variations of O-antigen synthesis and structure in an environmental Escherichia coli isolate, 4s, obtained from horse feces, and its mutants selected for resistance to bacteriophage G7C, isolated from the same fecal sample. The 4s O antigen was found to be serologically, structurally, and genetically related to the O antigen of E. coli O22, differing only in side-chain α-D-glucosylation in the former, mediated by a gtr locus on the chromosome. Spontaneous mutations of E. coli 4s occurring with an unusually high frequency affected either O-antigen synthesis or O-acetylation due to the inactivation of the gene encoding the putative glycosyltransferase WclH or the putative acetyltransferase WclK, respectively, by the insertion of IS1-like elements. These mutations induced resistance to bacteriophage G7C and also modified interactions of E. coli 4s with several other bacteriophages conferring either resistance or sensitivity to the host. These findings suggest that O-antigen synthesis and O-acetylation can both ensure the specific recognition of the O-antigen receptor following infection by some phages and provide protection of the host cells against attack by other phages.

Development of a new molecular subtyping tool for Salmonella enterica serovar Enteritidis based on single nucleotide polymorphism genotyping using PCR

The lack of a sufficiently discriminatory molecular subtyping tool for Salmonella enterica serovar Enteritidis has hindered source attribution efforts and impeded regulatory actions required to disrupt its food-borne transmission. The underlying biological reason for the ineffectiveness of current molecular subtyping tools such as pulsed-field gel electrophoresis (PFGE) and phage typing appears to be related to the high degree of clonality of S. Enteritidis. By interrogating the organism's genome, we previously identified single nucleotide polymorphisms (SNP) distributed throughout the chromosome and have designed a highly discriminatory PCR-based SNP typing test based on 60 polymorphic loci. The application of the SNP-PCR method to DNA samples from S. Enteritidis strains (n = 55) obtained from a variety of sources has led to the differentiation and clustering of the S. Enteritidis isolates into 12 clades made up of 2 to 9 isolates per clade. Significantly, the SNP-PCR assay was able to further differentiate predominant PFGE types (e.g., XAI.0003) and phage types (e.g., phage type 8) into smaller subsets. The SNP-PCR subtyping test proved to be an accurate, precise, and quantitative tool for evaluating the relationships among the S. Enteritidis isolates tested in this study and should prove useful for clustering related S. Enteritidis isolates involved in outbreaks.

Phage-host interplay: examples from tailed phages and Gram-negative bacterial pathogens

Complex interactions between bacteriophages and their bacterial hosts play significant roles in shaping the structure of environmental microbial communities, not only by genetic transduction but also by modification of bacterial gene expression patterns. Survival of phages solely depends on their ability to infect their bacterial hosts, most importantly during phage entry. Successful dynamic adaptation of bacteriophages when facing selective pressures, such as host adaptation and resistance, dictates their abundance and diversification. Co-evolution of the phage tail fibers and bacterial receptors determine bacterial host ranges, mechanisms of phage entry, and other infection parameters. This review summarizes the current knowledge about the physical interactions between tailed bacteriophages and bacterial pathogens (e.g., Salmonella enterica and Pseudomonas aeruginosa) and the influences of the phage on host gene expression. Understanding these interactions can offer insights into phage-host dynamics and suggest novel strategies for the design of bacterial pathogen biological controls.

Complete genome sequence of enterobacteria phage 4MG, a new member of the subgroup "PVP-SE1-like phage" of the "rV5-like viruses"

A novel virulent enterobacteria phage, 4MG, which was isolated from soil near a sewer, belongs to the family Myoviridae, as it possesses an isometric head and a long contractile tail. The complete genome of 4MG consists of a double-stranded DNA with a length of 148,567 bp, a G + C content of 46.3 %, 271 open reading frames (ORFs), and 21 tRNAs. Bioinformatic analysis revealed that 4MG highly resembles "rV5-like viruses" but can be separated, together with Salmonella phage PVP-SE1 and Cronobacter sakazakii phage vB_CsaM_GAP31, as part of the subgroup "PVP-SE1-like phage".

Development of an engineered bioluminescent reporter phage for the sensitive detection of viable Salmonella typhimurium

Because foodborne illnesses continuously threaten public health, rapid and sensitive detection of pathogens in food has become an important issue. As an alternative to time-consuming and laborious conventional detection methods, a technique using recombinant reporter phages has been developed. Here, we developed an advanced bioluminescent reporter phage SPC32H-CDABE by inserting a bacterial luxCDABE operon into the Salmonella temperate phage SPC32H genome. Whole SPC32H genome sequencing enabled the selection of nonessential genes, which can be replaced with approximately 6-kb luxCDABE operon, which provides both luciferase (LuxAB) and its substrate, fatty aldehyde, as generated by fatty acid reductase (LuxCDE). Thus, the SPC32H-CDABE detection assay is simpler and more efficient compared to the luxAB-based assay because the substrate addition step is excluded. At least 20 CFU/mL of pure S. Typhimurium culture was detectable using SPC32H-CDABE within 2 h, and the signals increased proportionally to the number of cells contaminated in lettuce, sliced pork, and milk. These results thereby demonstrate that this phage successfully detects live Salmonella without appreciable interference from food components. Furthermore, the presented data suggest that SPC32H-CDABE represents a promising easy-to-use diagnostic tool for the detection of Salmonella contamination in food.

Bacteriophage-aided intracellular killing of engulfed methicillin-resistant Staphylococcus aureus (MRSA) by murine macrophages

Phages are known to effectively kill extracellularly multiplying bacteria as they do not have the ability of intracellular penetration within the animal cells. However, the present manuscript focuses on studying the impact of surface-adsorbed phage particles on the killing of engulfed Staphylococcus aureus inside phagocytic cells. Mouse peritoneal macrophages were isolated and cultured, followed by evaluation of their ability of bacterial uptake and killing. The intracellular killing potential of macrophages in the presence of unadsorbed free phage as well as phage adsorbed onto S. aureus 43300 was studied. Phage added alone to macrophage preparation did not influence intracellular killing of engulfed S. aureus by macrophages. However, phage adsorbed onto host bacterial cells (utilizing host bacteria as a vehicle to carry the lytic phage into the phagocytic compartment) brought about time-dependent and titre-dependent significant reduction in the number of viable intracellular cocci. Phage particles that shuttled inside the macrophage along with bacteria also significantly reduced cytotoxic damage caused by methicillin-resistant S. aureus (MRSA). This in turn enhanced the bactericidal killing potential of phagocytic cells. In earlier studies the inability of phages to kill intracellular bacteria has been thought to be a major drawback of phage therapy. For the first time results of this study confirm the killing ability of the broad host range lytic phage MR-5 of both extracellular as well as intracellular engulfed S. aureus inside macrophages. This approach shall not only restrict intracellular proliferation of staphylococci within the myeloid cells but also protect the host from further relapse of infection and treatment failures.

Genomic investigation of lysogen formation and host lysis systems of the Salmonella temperate bacteriophage SPN9CC

To understand phage infection and host cell lysis mechanisms in pathogenic Salmonella, a novel Salmonella enterica serovar Typhimurium-targeting bacteriophage, SPN9CC, belonging to the Podoviridae family was isolated and characterized. The phage infects S. Typhimurium via the O antigen of lipopolysaccharide (LPS) and forms clear plaques with cloudy centers due to lysogen formation. Phylogenetic analysis of phage major capsid proteins revealed that this phage is a member of the lysogen-forming P22-like phage group. However, comparative genomic analysis of SPN9CC with P22-like phages indicated that their lysogeny control regions and host cell lysis gene clusters show very low levels of identity, suggesting that lysogen formation and host cell lysis mechanisms may be diverse among phages in this group. Analysis of the expression of SPN9CC host cell lysis genes encoding holin, endolysin, and Rz/Rz1-like proteins individually or in combinations in S. Typhimurium and Escherichia coli hosts revealed that collaboration of these lysis proteins is important for the lysis of both hosts and that holin is a key protein. To further investigate the role of the lysogeny control region in phage SPN9CC, a ΔcI mutant (SPN9CCM) of phage SPN9CC was constructed. The mutant does not produce a cloudy center in the plaques, suggesting that this mutant phage is virulent and no longer temperate. Subsequent comparative one-step growth analysis and challenge assays revealed that SPN9CCM has shorter eclipse/latency periods and a larger burst size, as well as higher host cell lysis activity, than SPN9CC. The present work indicates the possibility of engineering temperate phages as promising biocontrol agents similar to virulent phages.

Core lipopolysaccharide-specific phage SSU5 as an Auxiliary Component of a Phage Cocktail for Salmonella biocontrol

Salmonella spp. are among the major food-borne pathogens that cause mild diarrhea to severe bacteremia. The use of bacteriophages to control various food-borne pathogens, including Salmonella, has emerged as a promising alternative to traditional chemotherapy. We isolated the Siphoviridae family phage SSU5, which can infect only rough strains of Salmonella. The blocking of SSU5 adsorption by periodate treatment of host Salmonella cells and spotting and adsorption assays with mutants that contain various truncations in their lipopolysaccharide (LPS) cores revealed that the outer core region of the LPS is a receptor of SSU5. SSU5 could infect O-antigen (O-Ag)-deficient Salmonella mutants that developed by challenging of O-Ag-specific phages, and consequently, it delayed the emergence of the phage-resistant Salmonella population in broth culture when treated together with phages using O-Ag as a receptor. Therefore, these results suggested that phage SSU5 would be a promising auxiliary component of a phage cocktail to control rough strains of Salmonella enterica serovar Typhimurium, which might emerge as resistant mutants upon infection by phages using O-Ag as a receptor.

Hurdles in bacteriophage therapy: deconstructing the parameters

Bacterial infections in animals impact our food production, leading to economic losses due to food rejection and the need for preventive and curative measures. Since the onset of the antibiotic era, the rise of antibiotic-resistant pathogens is causing scares in health care and food producing facilities worldwide. In the search of new therapeutics, re-evaluation of bacteriophage (phage) therapy, using naturally occurring bacterial viruses to tackle infections, is gaining interest. Many studies report about phage therapy success, showing the value and power of these natural viruses. Although phages carry some interesting traits and their basic biology is now well understood, this review argues that phage therapy has not revealed all of its secrets and many parameters remain understudied, making the outcome of phage therapy highly variable depending on the disease incidence. These difficulties include poorly understood mechanisms of phage penetration and distribution throughout the body, the variable expression and accessibility of phage receptors on the bacterial host in in vivo conditions and the unusual (non-linear) phage pharmacokinetics. These parameters are not easily measured in realistic in vivo settings, but are nevertheless important hurdles to overcome the high variability of phage therapy trials. This critical approach is in accordance with Goethe's statement; "Difficulties increase the nearer we get to the goal". However, since the importance of the goal itself also rises, both difficulties and goal justify the need for additional in depth research in this domain.

Antirepression system associated with the life cycle switch in the temperate podoviridae phage SPC32H

Prophages switch from lysogenic to lytic mode in response to the host SOS response. The primary factor that governs this switch is a phage repressor, which is typically a host RecA-dependent autocleavable protein. Here, in an effort to reveal the mechanism underlying the phenotypic differences between the Salmonella temperate phages SPC32H and SPC32N, whose genome sequences differ by only two nucleotides, we identified a new class of Podoviridae phage lytic switch antirepressor that is structurally distinct from the previously reported Sipho- and Myoviridae phage antirepressors. The SPC32H repressor (Rep) is not cleaved by the SOS response but instead is inactivated by a small antirepressor (Ant), the expression of which is negatively controlled by host LexA. A single nucleotide mutation in the consensus sequence of the LexA-binding site, which overlaps with the ant promoter, results in constitutive Ant synthesis and consequently induces SPC32N to enter the lytic cycle. Numerous potential Ant homologues were identified in a variety of putative prophages and temperate Podoviridae phages, indicating that antirepressors may be widespread among temperate phages in the order Caudovirales to mediate a prudent prophage induction.

Revenge of the phages: defeating bacterial defences

Bacteria and their viral predators (bacteriophages) are locked in a constant battle. In order to proliferate in phage-rich environments, bacteria have an impressive arsenal of defence mechanisms, and in response, phages have evolved counter-strategies to evade these antiviral systems. In this Review, we describe the various tactics that are used by phages to overcome bacterial resistance mechanisms, including adsorption inhibition, restriction-modification, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems and abortive infection. Furthermore, we consider how these observations have enhanced our knowledge of phage biology, evolution and phage-host interactions.

Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity

The immunodominant lipopolysaccharide is a key antigenic factor for Gram-negative pathogens such as salmonellae where it plays key roles in host adaptation, virulence, immune evasion, and persistence. Variation in the lipopolysaccharide is also the major differentiating factor that is used to classify Salmonella into over 2600 serovars as part of the Kaufmann-White scheme. While lipopolysaccharide diversity is generally associated with sequence variation in the lipopolysaccharide biosynthesis operon, extraneous genetic factors such as those encoded by the glucosyltransferase (gtr) operons provide further structural heterogeneity by adding additional sugars onto the O-antigen component of the lipopolysaccharide. Here we identify and examine the O-antigen modifying glucosyltransferase genes from the genomes of Salmonella enterica and Salmonella bongori serovars. We show that Salmonella generally carries between 1 and 4 gtr operons that we have classified into 10 families on the basis of gtrC sequence with apparent O-antigen modification detected for five of these families. The gtr operons localize to bacteriophage-associated genomic regions and exhibit a dynamic evolutionary history driven by recombination and gene shuffling events leading to new gene combinations. Furthermore, evidence of Dam- and OxyR-dependent phase variation of gtr gene expression was identified within eight gtr families. Thus, as O-antigen modification generates significant intra- and inter-strain phenotypic diversity, gtr-mediated modification is fundamental in assessing Salmonella strain variability. This will inform appropriate vaccine and diagnostic approaches, in addition to contributing to our understanding of host-pathogen interactions.

Bacterial pathogens frequently evolve mechanisms to vary the composition of their surface structures. The consequence is enhanced long-term survival by facilitating persistence and evasion of the host immune system. Salmonella sp., cause severe infections in a range of mammalian hosts and guard themselves with a protective coat, termed the O-antigen. Through genome sequence analyses we found that Salmonella have acquired an unprecedented repertoire of genetic sequences for modifying their O-antigen coat. There is strong evidence that these genetic factors have a dynamic evolutionary history and are spread through the bacterial population by bacteriophage. In addition to this genetic repertoire, we determined that Salmonella can and often do employ stochastic mechanisms for expression of these genetic factors. This means that O-antigen coat diversity can be generated within a Salmonella population that otherwise has a common genome. Our data significantly enhance our appreciation of the genetic and regulatory characteristics underpinning Salmonella O-antigen diversity. The role attributed to bacteriophage in generating this diversity highlights that Salmonella are acquiring an extensive repertoire of O-antigen modifying traits that may enhance the pathogen's ability to persist and cause disease in mammalian hosts. Such genetic traits may make useful markers for defining new epidemiological and diagnostic tools.