Analysis host-recognition mechanism of staphylococcal kayvirus ɸSA039 reveals a novel strategy that protects Staphylococcus aureus against infection by Staphylococcus pseudintermedius Siphoviridae phages

Characterisation of a colourimetric biosensor SapYZUM13@Mn3O4-NH2 reveals the mechanisms underlying its rapid and sensitive detection of viable Staphylococcus aureus in food

In this study, a colourimetric biosensor based on bacteriophage SapYZUM13 and an aminated Mn3O4 (Mn3O4-NH2) nanozyme was constructed and evaluated for its ability to detect Staphylococcus aureus in food. The biosensor had a detection time of 20 min, with a detection limit of 2 × 101 CFU/mL and recovery rate of 92.42-106.96%, indicating its high reliability and accuracy in detecting the food pathogen. Mechanistically, SapYZUM13@Mn3O4-NH2 exhibited oxidase-mimicking capability, producing O2•- free radicals which oxidise 3,3',5,5'-tetramethylbenzidine (TMB) to yield blue-coloured oxTMB. In the presence of S. aureus, the oxidase activity decreased remarkably owing to shielding of the nanozyme active sites. Moreover, SapYZUM13@Mn3O4-NH2 could detect viable S. aureus from various sources, likely because of the special receptor-binding proteins of SapYZUM13 adsorbing to the wall teichoic acids on the S. aureus cell surface. Thus, SapYZUM13@Mn3O4-NH2 has broad application prospects for the detection of viable S. aureus in various foods.

Beyond Antibiotics: What the Future Holds

The prevalence of multidrug resistance (MDR) and stagnant drug-development pipelines have led to the rapid rise of hard-to-treat antibiotic-resistant bacterial infections. These infectious diseases are no longer just nosocomial but are also becoming community-acquired. The spread of MDR has reached a crisis level that needs immediate attention. The landmark O'Neill report projects that by 2050, mortality rates associated with MDR bacterial infections will surpass mortality rates associated with individuals afflicted with cancer. Since conventional antimicrobials are no longer very reliable, it is of great importance to investigate different strategies to combat these life-threatening infectious diseases. Here, we provide an overview of recent advances in viable alternative treatment strategies mainly targeting a pathogen's virulence capability rather than viability. Topics include small molecule and immune inhibition of virulence factors, quorum sensing (QS) quenching, inhibition of biofilm development, bacteriophage-mediated therapy, and manipulation of an individual's macroflora to combat MDR bacterial infections.

Characterisation of a SapYZU11@ZnFe2O4 biosensor reveals its mechanism for the rapid and sensitive colourimetric detection of viable Staphylococcus aureus in food matrices

Although bacteriophage-based biosensors hold promise for detecting Staphylococcus aureus in food products in a timely, simple, and sensitive manner, the associated targeting mechanism of the biosensors remains unclear. Herein, a colourimetric biosensor SapYZU11@ZnFe2O4, based on a broad-spectrum S. aureus lytic phage SapYZU11 and a ZnFe2O4 nanozyme, was constructed, and its capacity to detect viable S. aureus in food was evaluated. Characterisation of SapYZU11@ZnFe2O4 revealed its effective immobilisation, outstanding biological activity, and peroxidase-like capability. The peroxidase activity of SapYZU11@ZnFe2O4 significantly decreased after the addition of S. aureus, potentially due to blockage of the nanozyme active sites. Moreover, SapYZU11@ZnFe2O4 can detect S. aureus from various sources and S. aureus isolates that phage SapYZU11 could not lyse. This may be facilitated by the adsorption of the special receptor-binding proteins on the phage tail fibre and wall teichoic acid receptors of S. aureus. Besides, SapYZU11@ZnFe2O4 exhibited remarkable sensitivity and specificity when employing colourimetric techniques to rapidly determine viable S. aureus counts in food samples, with a detection limit of 0.87 × 102 CFU/mL. Thus, SapYZU11@ZnFe2O4 has broad application prospects for the detection of viable S. aureus cells on food substrates.

Bacteriophage Therapy in Companion and Farm Animals

Bacteriophages, which are viruses with restricted tropism for bacteria, have been employed for over a century as antimicrobial agents; they have been largely abandoned in Western countries but are constantly used in Eastern European countries with the advent of antibiotics. In recent decades, the growing spread of multidrug-resistant bacteria, which pose a serious threat to worldwide public health, imposed an urgent demand for alternative therapeutic approaches to antibiotics in animal and human fields. Based on this requirement, numerous studies have been published on developing and testing bacteriophage-based therapy. Overall, the literature largely supports the potential of this perspective but also highlights the need for additional research as the current standards are inadequate to receive approval from regulatory authorities. This review aims to update and critically revise the current knowledge on the application of bacteriophages to treat bacterial-derived infectious diseases in animals in order to provide topical perspectives and innovative advances.

Biological properties of Staphylococcus virus ΦSA012 for phage therapy

Staphylococcus virus ΦSA012 has a wide host range and efficient lytic activity. Here, we assessed the biological stability of ΦSA012 against temperature, freeze-thawing, and pH to clinically apply the phage. In addition, inoculation of ΦSA012 through i.p. and i.v. injections into mice revealed that phages were reached the limit of detection in serum and accumulated notably spleens without inflammation at 48 h post-inoculation. Furthermore, inoculation of ΦSA012 through s.c. injections in mice significantly induced IgG, which possesses neutralizing activity against ΦSA012 and other Staphylococcus viruses, ΦSA039 and ΦMR003, but not Pseudomonas viruses ΦS12-3 and ΦR18 or Escherichia viruses T1, T4, and T7 in vitro. Immunoelectron microscopic analysis showed that purified anti-phage IgG recognizes the long-tail fiber of staphylococcus viruses. Although S. aureus inoculation resulted in a 25% survival rate in a mouse i.p. model, ΦSA012 inoculation (i.p.) improved the survival rate to 75%; however, the survival rate of ΦSA012-immunized mice decreased to less than non-immunized mice with phage i.v. injection at a MOI of 100. These results indicated that ΦSA012 possesses promise for use against staphylococcal infections but we should carefully address the appropriate dose and periods of phage administration. Our findings facilitate understandings of staphylococcus viruses for phage therapy.

Discovery of the First Lytic Staphylococcus pseudintermedius/Staphylococcus aureus Polyvalent Bacteriophages

Background

There are no verified lytic Staphylococcus pseudintermedius phages in the literature and few temperate phage genomes in databases. S. pseudintermedius is an opportunistic zoonotic pathogen of great importance in veterinary and human medicine.

Materials and Methods

We discovered phages against canine-derived S. pseudintermedius isolates by screening dog feces, hair, and skin swabs. Fourteen new phages were isolated and characterized by genomic analysis, transmission electron microscopy, and host range determination.

Results

Three phages-DH2, DH5, and DS10, a phage K variant-were predicted lytic by sequencing, a designation supported by mitomycin C induction. All three are S. pseudintermedius and Staphylococcus aureus polyvalent phages, with DH2 and DS10 being strong killers of both species.

Conclusions

We report discovery of the first verified lytic S. pseudintermedius phages and suggest dog hair as a novel reservoir. DH2, DH5, and DS10 are promising candidates toward developing an anti-Staphylococcal phage cocktail.

Understanding the Mechanisms That Drive Phage Resistance in Staphylococci to Prevent Phage Therapy Failure

Despite occurring at the microscopic scale, the armed race between phages and their bacterial hosts involves multiple mechanisms, some of which are just starting to be understood. On the one hand, bacteria have evolved strategies that can stop the viral infection at different stages (adsorption, DNA injection and replication, biosynthesis and assembly of the viral progeny and/or release of the newly formed virions); on the other, phages have gradually evolved counterattack strategies that allow them to continue infecting their prey. This co-evolutionary process has played a major role in the development of microbial populations in both natural and man-made environments. Notably, understanding the parameters of this microscopic war will be paramount to fully benefit from the application of phage therapy against dangerous, antibiotic-resistant human pathogens. This review gathers the current knowledge regarding the mechanisms of phage resistance in the Staphylococcus genus, which includes Staphylococcus aureus, one of the most concerning microorganisms in terms of antibiotic resistance acquisition. Some of these strategies involve permanent changes to the bacterial cell via mutations, while others are transient, adaptive changes whose expression depends on certain environmental cues or the growth phase. Finally, we discuss the most plausible strategies to limit the impact of phage resistance on therapy, with a special emphasis on the importance of a rational design of phage cocktails in order to thwart therapeutic failure.

Bacteriophage Technology and Modern Medicine

The bacteriophage (or phage for short) has been used as an antibacterial agent for over a century but was abandoned in most countries after the discovery and broad use of antibiotics. The worldwide emergence and high prevalence of antimicrobial-resistant (AMR) bacteria have led to a revival of interest in the long-forgotten antibacterial therapy with phages (phage therapy) as an alternative approach to combatting AMR bacteria. The rapid progress recently made in molecular biology and genetic engineering has accelerated the generation of phage-related products with superior therapeutic potentials against bacterial infection. Nowadays, phage-based technology has been developed for many purposes, including those beyond the framework of antibacterial treatment, such as to suppress viruses by phages, gene therapy, vaccine development, etc. Here, we highlighted the current progress in phage engineering technology and its application in modern medicine.

The Complex Diseases of Staphylococcus pseudintermedius in Canines: Where to Next?

Staphylococcus pseudintermedius is a pathogenic bacterium of concern within the veterinary sector and is involved in numerous infections in canines, including topical infections such as canine pyoderma and otitis externa, as well as systemic infections within the urinary, respiratory and reproductive tract. The high prevalence of methicillin-resistant Staphylococcus pseudintermedius (MRSP) within such infections is a growing concern. Therefore, it is crucial to understand the involvement of S. pseudintermedius in canine disease pathology to gain better insight into novel treatment avenues. Here, we review the literature focused on S. pseudintermedius infection in multiple anatomic locations in dogs and the role of MRSP in treatment outcomes at these niches. Multiple novel treatment avenues for MRSP have been pioneered in recent years and these are discussed with a specific focus on vaccines and phage therapy as potential therapeutic options. Whilst both undertakings are in their infancy, phage therapy is versatile and has shown high success in both animal and human medical use. It is clear that further research is required to combat the growing problems associated with MRSP in canines.

Lytic Activity of Polyvalent Staphylococcal Bacteriophage PhiSA012 and Its Endolysin Lys-PhiSA012 Against Antibiotic-Resistant Staphylococcal Clinical Isolates From Canine Skin Infection Sites

The spread of antibiotic-resistant bacteria (ARB) in human and veterinary medicine is of global concern. Notably, the emergence of methicillin-resistant Staphylococcus pseudintermedius has become a serious problem. In this context, bacteriophages and their lytic enzymes, endolysins, have received considerable attention as therapeutics for infectious diseases in place of antibiotics. The aim of the present study was to investigate the antibiotic-resistance patterns of staphylococcal species isolated from canine skin at a primary care animal hospital in Tokyo, Japan and evaluate the lytic activity of the staphylococcal bacteriophage phiSA012 and its endolysin Lys-phiSA012 against isolated antibiotic-resistant staphylococcal strains. Forty clinical staphylococcal samples were isolated from infection sites of dogs (20 from skin and 20 from the external ear canal). Susceptibility to antimicrobial agents was determined by a disk diffusion method. The host range of phiSA012 was determined by using a spot test against staphylococcal isolates. Against staphylococcal isolates that showed resistance toward five classes or more of antimicrobials, the lytic activity of phiSA012 and Lys-phiSA012 was evaluated using a turbidity reduction assay. Twenty-three S. pseudintermedius, 16 Staphylococcus schleiferi, and 1 Staphylococcus intermedius were detected from canine skin and ear infections, and results revealed 43.5% methicillin resistance in S. pseudintermedius and 31.3% in S. schleiferi. In addition, the prevalence multidrug resistance (MDR) S. pseudintermedius was 65.2%. PhiSA012 could infect all staphylococcal isolates by spot testing, but showed little lytic activity by turbidity reduction assay against MDR S. pseudintermedius isolates. On the other hand, Lys-phiSA012 showed lytic activity and reduced significantly the number of staphylococcal colony-forming units. These results demonstrated that ARB issues underlying in small animal hospital and proposed substitutes for antibiotics. Lys-phiSA012 has broader lytic activity than phiSA012 against staphylococcal isolates; therefore, Lys-phiSA012 is a more potential candidate therapeutic agent for several staphylococcal infections including that of canine skin.

New Genus Fibralongavirus in Siphoviridae Phages of Staphylococcus pseudintermedius

Bacteriophages of the significant veterinary pathogen Staphylococcus pseudintermedius are rarely described morphologically and genomically in detail, and mostly include phages of the Siphoviridae family. There is currently no taxonomical classification for phages of this bacterial species. Here we describe a new phage designated vB_SpsS_QT1, which is related to phage 2638A originally described as a Staphylococcus aureus phage. Propagating strain S. aureus 2854 of the latter was reclassified by rpoB gene sequencing as S. pseudintermedius 2854 in this work. Both phages have a narrow but different host range determined on 54 strains. Morphologically, both of them belong to the family Siphoviridae, share the B1 morphotype, and differ from other staphylococcal phage genera by a single long fibre at the terminus of the tail. The complete genome of phage vB_SpsS_QT1 was sequenced with the IonTorrent platform and expertly annotated. Its linear genome with cohesive ends is 43,029 bp long and encodes 60 predicted genes with the typical modular structure of staphylococcal siphophages. A global alignment found the genomes of vB_SpsS_QT1 and 2638A to share 84% nucleotide identity, but they have no significant similarity of nucleotide sequences with other phage genomes available in public databases. Based on the morphological, phylogenetic, and genomic analyses, a novel genus Fibralongavirus in the family Siphoviridae is described with phage species vB_SpsS_QT1 and 2638A.

Biological challenges of phage therapy and proposed solutions: a literature review

Introduction: In light of the emergence of antibiotic-resistant bacteria, phage (bacteriophage) therapy has been recognized as a potential alternative or addition to antibiotics in Western medicine for use in humans.Areas covered: This review assessed the scientific literature on phage therapy published between 1 January 2007 and 21 October 2019, with a focus on the successes and challenges of this prospective therapeutic.Expert opinion: Efficacy has been shown in animal models and experimental findings suggest promise for the safety of human phagotherapy. Significant challenges remain to be addressed prior to the standardization of phage therapy in the West, including the development of phage-resistant bacteria; the pharmacokinetic complexities of phage; and any potential human immune response incited by phagotherapy.

Silviavirus phage ɸMR003 displays a broad host range against methicillin-resistant Staphylococcus aureus of human origin

The emergence of life-threatening methicillin-resistant Staphylococcus aureus (MRSA) has led to increased interest in the use of bacteriophages as an alternative therapy to antibiotics. The success of phage therapy is greatly dependent on the selected phage possessing a wide host range. This study describes phage ɸMR003 isolated from sewage influent at a municipal wastewater treatment plant in Tokyo, Japan. ɸMR003 could infect 97% of 104 healthcare- and community-associated MRSA strains tested, compared with 73% for phage ɸSA012, which has a broad host range against bovine mastitis S. aureus. Genome analysis revealed that ɸMR003 belongs to the genus Silviavirus which has not been studied extensively. ɸMR003 recognizes and binds to wall teichoic acid (WTA) of S. aureus during infection. In silico comparisons of the genomes of ɸMR003 and ɸSA012 revealed that ORF117 and ORF119 of ɸMR003 are homologous to the putative receptor-binding proteins ORF103 and ORF105 of ɸSA012, with amino acid similarities of 75% and 72%, respectively. ORF104, which is an N-acetylglucosaminidase found in the ɸMR003 tail, may facilitate phage's infection onto the WTA-null S. aureus RN4220. The differences in tail and baseplate proteins may be key contributing factors to the different host specificities of ɸMR003 and ɸSA012. ɸMR003 showed strong adsorptivity, but not infectivity, against S. aureus SA003, which may be influenced by the bacterium's restriction modification system. This study expands our knowledge of the genomic diversity and host specificity of Silviavirus, which is a potential phage therapy candidate for MRSA infections.