Antibiotic resistance in bacteria has become so important that it has justified the prediction of a "post-antibiotic" era in the 21^st century. Prudent estimates on the impact of antibiotic resistance showed that currently the deaths attributable to this cause are 700,000/year, and that this number is expected to rise to 10 million in 2050. As an example, this means that the number of deaths due to antibiotic resistance could be even higher than the sum of those currently registered for cancer (8.2 million) and car accidents (1.2 million) (https: // amr-review.org/sites/default/files/160518_Final%20paper_with%20cover.pdf). In addition, the problem of antibiotic resistance involves not only the fields of human and animal health, but also the environment. In order to limit as much as possible the use of antibiotics and the consequent selective pressure that promotes the exchange and selection of resistance, the possibility of using bacteriophages has gained a renewed importance in the search for alternative solutions. We have engaged in this research field by looking for virulent bacteriophages against bacteria of both medical and agricultural interest. Our research has led to the isolation and characterization of bacteriophages active against Pseudomonas syringae pathovar actinidiae and Klebsiella pneumoniae.

Research in this field is mainly carried by Marco Maria D’Andrea and Gustavo Di Lallo, with the unvaluable contribution of Prof. Gian Maria Rossolini (University of Florence) and his team.

Some of the preliminary results on K. pneumoniae were awarded at the national Congress of the Italian Society of Microbiology (2014, Turin, Italy) and at the Bacteriophage 2016 Conference (London, UK).

 

Poerio N., Olimpieri T., Henrici De Angelis L., De Santis F., Thaller M.C., D’Andrea M.M., Fraziano M. (2022). Fighting MDR-Klebsiella pneumoniae Infections by a Combined Host and Pathogen-Directed Therapeutic Approach. Frontiers in Immunology, 13:835417. DOI: 10.3389/fimmu.2022.835417

Klebsiella pneumoniae is an opportunistic pathogen that is very difficult to treat mainly due to its high propensity to acquire complex resistance traits. Notably, multidrug resistance (MDR)-Klebsiella pneumoniae (KP) infections are responsible for 22%–72% of mortality among hospitalized and immunocompromised patients. Although treatments with new drugs or with combined antibiotic therapies have some degree of success, there is still the urgency to investigate and develop an efficient approach against MDR-KP infections. In this study, we have evaluated, in an in vitro model of human macrophages, the efficacy of a combined treatment consisting of apoptotic body-like liposomes loaded with phosphatidylinositol 5-phosphate (ABL/PI5P) and φBO1E, a lytic phage specific for the major high-risk clone of KPC-positive MDR-KP. Results show that ABL/PI5P did not affect in a direct manner KKBO-1 viability, being able to reduce only the intracellular KKBO-1 bacterial load. As expected, φBO1E was effective mainly on reducing extracellular bacilli. Importantly, the combination of both treatments resulted in a simultaneous reduction of both intracellular and extracellular bacilli. Moreover, the combined treatment of KKBO-1-infected cells reduced proinflammatory TNF- and IL-1β cytokines and increased anti-inflammatory TGF-β cytokine production. Overall, our data support the therapeutic value of a combined host- and pathogen-directed therapy as a promising approach, alternative to single treatments, to simultaneously target intracellular and extracellular pathogens and improve the clinical management of patients infected with MDR pathogens such as MDR-KP.

Henrici De Angelis L., Poerio N., Di Pilato V., De Santis F., Antonelli A., Thaller M.C., Fraziano M., Rossolini G.M., D’Andrea M.M. (2021). Phage Resistance Is Associated with Decreased Virulence in KPC-Producing Klebsiella pneumoniae of the Clonal Group 258 Clade II Lineage. Microorganisms, 9(4), 762.DOI: 10.3390/microorganisms9040762

Phage therapy is now reconsidered with interest in the treatment of bacterial infections. A major piece of information for this application is the definition of the molecular targets exploited by phages to infect bacteria. Here, the genetic basis of resistance to the lytic phage φBO1E by its susceptible host Klebsiella pneumoniae KKBO-1 has been investigated. KKBO-1 phage-resistant mutants were obtained by infection at high multiplicity. One mutant, designated BO-FR-1, was selected for subsequent experiments, including virulence assessment in a Galleria mellonella infection model and characterization by whole-genome sequencing. Infection with BO-FR-1 was associated with a significantly lower mortality when compared to that of the parental strain. The BO-FR-1 genome differed from KKBO-1 by a single nonsense mutation into the wbaP gene, which encodes a glycosyltransferase involved in the first step of the biosynthesis of the capsular polysaccharide (CPS). Phage susceptibility was restored when BO-FR-1 was complemented with the constitutive wbaP gene. Our results demonstrated that φBO1E infects KKBO-1 targeting the bacterial CPS. Interestingly, BO-FR-1 was less virulent than the parental strain, suggesting that in the context of the interplay among phage, bacterial pathogen and host, the emergence of phage resistance may be beneficial for the host.

 

Marmo P., Thaller M.C., Di Lallo G., Henrici De Angelis L., Poerio N., De Santis F., Fraziano M., Migliore L., D’Andrea M.M. (2020). CHARACTERIZATION OF VB_STUS_MMDA13, A NEWLY DISCOVERED BACTERIOPHAGE INFECTING THE AGAR-DEGRADING SPECIES SPHINGOMONAS TURRISVIRGATAE. Viruses, 12(8): 894. DOI: 10.3390/v12080894

Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, we describe and characterize a lytic bacteriophage, named vB_StuS_MMDA13, able to infect the Sphingomonas turrisvirgatae MCT13 type strain. Physiological characterization demonstrated that vB_StuS_MMDA13 has a narrow host range, a long latency period, a low burst size, and it is overall stable to both temperature and pH variations. The phage has a double-stranded DNA genome of 63,743 bp, with 89 open reading frames arranged in two opposite arms separated by a 1186 bp non-coding region and shows a very low global similarity to any other known phages. Interestingly, vB_StuS_MMDA13 is endowed with an original nucleotide modification biosynthetic gene cluster, which greatly differs from those of its most closely related phages of the Nipunavirus genus. vB_StuS_MMDA13 is the first characterized lytic bacteriophage of the Siphoviridae family infecting members of the Sphingomonas genus.

  

D'Andrea M.M., Frezza D., Romano E., Marmo P., Henrici De Angelis L., Perini N., Thaller M.C. and Di Lallo G. (2019) - THE LYTIC BACTERIOPHAGE VB_EFAH_EF1TV, A NEW MEMBER OF THE HERELLEVIRIDAE FAMILY, DISRUPTS BIOFILM PRODUCED BY ENTEROCOCCUS FAECALIS CLINICAL STRAINS. Journal of Global Antimicrobial Resistance, PII S2213-7165(19)30273-5. DOI: 10.1016/j.jgar.2019.10.019

 

Objectives. The aim of this study is to characterize a new bacteriophage able to infect Enterococcus faecalis, and to evaluate its ability to disrupt biofilm.

Methods. The vB_EfaH_EF1TV (EF1TV) host-range was determined by spot test and efficiency of plating using a collection of 15 E. faecalis clinical strains. The phage genome was sequenced with a next generation sequencing approach. Anti-biofilm activity was tested by crystal violet method and confocal laser scanning microscopy. Phage-resistant mutants were selected and sequenced to investigate receptors exploited by phage for infection.

Results. EF1TV is a newly discovered E. faecalis phage which belongs to the Herelleviridae family. EF1TV, whose genome is 98% identical to φEF24C, is characterized by a linear dsDNA genome of 143,507 bp with direct terminal repeats of 1,911 bp. The phage is able to infect E. faecalis and shows also the ability to degrade biofilm produced by strains of this species. The results were confirmed by confocal laser scanning microscopy analyzing the biofilm reduction in the same optical field before and after phage infection.

Conclusions. The EF1TV phage shows promising features such as an obligatory lytic nature, an anti-biofilm activity and the absence of integration-related proteins, antibiotic resistance determinants and virulence factors, and therefore could be a promising tool for therapeutic applications.

Ciacci N., D’Andrea M.M., Marmo P., Demattè E., Amisano F., Di Pilato V., Fraziano M., Lupetti P., Rossolini G.M. and Thaller M.C. (2018) - CHARACTERIZATION OF VB_KPN_F48, A NEWLY DISCOVERED LYTIC BACTERIOPHAGE FOR KLEBSIELLA PNEUMONIAE OF SEQUENCE TYPE 101. Viruses, 10(9): 482-497. DOI: 10.3390/v10090482

Resistance to carbapenems in Enterobacteriaceae, including Klebsiella pneumoniae, represents a major clinical problem given the lack of effective alternative antibiotics. Bacteriophages could provide a valuable tool to control the dissemination of antibiotic resistant isolates, for the decolonization of colonized individuals and for treatment purposes. In this work, we have characterized a lytic bacteriophage, named vB_Kpn_F48, specific for K. pneumoniaeisolates belonging to clonal group 101. Phage vB_Kpn_F48 was classified as a member of Myoviridae, order Caudovirales, on the basis of transmission electron microscopy analysis. Physiological characterization demonstrated that vB_Kpn_F48 showed a narrow host range, a short latent period, a low burst size and it is highly stable to both temperature and pH variations. High throughput sequencing and bioinformatics analysis revealed that the phage is characterized by a 171 Kb dsDNA genome that lacks genes undesirable for a therapeutic perspective such integrases, antibiotic resistance genes and toxin encoding genes. Phylogenetic analysis suggests that vB_Kpn_F48 is a T4-like bacteriophage which belongs to a novel genus within the Tevenvirinae subfamily, which we tentatively named “F48virus”. Considering the narrow host range, the genomic features and overall physiological parameters phage vB_Kpn_F48 could be a promising candidate to be used alone or in cocktails for phage therapy applications.

D'Andrea M., Marmo P., Henrici De Angelis L., Palmieri M., Ciacci N., Di Lallo G., Demattè E., Vannuccini E., Lupetti P., Rossolini G.M., Thaller M.C. (2017) - ΦBO1E, A NEWLY DISCOVERED LYTIC BACTERIOPHAGE TARGETING CARBAPENEMASE-PRODUCING KLEBSIELLA PNEUMONIAE OF THE PANDEMIC CLONAL GROUP 258 CLADE II LINEAGE. Scientific Reports 7(1): 2614. DOI: 10.1038/s41598-017-02788-9

 The pandemic dissemination of KPC carbapenemase-producing Klebsiella pneumoniae (KPC-KP) represents a major public health problem, given their extensive multidrug resistance profiles and primary role in causing healthcare-associated infections. This phenomenon has largely been contributed by strains of Clonal Group (CG) 258, mostly of clade II, which in some areas represent the majority of KPC-KP isolates. Here we have characterized a newly discovered lytic Podoviridae, named φBO1E, targeting KPC-KP strains of clade II lineage of CG258. Genomic sequencing revealed that φBO1E belongs to the Kp34virus genus (87% nucleotide identity to vB_KpnP_SU552A). ΦBO1E was stable over a broad pH and temperature range, exhibited strict specificity for K. pneumoniae strains of clade II of CG258, and was unable to establish lysogeny. In a Galleria mellonella infection model, φBO1E was able to protect larvae from death following infection with KPC-KP strains of clade II of CG258, including one colistin resistant strain characterized by a hypermucoviscous phenotype. To our best knowledge φBO1E is the first characterized lytic phage targeting K. pneumoniae strains of this pandemic clonal lineage. As such, it could be of potential interest to develop new agents for treatment of KPC-KP infections and for decolonization of subjects chronically colonized by these resistant superbugs.