Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii

Acinetobacter baumannii is a critical priority nosocomial pathogen that produces a variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, the mechanism of specific cleavage of corresponding A. baumannii capsular polysaccharides (CPSs) was established. The structures of oligosaccharide fragments derived from K9, K14, K16, K37/K3-v1, K86, K127, and K128 CPSs degradation by the recombinant depolymerases have been determined. The crystal structures of three of the studied TSDs were obtained. A significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type was shown in the example of recombinant TSD APK09_gp48. The data obtained will provide a better understanding of the interaction of phage-bacterial host systems and will contribute to the formation of principles of rational usage of lytic phages and phage-derived enzymes as antibacterial agents.

Complete Genome Sequence of Klebsiella pneumoniae Bacteriophage KpS110, Encoding Five Tail-Associated Proteins with Putative Polysaccharide Depolymerase Domains

We report the genome sequence of bacteriophage KpS110, which infects Klebsiella pneumoniae, a multidrug-resistant encapsulated bacterium that causes severe community-acquired and hospital-acquired infections. The phage genome is 156,801 bp, with 201 open reading frames. KpS110 is most closely related to phages of the family Ackermannviridae at the genome and proteome levels.

Comparison of the therapeutic potential of bacteriophage KpV74 and phage-derived depolymerase (β-glucosidase) against Klebsiella pneumoniae capsular type K2

Bacteriophages and phage polysaccharide-degrading enzymes (depolymerases) are garnering attention as possible alternatives to antibiotics. Here, we describe the antimicrobial properties of bacteriophage KpV74 and phage depolymerase Dep_kpv74 specific to the hypervirulent Klebsiella pneumoniae of the K2 capsular type. The depolymerase Dep_kpv74 was identified as a specific glucosidase that cleaved the K2 type capsular polysaccharides of the K. pneumoniae by a hydrolytic mechanism. This depolymerase was effective against thigh soft tissue K. pneumoniae infection in mice without inducing adverse behavioral effects or toxicity. The depolymerase efficiency was similar to or greater than the bacteriophage efficiency. The phage KpV74 had a therapeutic effect only for treating the infection caused by the phage-propagating K. pneumoniae strain and was completely inactive against the infection caused by the K. pneumoniae strain that did not support phage multiplication. The depolymerase was effective in both cases. A mutant resistant to phage and depolymerase was isolated during the treatment of mice with bacteriophage. A confirmed one-base deletion in the flippase-coding wzx gene of this mutant is assumed to affect the polysaccharide capsule, abolishing the KpV74 phage adsorption and reducing the K. pneumoniae virulence.

Novel Klebsiella pneumoniae K23-Specific Bacteriophages From Different Families: Similarity of Depolymerases and Their Therapeutic Potential

Antibiotic resistance is a major public health concern in many countries worldwide. The rapid spread of multidrug-resistant (MDR) bacteria is the main driving force for the development of novel non-antibiotic antimicrobials as a therapeutic alternative. Here, we isolated and characterized three virulent bacteriophages that specifically infect and lyse MDR Klebsiella pneumoniae with K23 capsule type. The phages belonged to the Autographiviridae (vB_KpnP_Dlv622) and Myoviridae (vB_KpnM_Seu621, KpS8) families and contained highly similar receptor-binding proteins (RBPs) with polysaccharide depolymerase enzymatic activity. Based on phylogenetic analysis, a similar pattern was also noted for five other groups of depolymerases, specific against capsule types K1, K30/K69, K57, K63, and KN2. The resulting recombinant depolymerases Dep622 (phage vB_KpnP_Dlv622) and DepS8 (phage KpS8) demonstrated narrow specificity against K. pneumoniae with capsule type K23 and were able to protect Galleria mellonella larvae in a model infection with a K. pneumoniae multidrug-resistant strain. These findings expand our knowledge of the diversity of phage depolymerases and provide further evidence that bacteriophages and phage polysaccharide depolymerases represent a promising tool for antimicrobial therapy.

Characterization and Therapeutic Potential of Bacteriophage-Encoded Polysaccharide Depolymerases with β Galactosidase Activity against Klebsiella pneumoniae K57 Capsular Type

Bacteriophages and phage enzymes are considered as possible alternatives to antibiotics in the treatment of infections caused by antibiotic-resistant bacteria. Due to the ability to cleave the capsular polysaccharides (CPS), one of the main virulence factors of Klebsiella pneumoniae, phage depolymerases, has potential in the treatment of K. pneumoniae infections. Here, we characterized in vivo two novel phage-encoded polysaccharide depolymerases as therapeutics against clinical isolates of K. pneumoniae. The depolymerases Dep_kpv79 and Dep_kpv767 encoded by Klebsiella phages KpV79 (Myoviridae; Jedunavirus) and KpV767 (Autographiviridae, Studiervirinae, Przondovirus), respectively, were identified as specific β-galactosidases that cleave the K. pneumoniae K57 type CPS by the hydrolytic mechanism. They were found to be highly effective at combating sepsis and hip infection caused by K. pneumoniae in lethal mouse models. Here, 80–100% of animals were protected against death by a single dose (e.g., 50 μg/mouse) of the enzyme injected 0.5 h after infection by K. pneumoniae strains of the K57 capsular type. The therapeutic effect of the depolymerases is because they strip the capsule and expose the underlying bacterium to the immune attack such as complement-mediated killing. These data provide one more confirmation that phage polysaccharide depolymerases represent a promising tool for antimicrobial therapy.

Emergence of Five Genetic Lines ST395NDM-1, ST13OXA-48, ST3346OXA-48, ST39CTX-M-14, and Novel ST3551OXA-48 of Multidrug-Resistant Clinical Klebsiella pneumoniae in Russia

Aims: The objective of this study was phenotypic and genotypic characterization of antibacterial-resistant Klebsiella pneumoniae clinical strains isolated in Moscow Transplantology Intensive Care Unit in 2017-2019. Results: Major strains among K. pneumoniae (n = 63) isolated from 30 patients were recognized as extensive drug-resistant (n = 55) pathogens, and remaining strains were recognized as multidrug-resistant (n = 8) pathogens. The beta-lactamase genes bla_{SHV-1,-2a,-11,-27,-67,-187} (n = 63), bla_CTX-M-14,-15 (n = 61), bla_TEM-1 (n = 54), bla_OXA-48 (n = 52), and bla_NDM-1 (n = 2), as well as class 1 integrons (n = 19) carried gene cassette arrays aacA4 (n = 2), dfrA1-orfC (n = 6), aadB-aadA1 (n = 9), dfrA15-aadA1 (n = 3), and dfrA12-orfF-aadA2 (n = 1) were identified in the strains. All strains carried four virulence genes: wabG, fimH, uge, and allS, but two strains had additionally kfu gene. Six known sequence types (STs) of K. pneumoniae ST395 (n = 44), ST377 (n = 3), ST307 (n = 4), ST13 (n = 2), ST39 (n = 2), ST3346 (n = 1), and a novel sequence-type ST3551 (n = 7) were identified. Phylogenetic analysis showed that ST3551 belonged to the cluster of clonal group CG147, and the remaining six STs to the another cluster consisting of four subgroups. The emergence of K. pneumoniae genetic lines carrying epidemiologically significant beta-lactamase genes ST395^NDM-1, ST13^OXA-48, ST3346^{OXA-48/CTX-M-14}, ST3551^OXA-48, and ST39^CTX-M-14 was the first case of detection in Russia. Conclusion: The emergence of novel carbapenemase-producing K. pneumoniae genetic lines in Russia highlights the global negative tendency of multidrug-resistant pathogens spread in high-technological medical centers.

Structure and gene cluster of the capsular polysaccharide of multidrug resistant carbapenemase OXA-48-producing Klebsiella pneumoniae strain KPB536 of the genetic line ST147

The Gram-negative opportunistic pathogen Klebsiella pneumoniae is a significant cause of community-acquired and healthcare-associated infections for which multidrug resistance is a concern worldwide. A major virulence determinant of K. pneumoniae is a polysaccharide capsule (CPS) which forms a barrier around the bacterial cell wall, providing protection from environmental pressures and immune responses of eukaryotic organisms. More than 70 chemical capsule structures of serologically typeable K. pneumoniae strains are known. However, there are little data on the CPS structure and cps gene cluster organization of clinical multidrug resistant K. pneumoniae strains. Our investigation of multidrug resistant carbapenemase OXA-48-producing K. pneumoniae strain KPB536 identified a capsular type that was structurally similar to K. pneumoniae K10 but different from any K. pneumoniae CPS reported so far. The content and organization of the cps gene cluster in K. pneumoniae KPB536 also was determined. The catalytic functions of glycosyltransferases coded by the cps_KPB536 gene cluster were assigned by comparison with those responsible for the synthesis of glycoside linkages in the CPSs of K. pneumoniae types K10 and K61.

[Diagnostic bacteriophage V32 as a tool for the rapid identification of Escherichia coli serogroup O157.]

Bacteriophage V32, a representative of bacterial viruses of the Myoviridae family Ounavirinae subfamily, is proposed for search and identification of E. coli O₁₅₇ serogroup, including Shiga-toxin producing E. coli O₁₅₇:H₇ (STEC O₁₅₇:H₇), among cultures of enterobacteria from the primary seeding of the material studied. Phage genome containes a linear double-stranded DNA of 87875 base pairs with G/C-content of 38.9% and includes 132 open reading frames (ORF). In the genome, there are no determinants of antibiotic resistance, virulence genes of STEC and other well-known pathogroups of E. coli. It has been established that phage V32 has lytic activity against all studied cultures of E. coli O₁₅₇ serogroup (n=183) isolated from people and farm animals in various regions of the Russian Federation, as well as in Japan and Italy. At the same time, the phage lyses only 6 of 182 strains (3.3%) of E. coli not belonging to the O₁₅₇ serogroup and is not active against strains of other enterobacteria. That is, the phage has a high specificity. The use of bacteriophage V32 as a diagnostic tool is a highly efficient, fast, cheap and simple method for identifying E. coli serogroup O₁₅₇, including the serotype E. coli O₁₅₇: H₇, in any bacteriological laboratory without special equipment and special training of performers.

Characterization of myophage AM24 infecting Acinetobacter baumannii of the K9 capsular type

In the present study, we investigate the biological properties and genomic organization of virulent bacteriophage AM24, which specifically infects multidrug-resistant clinical Acinetobacter baumannii strains with a K9 capsular polysaccharide structure. The phage was identified as a member of the family Myoviridae by transmission electron microscopy. The AM24 linear double-stranded DNA genome of 97,177 bp contains 167 open reading frames. Putative functions were assigned for products of 40 predicted genes, including proteins involved in nucleotide metabolism and DNA replication, packaging of DNA into the capsid, phage assembly and structural proteins, and bacterial cell lysis. The gene encoding the tailspike, which possesses depolymerase activity towards the corresponding capsular polysaccharides, is situated in the phage genome outside of the structural module, upstream of the genes responsible for packaging of DNA into the capsid. The data on characterization of depolymerase-carrying phage AM24 contributes to our knowledge of the diversity of viruses infecting different capsular types of A. baumannii.

Comparative analysis of Klebsiella pneumoniae strains isolated in 2012-2016 that differ by antibiotic resistance genes and virulence genes profiles

The antibacterial resistance and virulence genotypes and phenotypes of 148 non-duplicate Klebsiella pneumoniae strains collected from 112 patients in Moscow hospitals in 2012-2016 including isolates from the respiratory system (57%), urine (30%), wounds (5%), cerebrospinal fluid (4%), blood (3%), and rectal swab (1%) were determined. The majority (98%) were multidrug resistant (MDR) strains carrying bla_SHV (91%), bla_CTX-M (74%), bla_TEM (51%), bla_OXA (38%), and bla_NDM (1%) beta-lactamase genes, class 1 integrons (38%), and the porin protein gene ompK36 (96%). The beta-lactamase genes bla_TEM-1, bla_SHV-1, bla_SHV-11, bla_SHV-110, bla_SHV-190, bla_CTX-M-15, bla_CTX-M-3, bla_CTX-M-55, bla_OXA-48, bla_OXA-244, and bla_NDM-1 were detected; class 1 integron gene cassette arrays (aadA1), (dfrA7), (dfrA1-orfC), (aadB-aadA1), (dfrA17-aadA5), and (dfrA12-orfF-aadA2) were identified. Twenty-two (15%) of clinical K. pneumoniae strains had hypermucoviscous (HV) phenotype defined as string test positive. The rmpA gene associated with HV phenotype was detected in 24% of strains. The intrapersonal mutation of rmpA gene (deletion of one nucleotide at the polyG tract) was a reason for negative hypermucoviscosity phenotype and low virulence of rmpA-positive K. pneumoniae strain KPB584. Eighteen virulent for mice strains with LD₅₀ ≤ 10⁴ CFU were attributed to sequence types ST23, ST86, ST218, ST65, ST2174, and ST2280 and to capsular types K1, K2, and K57. This study is the first report about hypervirulent K. pneumoniae strain KPB2580-14 of ST23^K1 harboring extended-spectrum beta-lactamase CTX-M-15 and carbapenemase OXA-48 genes located on pCTX-M-15-like and pOXA-48-like plasmids correspondingly.

Genome sequencing and comparative analysis of three hypermucoviscous Klebsiella pneumoniae strains isolated in Russia

The prevalence and characteristics of hypermucoviscous (HV) strains among Klebsiella pneumoniae isolated in Russian hospitals were investigated. The HV strains accounted for 11% of the K. pneumoniae isolates collected in the period from 2011 to 2016, and were characterized as belonging to the K1, K2, K20 and K57 serotypes. Whole genome sequences (WGSs) of K. pneumoniae HV clinical strains KPi261 (SCPM-O-B-7850) and KPB4010 (SCPM-O-B-7846) belonging to the K1 and K2 capsular types, as well as WGSs of K. pneumoniae strain KPM9 (SCPM-O-B-7749) of the K20 capsular type isolated from freshwater, were completed. The final draft genome sequences of KPi261, KPB4010 and KPM9 strains consisted of 5 719 189, 5 431 785 and 5 427 926 bp with 57.0, 57.1 and 57.4% GC content, respectively. The chromosomal and plasmid genes associated with K. pneumoniae virulence including the capsular polysaccharide synthesis gene cluster, mucoid phenotype regulator rmpA and transcriptional activator rmpA2, the all operon associated with allantoin metabolism, the kfu operon involved in iron uptake, the aerobactin-producing system iucABCDiutA, and the iron-transport systems iroBCDN and fecIRA were detected.

Identification of IS1R and IS10R elements inserted into ompk36 porin gene of two multidrug-resistant Klebsiella pneumoniae hospital strains

Hospital Klebsiella pneumoniae strains (n = 196) were collected in 2012-16 from the patients of a Moscow neurosurgical intensive care unit. Klebsiella pneumoniae strains were multidrug-resistant and carried beta-lactamase genes blaSHV (97.4% of strains), blaCTX-M (84.7%), blaTEM (56.1%), blaOXA-48-like (49.0%) and blaNDM-1 (one strain), class 1 integrons (43.4% of strains) and porin protein ompK36 gene (100% of strains). The ompK36 porin protein gene disruption by insertion sequence (IS) elements and OmpK36 production loss in two strains were detected in this study. Outer membrane proteins were isolated according to Carlone et al. (Rapid microprocedure for isolating detergent-insoluble outer membrane proteins from Haemophilus species. J Clin Microbiol 1986;24:330-2). The IS10R element belonging to the IS4 family, IS10 group was detected at the position of the 41st nucleotide of the ompK36 gene in K. pneumoniae strain KPB-2304K/15 (the first report for a certain IS element in K. pneumoniae). The IS1R element belonging to the IS1 family was identified at the position of the 86th nucleotide of the ompK36 gene in the K. pneumoniae strain KPB-367K/15 (novel insertion site for IS1 element into ompK36 gene). DNA transfer of the intact ompK36 gene into the strain KPB-367K/15 by vector plasmid restored OmpK36 porin protein production and resulted in a decrease of imipenem minimal inhibitory concentration. Such data confirm the importance of IS elements in ongoing multidrug-resistant evolution in hospital Klebsiella.

Complete genome sequence of novel T7-like virus vB_KpnP_KpV289 with lytic activity against Klebsiella pneumoniae

A novel bacteriophage, vB_KpnP_KpV289, lytic for hypermucoviscous strains of Klebsiella pneumoniae, was attributed to the family Podoviridae, subfamily Autographivirinae, genus T7likevirus based on transmission electron microscopy and genome analysis. The complete genome of the bacteriophage vB_KpnP_KpV289 consists of a linear double-stranded DNA of 41,054 bp including 179-bp direct-repeat sequences at the ends and 51 open reading frames (ORFs). The G+C content is 52.56 %. The phage was shown to lyse 15 out of 140 (10.7 %) K. pneumoniae strains belonged to the capsular types K-1, K-2, and K-57 and strains without a determined capsular type, including a hypermucoviscous strain of the novel sequence type ST-1554.

The spread of bla OXA-48 and bla OXA-244 carbapenemase genes among Klebsiella pneumoniae, Proteus mirabilis and Enterobacter spp. isolated in Moscow, Russia

Background

The spread of carbapenemase-producing Enterobacteriaceae (CPE) is a great problem of healthcare worldwide. Study of the spread for bla_OXA-48-like genes coding epidemically significant carbapenemases among hospital pathogens is important for the regional and global epidemiology of antimicrobial resistance.

Methods

Antibacterial resistant isolates of Klebsiella pneumoniae (n = 95) from 54 patients, P.mirabilis (n = 32) from 20 patients, Enterobacter aerogenes (n = 6) from four patients, and Enterobacter cloacae (n = 4) from four patients were collected from January, 2013 to October, 2014 in neurosurgical intensive care unit (ICU) of the Burdenko Neurosurgery Institute, Moscow. Characteristics of the isolates were done using susceptibility tests, PCR detection of the resistance genes, genotyping, conjugation, DNA sequencing, and bioinformatic analysis.

Results

Major strains under study were multi drug resistant (MDR), resistant to three or more functional classes of drugs simultaneously—98.9 % K. pneumoniae, 100 % P.mirabilis, one E.aerogenes isolate, and one E.cloacae isolate. Molecular-genetic mechanism of MDR in K.pneumoniae and P.mirabilis isolates were based on carrying of epidemic extended-spectrum beta-lactamase bla_CTX-M-15 gene (87.2 and 90.6 % accordingly), carbapenemase bla_OXA-48-like gene (55.3 and 23.3 % accordingly), and class 1 (54.8 and 31.3 % accordingly) and class 2 (90.6 % P. mirabilis) integrons. The bla_OXA-48-like-positive K. pneumoniae were collected during whole two-year surveillance period, while P. mirabilis and Enterobacter spp. carrying bla_OXA-48-like genes were detected only after four and 18 months after the research start, respectively. The bla_OXA-48-like gene acquisition was shown for P. mirabilis isolates collected from five patients and for E. cloacae isolate collected from one patient during their stay in the ICU, presumably from bla_OXA-48-like-positive K. pneumoniae. The source of the bla_OXA-244 gene acquired by E. aerogenes isolates and the time of this event were not recognized.

Conclusions

The expanding of CPE in the surveyed ICU was associated with the spread of bla_OXA-48 and bla_OXA-244 carbapenemase genes documented not only among K.pneumoniae, well-known bacterial host for such genes, but among P.mirabilis, E.aerogenes, and E. cloacae.

A small-scale experiment of using phage-based probiotic dietary supplement for prevention of E. coli traveler's diarrhea

Traveler's diarrhea (TD) is caused by Escherichia coli in 30% of cases. We have developed a phage cocktail for prophylaxis of TD caused by E.coli, Shigella flexneri, Shigella sonnei, Salmonella enterica, Listeria monocytogenes or Staphylococcus aureus, and investigated its effectiveness against infection caused by the non-pathogenic Lac (-) strain of E.coli K12 C600 in animal and human trials. On the 6th day of both animal and human trials E. coli K12 C600 strain was detected in titer of 10⁴ CFU/g of mice feces and 10⁶ CFU/g of human feces in the control (untreated) groups, while it was not detected in the samples of either of the study (phage-treated) groups. These results have great significance because the original coliphages included in the cocktail have a broad host-range including ETEC, EAEC and EHEC strains which cause severe cases of TD.

Structure elucidation of the capsular polysaccharide of Acinetobacter baumannii AB5075 having the KL25 capsule biosynthesis locus

Capsular polysaccharide was isolated by the phenol-water extraction of Acinetobacter baumannii AB5075 and studied by 1D and 2D (1)H and (13)C NMR spectroscopy. The following structure of the linear trisaccharide repeating unit was established: → 3)-β-D-ManpNAcA-(1 → 4)-β-D-ManpNAcA-(1 → 3)-α-D-QuipNAc4NR-(1 → where R indicates (S)-3-hydroxybutanoyl or acetyl in the ratio ∼ 2.5:1. The genes in the polysaccharide biosynthesis locus designated KL25 are appropriate to the established CPS structure.

Structure of a new pseudaminic acid-containing capsular polysaccharide of Acinetobacter baumannii LUH5550 having the KL42 capsule biosynthesis locus

The capsular polysaccharide from Acinetobacter baumannii LUH5550 was studied by 1D and 2D (1)H and (13)C NMR spectroscopy. The following structure of the branched trisaccharide repeating unit was established: [structure: see text] where Pse5Ac7RHb indicates 5-acetamido-3,5,7,9-tetradeoxy-7-[(R)-3-hydroxybutanoylamino]-L-glycero-L-manno-non-2-ulosonic acid. The genes in the capsule biosynthesis locus designated KL42 are consistent with the structure established.

[Genotypic differences between Corynebacterium diphtheriae biovar gravis and mitis strains]

AIM

Study structure ofa genetic determinant of amylase activity (amygene) in Corynebacterium diphtheriae biovar gravis and mitis strains.

MATERIALS AND METHODS

87 C. diphtheriae strains (31 gravis biovar strains and 56 mitis biovar strains) as well as C. diphtheriae PW8 strain were analyzed to detect structural features of C. diphtheriae strains of various biovars. 10 pairs of primers were used in PCR that flank mutually overlapping regions within DIP0357 locus as well as additional primers that flank DIP0353-DIP0354, DIP0357 and DIP0358 loci.

RESULTS

All the C. diphtheriae biovar gravis strains were established to contain a full-size DIP0357 locus (amy gene) whereas in all the mitis biovar strains this genome fragment is absent. All the studied C. diphtheriae biovar gravis strains do not have significant changes within DIP0354-DIP0357 loci (amy gene) whereas in genome of 57 studied C. diphtheriae biovar mitis strains the major part of this fragment including the complete nucleotide sequence of amy gene is absent.

CONCLUSION

C. diphtheriae biovar gravis strains have a genetically determined ability to produce amylase that can be viewed as an additional pathogenicity factor giving microorganisms wider capabilities to colonize the mucous membrane of oropharynx.

Atomic force microscopy analysis of the Acinetobacter baumannii bacteriophage AP22 lytic cycle

Background

Acinetobacter baumannii is known for its ability to develop resistance to the major groups of antibiotics, form biofilms, and survive for long periods in hospital environments. The prevalence of infections caused by multidrug-resistant A. baumannii is a significant problem for the modern health care system, and application of lytic bacteriophages for controlling this pathogen may become a solution.

Methodology/Principal Findings

In this study, using atomic force microscopy (AFM) and microbiological assessment we have investigated A. baumannii bacteriophage AP22, which has been recently described. AFM has revealed the morphology of bacteriophage AP22, adsorbed on the surfaces of mica, graphite and host bacterial cells. Besides, morphological changes of bacteriophage AP22-infected A. baumannii cells were characterized at different stages of the lytic cycle, from phage adsorption to the cell lysis. The phage latent period, estimated from AFM was in good agreement with that obtained by microbiological methods (40 min). Bacteriophage AP22, whose head diameter is 62±1 nm and tail length is 88±9 nm, was shown to disperse A. baumannii aggregates and adsorb to the bacterial surface right from the first minute of their mutual incubation at 37°C.

Conclusions/Significance

High rate of bacteriophage AP22 specific adsorption and its ability to disperse bacterial aggregates make this phage very promising for biomedical antimicrobial applications. Complementing microbiological results with AFM data, we demonstrate an effective approach, which allows not only comparing independently obtained characteristics of the lytic cycle but also visualizing the infection process.

Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae

Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium responsible for human food-borne disease as well as non-food-borne human, animal and poultry diseases. Because bacteriophages or their gene products could be applied to control bacterial diseases in a species-specific manner, they are potential important alternatives to antibiotics. Consequently, poultry intestinal material, soil, sewage and poultry processing drainage water were screened for virulent bacteriophages that lysed C. perfringens. Two bacteriophages, designated ΦCPV4 and ΦZP2, were isolated in the Moscow Region of the Russian Federation while another closely related virus, named ΦCP7R, was isolated in the southeastern USA. The viruses were identified as members of the order Caudovirales in the family Podoviridae with short, non-contractile tails of the C1 morphotype. The genomes of the three bacteriophages were 17.972, 18.078 and 18.397 kbp respectively; encoding twenty-six to twenty-eight ORF's with inverted terminal repeats and an average GC content of 34.6%. Structural proteins identified by mass spectrometry in the purified ΦCP7R virion included a pre-neck/appendage with putative lyase activity, major head, tail, connector/upper collar, lower collar and a structural protein with putative lysozyme-peptidase activity. All three podoviral bacteriophage genomes encoded a predicted N-acetylmuramoyl-L-alanine amidase and a putative stage V sporulation protein. Each putative amidase contained a predicted bacterial SH3 domain at the C-terminal end of the protein, presumably involved with binding the C. perfringens cell wall. The predicted DNA polymerase type B protein sequences were closely related to other members of the Podoviridae including Bacillus phage Φ29. Whole-genome comparisons supported this relationship, but also indicated that the Russian and USA viruses may be unique members of the sub-family Picovirinae.

Isolation and characterization of wide host range lytic bacteriophage AP22 infecting Acinetobacter baumannii

Acinetobacter baumannii plays a significant role in infecting patients admitted to hospitals. Many A. baumannii infections, including ventilation-associated pneumonia, wound, and bloodstream infections, are common for intensive care and burn units. The ability of the microorganism to acquire resistance to many antibiotics, disinfectants, and dehydration assures its long-term survival in hospital settings. The application of bacteriophages is a potential tool to control A. baumannii infections. Bacteriophage AP22 lytic for A. baumannii was isolated from clinical materials and classified as a member of the Myoviridae family. The phage had an icosahedral head of 64 nm in diameter and a contractile tail of 85-90 nm in length. According to restriction analysis, AP22 had 46-kb double-stranded DNA genome. The phage AP22 exhibited rapid adsorption (> 99% adsorbed in 5 min), a large burst size (240 PFU per cell), and stability to the wide range of pH. The bacteriophage was shown to specifically infect and lyse 68% (89 of 130) genotype-varying multidrug-resistant clinical A. baumannii strains by forming clear zones. Thus, it could be used as a candidate for making up phage cocktails to control A. baumannii-associated nosocomial infections.

[Molecular characterization of the multidrug-resistant Acinetobacter baumannii strains and assessment of their sensitivity to the phage AP22]

The molecular analysis of 130 multidrug-resistant nosocomial Acinetobacter baumannii strains was performed. The strains were obtained from patients admitted to different Russian hospitals (Chelyabinsk, Moscow, Nizhni Novgorod, and St. Petersburg) in 2005-2010. Species identification was performed using the amplified 16S rRNA gene restriction analysis and by determining intrinsic for A. baumannii blaQXA-51-like genes using PCR. The genetic typing of the strains was performed by RAPD-PCR. All strains fell into two clusters: A and B with dominant RAPD-groups A1 and B1, respectively, including 82% (107 of 130) of all studied strains. The susceptibility to the bacteriophage AP22 of the strains was determined. The phage was found to infect specifically and to constitute 69% of 130 strains and 82% (88 of 107) of the A. baumannii strains from the dominant RAPD groups. The ability of the bacteriophage AP22 to constitute a broad range of the clinically relevant A. baumannii strains makes it an attractive candidate for designing the phage cocktails intended to control the A. baumannii-associated nosocomial infections. Moreover, the phage can be used for the identification of A. baumannii in bacteriological analysis of clinical materials.

Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

Background

Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen.

Results

Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase) and a holin (PF04531). Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1) strongly significant host-specific sequence variation within the endolysin, and 2) a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical.

Conclusions

Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

Distribution and characterization of Campylobacter spp. from Russian poultry

The distribution of Campylobacter spp. on 13 poultry farms (broiler chicken, quail, pheasant, peacock, and turkey) from eight regions (Vladimir, Vologda, Voronezh, Kaluga, Liptsk, Moscow, Orenburg, and Orel) in Russia was surveyed. Intestinal materials were plated onto Campylobacter-selective medium and plates were incubated microaerobically at 42 degrees C for 24 or 48 h. Identification was based on colonial morphology, microscopic examination, and biochemical tests; latex agglutination assays were used for confirmation. In total, 116 isolates were derived from 370 samples. Isolation rates were similar, regardless of whether the birds were from small or large broiler production farms. Susceptibility of 48 representative (from these production sources) strains of Campylobacter spp. to 38 antimicrobial compounds was determined by disk diffusion assays. All strains tested were sensitive to amikacin, gentamycin, sisomycin, chloramphenicol, imipenem, oleandomycin, erythromycin, azitromycin, and ampicillin. The strains were also sensitive to 100 microg/disk of carbenicillin, fluoroquinolones, and to nitrofurans. Fluoroquinolone sensitivity was most notable and may be related to its limited application in poultry production within Russia. Hippurate and ribosomal RNA gene primers were developed and used to distinguish Campylobacter jejuni and Campylobacter coli and to provide a measure of strain discrimination. The combination of PCR analysis and randomly amplified polymorphic DNA (RAPD) typing were conducted for selected isolates. The various poultry species and the different locations yielded Campylobacter isolates with discrete randomly amplified polymorphic DNA patterns. The distribution and substantial diversity of Campylobacter spp. isolates appears similar to that previously reported in other countries.

[Corynebacterium diphtheriae nontoxigenic strain carrying the gene of diphtheria toxin]

Among 828 C. diphtheriae nontoxigenic cultures isolated in different region of Russia in 1994-2002, 114 cultures (13.8%) had the gene of diphtheria toxin (gene tox) and were thus called nontoxigenic tox-carrying (NTTC) strains. All NTTC strains were found to belong to biovar mitis and formed neither normal, nor "defective" diphtheria toxin. The most of NTTC strains (94%) belonged to ribotype "Moskva", not occurring among C. diphtheriae toxigenic strains. The incapacity of NNTC strains of forming diphtheria toxin was caused by mutation: the deletion of one nucleotide which led to the shift of the open reading frame and to the formation of the stop codon. The results of these studies are indicative of the fact that a sufficiently homogeneous and isolated group of C. diphtheriae nontoxigenic strains is spread in Russia. These strains carry the nonexpressing gene of diphtheria toxin and are of no epidemic importance in diphtheria infection.

[Effect of TRA-system of plasmids RP4 and R68.45 on pseudomonas mallei virulence]

In Pseudomonas mallei, spontaneous mutants (Tra- mutants) of the plasmids RP4 and R68.45, losing the ability to transfer at conjugation are formed. The plasmids RP4 and R68.45 with Tra(+)-phenotype caused a decrease in P. mallei virulence for laboratory animals. At the same time, Tra- mutants of these plasmids do not affect P. mallei virulence. The insertion of DNA fragment of about 1900 bp into the plasmid transfer gene regions (tra-2-tra-3) gave rise to RP4 and R68.45 tra mutations detectable on examination.

[Identification of the bacterium Pseudomonas mallei using Pseudomonas pseudomallei bacteriophages]

Phage production by Pseudomonas pseudomallei and Pseudomonas mallei strains has been studied. 32 P. pseudomallei bacteriophages have been isolated. Their spectrum of lytic action against P. pseudomallei, P. mallei and other Pseudomonas sp. has been defined. It has been shown that P. pseudomallei bacteriophages PP19, PP23, PP33 may be used for identification P. mallei among related Pseudomonas.

[Transduction of Pseudomonas mallei bacteria]

The transducing ability of 17 Pseudomonas pseudomallei bacteriophages has been studied. Five of them were found to be capable of transducing the transposon Tn7 markers TpR, SmR into the strain Pseudomonas mallei C-5. The transduced bacterial recipients became lysogenic and acquired resistance to trimethoprim and streptomycin. Transduction of transposon Tn7 has been confirmed by DNA-DNA hybridization.

[Transformation of pathogenic pseudomonas by plasmid DNA]

The possibility has been shown of the genetical transformation of Pseudomonas mallei strains by the purified DNA of the plasmids RSF1010, pES154, pBS222 and pBR325. The frequency of transformation varied from 1.2 x 10(1) to 2.0 x 10(2) depending on the plasmid DNA and transformation technique used in the experiments. Pseudomonas pseudomallei cells could not be transformed by the methods described in the paper.

[Integration of plasmid RP1 with the chromosome of Escherichia coli K-12 recA. 2 classes of Hfr strains]

Integration of broad host range RP1 plasmid into the chromosome of Escherichia coli K-12 recA- cells has been studied. Using temperature-sensitive for replication plasmids pVD1 and pVD3, the derivatives of RP1, it has been shown that integration of RP1 into the bacterial chromosome results in formation of two classes of Hfr strains. Properties of these Hfrs have been examined. From the data obtained, it has been concluded that the plasmid integration and formation of one of the Hfrs classes appear to be mediated by transposon Tn1 residing on RP1. The other class of Hfr strains is formed due to a stable integration of RP1. In the course of analysis of R+ transconjugants arising at low frequency in crosses between stable Hfrs and E. coli rec+ recipients, it has been found that the significant part of them contain plasmid-chromosome hybrids (R-prim plasmids). On the basis of the latter results, a new simple method for R' plasmids selection has been proposed. Using restriction endonuclease analysis, the structure of plasmids that were excised from chromosomes of the stable Hfr strains and were comparable in their size to RP1, has been investigated. Probable mechanisms of the stable Hfr strains formation are discussed.

[Formation of stable Hfr strains in R factor RP1 integration with the chromosome of E. coli K12 recA and their use for R-plasmid selection]

Analysis of thermoindependent derivatives of E. coli K12 JC1553 recA (p VD1) carrying a replication thermostable mutant pVD1 of R factor RP1 IncP Ap Km Tc showed that formation of about 5 per cent of them was associated with stable integration of the plasmid with the bacterial chromosome. The respective bacteria had the following features: (1) preserved all the markers of plasmid pVD1, (2) according to the data of the electrophoretic analysis had no extrachromosomal DNA on prolonged cultivation under nonselective conditions, (3) were effective donors of the chromosomal genes, (4) had a low rate of the plasmid marker transfer on crossing with R- recipient. The latter feature was suggested to be used as a test for identification of stable Hfr strains. Investigation of the properties of the transconjugants obtained on crossing of stable Hfr strains with R-recipients rec+ showed that same of them had plasmid DNA with a higher molecular mass as compared to that of plasmid pVD1 DNA. The presence of this DNA was connected with formation of R' plasmid as a result of an irregular exclusion of plasmid pVD1 from the chromosome of stable Hfr bacteria. On the basis of the results a simple method was proposed for selection of R' plasmids having a number of advantages over the classical ones. The perspectives of using thermostable derivatives of RP1 for cloning the chromosome genes are discussed.

[Restriction and electron microscopic analyses of deletion derivatives thermosensitive with respect to maintaining plasmid pEG1]

Temperature-independent deletion mutants of temperature-sensitive in self-maintenance plasmid pEG-1, derived from R-factor RP4, are mapped using the restriction endonucleases PstI, SmaI, EcoRI, BamHI and the heteroduplex analysis. The pEG1 derivatives under study are found to have deletions in the area of ampicillin transposon Tn1 and nearby genes. The left and the right ends of these deletions boundaries are localized between 37.5 MD and 7.6 MD in the RP4 map. Thus far, the area of plasmid RP4 (37.5-7.6 MD) with Tn1 and, presumably, inc gene(s) in it does not have any genes needed for stable maintenance of R-factor. A conclusion is made that the gene RP4, which carries the mutation determining thermosensitive character of pEG1 maintenance and of inhibition of the cell growth, is localized between the EcoRI site and transposon Tn1 at a distance less than 1.0 MD from the latter.

[Isolation and characteristics of deletion mutants of thermosensitive plasmid pEG1]

Phenotypic revertants of temperature-sensitive in self-maintenance plasmid pEG1 derived from R-factor RP4 were studied. The study indicated a sertain part of them to be variants without ampicillin resistance. The frequency of pEG1 ampicillin sensitive (Aps) derivatives is about 5.10(-7) and does not depend on the recA gene product. The Aps-derivatives of pEG1 plasmid can be classified in two phenotypic groups. The first group is temperature-independent and does not inhibit the growth of host cells by non-permissive temperature (43 degrees C). Agarose gel electrophoresis has revealed that plasmids of this group occur as a result of deletions in plasmid pEG1. The other group of Aps-derivatives still possess the property to be eliminated at 43 degrees C and they inhibit the growth of bacterial cells like pEG1. Agarose gel has demonstrated that some of them are deletion mutants while others are quite similar to pEG1 plasmid. The data obtained in the course of study of deletion mutants make it possible to suppose that the presence of gene with temperature sensitive mutation in pEG1 is not necessary for stable maintenance of R-factor.

[RP4 factor integration with E. coli chromosome]

Integration of R-factor RP4 with the chromosome of E. coli was studied with the use of replication thermosensitive mutant pEG1 of this factor. It was found that the frequency of integration of factor pEG1 containing the ampicillin transposone Tn1 with the chromosome of bacteria JC411 carrying transposone Tn1 previously inserted into it was very high and markedly exceeded that of its insertion into the same chromosome but not carrying this transposone. The frequency of factor pEG1 insertion into the chromosome of bacteria JC 1553 rec A defective with respect to genetic recombination was less than 2.10(-5) and did not depend on the presence of transposone Tn1 in it. Probably, insertion of factor RP4 into the bacterial chromosome may be realized through the rec A-dependent process of recombination between transposone Tn1 previously translocated into the chromosome and the same transposone contained in R-factor.