A new scheme for phage typing Salmonella bareilly and characterization of typing phages

A new phage typing scheme using wild bacteriophages isolated from sewage for phage typing Salmonella bareilly is described. Six hundred and thirty-seven strains of Salm. bareilly could be separated into 11 different phage types using five wild phages. Overall typability was 94.5%. These phages belonged to two different morphotypes. A1 and B1, and showed varying host range.     

Phage typing and lysogen typing of Staphylococcus aureus]

A comparison was made between the results of phage and lysogenic typing of S. aureus strains isolated during several outbreaks of staphylococcal infection and S. aureus cultures isolated from the same carriers at different periods. The study of the groups of strains having the same origin showed that the differences in the number of reactions were more pronounced in lysogenic typing than in phage typing. For this reason lysogenic typing can be recommended only for the identification of those strains which cannot be identified with the use of the phages of the International Basic Set. The results of the experiments with induced phages proliferating in a restriction-defective strain indicated that restriction and modification were mainly responsible for the specificity of lytic reactions.     

Evaluation of the international phage typing set and some experimental phages for typing of Listeria monocytogenes from poultry in Spain

AIMS: The validity of the international phage set and 13 experimental phages for subtyping Listeria monocytogenes strains isolated from poultry in Spain was investigated. METHODS AND RESULTS: Ninety-six L. monocytogenes strains (52 from serogroup 1/2 and 44 from serogroup 4) were phage-typed using the international phage set, 10 experimental phages for typing serogroup 1/2 strains (seven isolated in France: 1313, 9425, 1807, 351, 881, 717 and 586-, and three from Denmark: 5775, 12682 and 6223-) and three experimental phages isolated in France for typing serogroup 4 strains (2425 A, 4286 and 197). Percentages of serogroup 1/2, serogroup 4 and total phage-typeable strains were 57.7%, 52.3% and 55.2%, respectively. Important differences in the behaviour of the phages tested were found. The typeability rate, the specificity index and the percentage of strong reactions were greater in the phages of international set than in the experimental phages. The number of phage typeable strains and the number of phage types (42) were not modified by the use of experimental phages. CONCLUSIONS: The phage set used was not effective for typing L. monocytogenes strains from poultry in Spain, because a low typeability rate was found. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggest the importance of the availability of new phages specific to a geographical area in order to improve the typeability of the system.     

Phage typing of cholera vibrios with different sets of phages]

A comparative study was made of two sets of Mukerjee and Drozhevkina-Arutyunova's bacteriophages in typing 514 strains of the El Tor vibrios and 45 strains of clasic biotype. It was shown that the Mukerjee or Drozhevkina-Arutyunova's phages could be used for the typing of cholera vibrios. The phages of the latter set prove to detect more phage types (18 against 11); they determine both the phage type and the biotype at the same time. The typing of cholera vibrios of both biotypes is possible, and the percentage of nontyping strains left is comparatively low (5.2 against 23.5 after Mukerjee). A table of the phage correspondence was made; it permits to obtain comparable data in using any set of the typing phages.     

Phage typing of the coagulase-positive staphylococci isolated from various species of animals

More than 200 coagulase-positive strains of animal origin have been studied by means of Staphylococcus aureus typing phages, belonging to two international sets and intended for typing staphylococci isolated from large cattle and humans, and experimental "chicken" phage A 1591. Among S. aureus strains the cultures isolated from swine, cows, chickens, and belonging to biotypes B1, C1, B2, respectively, have been mostly (in 78.5-90.0% of cases) determined by phage typing. The strains belonging to one biotype have proved to be sensitive predominantly to the same phages. In this connection further differentiation of staphylococci within individual biotypes by means of the phages used in these experiments seems to be impracticable. S. intermedius strains have been found to be completely resistant to the above phages, which confirms that S. intermedius is rightly considered to be an independent species of coagulase-positive staphylococci.     

Bacteriophage typing of Listeria species.

A bacteriophage typing scheme for differentiating Listeria isolates from dairy products and various other foodstuffs was developed. Sixteen selected phages isolated from both environmental sources and lysogenic strains were used for typing and, according to their lytic spectra, divided into four groups. Thus far, 41 distinct patterns of lysis were seen when this set was used in typing 57 defined reference strains, representing all five confirmed species and 16 serotypes in addition to 454 Listeria isolates of primarily foodborne origin. Overall, typability was 84.5%; i.e., a strain was lysed by at least one phage at 100x routine test dilution. Strains belonging to serovar 3 were mostly resistant to lysis by the phages employed. The results were highly reproducible, as determined in retyping trials several weeks later. Some phages isolated from environmental sources showed a wider lytic spectrum than did those isolated from lysogenic strains. In accordance with this, the phages were found in different clusters within a computer-generated linkage map. Species specificity and serovar specificity of the lytic reaction were not found. None of the phages was able to lyse strains of Listeria grayi, Listeria murrayi or Jonesia denitrificans. This phage typing system may provide important information for a means of recognizing and eliminating sources of contamination by Listeria spp. within dairy plant equipment.     

Phage typing ofstaphylococcus aureus strains using experimentalS. aureus phage 292

The characteristics of a newStaphylococcus aureus phage, 292, are described. Phage 292 appears closely related to typing phage 96 of the basic international series and is serologically related to the group B staphylococcal phages. In typing studies, phage 292 further subdivided 44.4% (120/270) of the type 94/96 strains and 42.0% (68/162) of the type 96 strains. A comparison of the typing efficacy of phage 292 and four other phages (14, 15, 16, 17) is also presented.     

Proposals for optimization of the international phage typing system for Listeria monocytogenes: combined analysis of phage lytic spectrum and variability of typing results.

Combined analysis of 5,179 serial phage reactions of 20 Listeria monocytogenes propagating strains over 14 years and phage typing results from 2,659 further L. monocytogenes strains allowed us to estimate lytic spectrum specificity and the variability of the lytic reactions of 35 phages. These included the 26 phages recommended for the international method for phage typing defined in 1985 by Rocourt et al. (J. Rocourt, A. Audurier, A. L. Courtieu, J. Durst, S. Ortel, A. Schrettenbrunner, and A. G. Taylor, Zentralbl. Bakteriol. Abt. 1 Orig. A 259:489-497, 1985). The results are discussed individually for each phage. Proposals for modifying the present system are made with the aim of producing an optimal bacteriophage set for routine use.     

Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages

Background

Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age groups and disease severity. The aim of this study was to analyse the genome sequences of 16 (fourteen T4 and two T7) E. coli O157 typing phages and to determine the genes responsible for the subtle differences in phage type profiles.

Results

The typing phages were sequenced using paired-end Illumina sequencing at The Genome Analysis Centre and the Animal Health and Veterinary Laboratories Agency and bioinformatics programs including Velvet, Brig and Easyfig were used to analyse them. A two-way Euclidian cluster analysis highlighted the associations between groups of phage types and typing phages. The analysis showed that the T7 typing phages (9 and 10) differed by only three genes and that the T4 typing phages formed three distinct groups of similar genomic sequences: Group 1 (1, 8, 11, 12 and 15, 16), Group 2 (3, 6, 7 and 13) and Group 3 (2, 4, 5 and 14). The E. coli O157 phage typing scheme exhibited a significantly modular network linked to the genetic similarity of each group showing that these groups are specialised to infect a subset of phage types.

Conclusion

Sequencing the typing phage has enabled us to identify the variable genes within each group and to determine how this corresponds to changes in phage type.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1470-z) contains supplementary material, which is available to authorized users.     

Bacteriophage typing of Salmonella weltevreden

Salmonella weltevreden has been found to be one of the commonest Salmonella serotypes isolated from diverse sources in India and has also been isolated in a number of other countries. A phage typing scheme was developed for this serotype using a set of six typing phages. These phages had been selected out of 146 phage strains isolated and purified from stool samples of man, laboratory animals and other animals, sewage and surface water sources, and the lytic mutants of temperate phages from S. weltevreden.The phage typing scheme was applied systematically to type the 946 strains from India isolated during 1958–1974 and 148 strains originating from Australia, Burma, England, Gan Island, Holland, Hong Kong, Malaysia, New Zealand, Papua New Guinea, The Philippines, Thailand, The United States and Vietnam during 1953–1971. The scheme was particularly studied to evaluate its utility in mapping the epidemiologically related strains from various sources.The S. weltevreden strains could be classified into ten phage types. Phage types 2 and 7 were found exclusively amongst Indian strains, type 6 from Vietnam and type 8 from Burma, Thailand and Vietnam. Phage types were found to be stable and consistent with the independent epidemiological data available.     

Evaluation of the usefulness of three collections of bacteriophages for typing methicillin-resistant Staphylococcus aureus,isolated in Moscow hospitals

The typing of S. aureus methicillin-resistant strains, isolated in different hospitals of Moscow; was carried out with the use of three collections of phages: the International Set of Phages; the set of phages of the International Center of S. aureus phage typing in London (L); and the experimental collection of phages of the Gamaleya Institute of Epidemiology and Microbiology in Moscow (M). In this study made with the use of both the phages of the International Diagnostic Set and phages L in the standard typing dose of 1 TP about 6% of the cultures under study proved to be sensitive. When the typing dose was increased to 100 TP the phages of the international diagnostic set lyzed 75.5% of the cultures. The typed strains were found to belong to phage types 77 (71.7%), 77/84/85 (19.6%) and 94/96 (6.5%). At a concentration of 100 TP phages L lyzed 83.7% of the cultures, but the dominating phage types could not be determined due to a great variety of phage markers. In contrast to the two preceding collections, the third phage collection M was composed in such a way that in the study of the investigated culture the specificity of its restriction modification was primarily evaluated and only then the presence of antiphage immunity was determined. This latter collection was used in the evaluation of 93.1% of the cultures. By the specificity of their restriction specification system the majority of them were classified with two new groups, heretofore not described. Only this collection M made it possible to differentiate epidemic and sporadic strains and to evaluate the epidemic situation in all 6 hospitals.     

Host specificity of Salmonella weltevreden typing phages

The host range of the six S. weltevreden typing phages was studied on 1469 strains belonging to 37 different Salmonella serotypes. In addition to S. weltevreden, only S. nchanga, S. give, S. lexington and S. anatum, all belonging to O group E₁, showed varying degrees of susceptibility to the action of some of the typing phages.Typing phage VI lysed only one strain other than S. weltevreden. All serotypes tested other than S. weltevreden were resistant to phages III and IV even at 1000 times the routine test dilution. Thus, typing phages III and IV were specific for S. weltevreden. The sensitivity patterns of S. weltevreden typing phages were not found to bear much correlation with either somatic of flagellar antigens of Salmonellae.     

Coagulase-negative Staphylococci isolated from patients. III. Phage typing

Coagulase-negative staphylococci of clinical origin were subjected to phage typing by means of phages from the experimental Dutch (Verhoef) and American (Paris) sets. These sets of phages were used to study 153 and 378 strains, respectively. The Dutch phages could lyse 30.1%, and the American ones 19.6% of the cultures. The strains belonging to the species S. epidermidis were lysed in 34.3% and 32.4% of cases, respectively, which is indicative of the fact that the American phages possess a more pronounced specificity in respect to S. epidermidis. The unsufficient effectiveness of typing phages does not yet allow one to evaluate the outlook for the method of phage typing in the study of coagulase-negative staphylococci.     

Insertion sequence (IS) hybridization supports classification of Rhizobium meliloti by phage typing

Sixty-one isolates of Rhizobium meliloti from two field sites which had been previously classified into 15 phage types on the basis of sensitivity to 16 typing phages, were subjected to insertion sequence (IS) hybridization using DNA probes for ISR m 3 and ISR m 5. Isolates from all but one phage type contained ISR m 3 (apparent copy no. 1–11) and all isolates contained ISR m 5 (apparent copy no. 3–11). The isolates were placed into 24 IS classes based on differences in their respective ISR m 3 and ISR m 5 hybridization profiles. At either field site, isolates representing different phage types possessed IS hybridization profiles that differed from each other, while those comprising a specific type had identical or closely related profiles. Isolates from one phage type were unusual since they did not react with any of the typing phages and were shown by IS hybridization to constitute a heterogeneous group. Evidence for spatial effects were provided by isolates from two of six types present at both sites which fell into separate IS classes on the basis of their site of origin. These data have ecological implications and suggest that for a particular site, phage typing may be employed for the rapid assessment of the genetic diversity among field isolates.     

Phage typing set for differentiating Staphylococcus epidermidis

A phage typing set composed of 13 phages is described for characterizing Staphylococcus epidermidis. Isolates (372) from cases of bovine mastitis were used in this study. Of these, 350 or 94% were successfully delineated, and 63 phage types were observed. Twenty two cultures were not typeable.     

Results of typing staphylococci isolated from cows and their milk products using the basic set of phages and local phages]

The basic set of phages recommended for typing staphylococci from cattle and also of local phages were approbated. Staphylococci cultures (950 in all) isolated in various regions of the Soviet Union from milk, milk produce and from cows suffering from mastitis were studied. Percentage of cultures typed by the phages of the basic set proved to be 78.3. Thirty different phage patterns were revealed among staphylococcal cultures lysed by phages. Lytic activity was the greatest in phages of group IV of the basic set. It is suggested that local phage 34k can be used as an additional phage permitting to subdivide the prevailing phage types within group IV into a number of new ones.     

Multilocus sequence typing scheme for the characterization of 936-like phages infecting Lactococcus lactis

Lactococcus lactis phage infections are costly for the dairy industry because they can slow down the fermentation process and adversely impact product safety and quality. Although many strategies have been developed to better control phage populations, new virulent phages continue to emerge. Thus, it is beneficial to develop an efficient method for the routine identification of new phages within a dairy plant to rapidly adapt antiphage tactics. Here, we present a multilocus sequence typing (MLST) scheme for the characterization of the 936-like phages, the most prevalent phage group infecting L. lactis strains worldwide. The proposed MLST system targets the internal portion of five highly conserved genomic sequences belonging to the packaging, morphogenesis, and lysis modules. Our MLST scheme was used to analyze 100 phages with different restriction fragment length polymorphism (RFLP) patterns isolated from 11 different countries between 1971 and 2010. PCR products were obtained for all the phages analyzed, and sequence analysis highlighted the high discriminatory power of the MLST system, detecting 93 different sequence types. A conserved locus within the lys gene (coding for endolysin) was the most discriminative, with 65 distinct alleles. The locus within the mcp gene (major capsid protein) was the most conserved (54 distinct alleles). Phylogenetic analyses of the concatenated sequences exhibited a strong concordance of the clusters with the phage host range, indicating the clonal evolution of these phages. A public database has been set up for the proposed MLST system, and it can be accessed at http://pubmlst.org/bacteriophages/.     

Phage typing ofSalmonella Typhi in the Netherlands

Summary A survey has been given of the results of phage typing of strains ofS. typhi found in Holland. It has been shown, that type A includes a different group of strains in systems drawn up with different Vi phages. An auxiliary system — to be used besides the system ofCraigie andYen — and a few new types, have been described.     

Plaque morphology and antigenic relationship of the Salmonella weltevreden typing phages

The plaque morphology and antigenic relationship of the six typing phages of Salmonella weltevreden were studied. Under identical conditions of plating, the phages could be classified into three groups based on plaque morphology. Neutralization tests with anti-phage sera showed that typing phages phi I and phi II were antigenically similar. Phages phi III, phi IV and phi VI also showed antigenic similarity. Typing phage phi V was antigenically distinct from all other phages. Thus the phages could be classified into three groups on the basis of both plaque morphology on their respective indicator strains and velocities of neutralization by homologous/heterologous anti-sera.     

Evaluation of the usefulness of new international experimental phages for typing methicillin resistant Staphylococcus aureus (MRSA)

The aim of the study was to determine the usefulness of the set of experimental phages obtained from the Central Public Health Laboratory in London for typing of MRSA strains in Poland. The study was performed on 150 MRSA strains isolated from various clinical materials in various regions of the country. The set of 10 experimental phages and the international basic set of 23 phages were used for typing. The results of the study showed that 76.8% of MRSA strains were typing with the experimental set of phages. The frequency of inhibition reactions was 19.9%. Only 3.3% of the strains were nontypable with the new phages while nearly half of the studied strains were nontypable with the basic set of phages. The studied strains were divided into 19 phagotypes. There was a high frequency of typable strains among MRSA typable and nontypable strains and those inhibited by the basic set of phages (71.4%-85.7%). These data indicate that the set of 10 experimental phages is useful for typing of MRSA strains isolated in Poland except for phage M3 which failed to react with almost all the strains and should be excluded from the proposed set.