Phage Strains Research Articles

SENSITIVITY OF <i>KLEBSIELLA PNEUMONIAE</i> CLINICAL ISOLATES WITH VARIOUS LEVELS OF ANTIBIOTIC RESISTANCE TO BACTERIORAGE PREPARATIONS

Objective : to assess sensitivity of K. pneumoniae clinical isolates with different levels of antibiotic resistance to commercial bacteriophage preparations. Material and methods . We have performed re-identification and determination of the sensitivity to antibiotics and bacteriophage preparations of 109 K. pneumoniae clinical isolates isolated from patients hospitalized in medical institutions of three regions of Belarus. The presence of carbapenemase genes has been deteсted by real-time PCR. Results . The study has shown awidespread prevalence of extreme antibiotic resistance among K. pneumoniae associated with the production of NDM and OXA-48 carbapenemases and has found an insufficient lytic activity of bacteriophage preparations against K. pneumoniae strains. The preparation «Sextafag», which lysed with a high activity of 28.4% of Klebsiella isolates possessed the widest spectrum of activity. Conclusion . Bacteriophage preparations can be considered as a possible alternative to antibiotics in the treatment of infections caused by extremely antibiotic-resistant K. pneumoniae isolates.It is necessary to supplement the composition of commercial preparations with phage strains that are active against Klebsiella isolates producing carbapenemases.

Experimental study of the antibacterial activity of the lytic Staphylococcus aureus bacteriophage ph20 and lytic Pseudomonas aeruginosa bacteriophage ph57 during modelling of its impregnation into poly(methylmetacrylate) orthopedic implants (bone cement)

Background: The problem of bacterial colonization of implants used in medical practice continues to be relevant regardless of the material of the implant. Particular attention deserves polymeric implants, which are prepared ex tempore from polymethyl methacrylate, for example - duting orthopedic surgical interventions (so-called "bone cement"). The protection of such implants by antibiotic impregnation is subjected to multiple criticisms, therefore, as an alternative to antibiotics, lytic bacteriophages with a number of unique advantages can be used - however, no experimental studies have been published on the possibility of impregnating bacteriophages into polymethyl methacrylate and their antibacterial activity assessment under such conditions.Aims: to evaluate the possibility of physical placement of bacteriophages in polymethylmethacrylate and to characterize the lytic antibacterial effect of two different strains of bacteriophages when impregnated into polymer carrier ex tempore during the polymerization process in in vitro model.Materials and methods: First stage - Atomic force microscopy (AFM) of polymethyl methacrylate samples for medical purposes was used to determine the presence and size of caverns in polymethyl methacrylate after completion of its polymerization at various reaction temperatures (+6…+25°C and +18…+50°C).The second stage was performed in vitro and included an impregnation of two different bacteriophage strains (phage ph20 active against S. aureus and ph57 active against Ps. aeruginosa) into polymethyl methacrylate during the polymerization process, followed by determination of their antibacterial activity.Results: ACM showed the possibility of bacteriophages placement in the cavities of polymethyl methacrylate - the median of the section and the depth of cavities on the outer surface of the polymer sample polymerized at +18…+50°C were 100.0 and 40.0 nm, respectively, and on the surface of the transverse cleavage of the sample - 120.0 and 100.0 nm, respectively, which statistically did not differ from the geometric dimensions of the caverns of the sample polymerized at a temperature of +6…+25°C.The study of antibacterial activity showed that the ph20 bacteriophage impregnated in polymethyl methacrylate at +6…+25°C lost its effective titer within the first six days after the start of the experiment, while the phage ph57 retained an effective titer for at least 13 days.Conclusion: the study confirmed the possibility of bacteriophages impregnation into medical grade polymethyl methacrylate, maintaining the effective titer of the bacteriophage during phage emission into the external environment, which opens the way for the possible application of this method of bacteriophage delivery in clinical practice. It is also assumed that certain bacteriophages are susceptible to aggressive influences from the chemical components of "bone cement" and / or polymerization reaction products, which requires strict selection of bacteriophage strains that could be suitable for this method of delivery.

Молекулярно-генетическая характеристика штаммов протейных бактериофагов .

Молекулярно-генетическая характеристика штаммов протейных бактериофагов .

Antibacterial Activity of Novel Strains of Bacteriophages: An Experimental Approach.

The evolution of antibiotic resistance in bacteria has increased research in the development of alternative therapies to conventional drugs. In this study, isolated phages were characterized and antibacterial activity was determined by standard agar disc diffusion method. The phages showed maximum propagation at 37°C to 40°C and highest viability at pH 7. Sugars influenced the bacteriophage viability. Sodium chloride decreased the phage propagation. Calcium chloride and magnesium chloride increased the phage propagation up to a certain limit. SDS-PAGE analysis confirmed the presence of protein cover and showed the various bands ranging from 10 to 200 kDa. Nucleic acid analysis confirmed the presence of RNA with a size of approximately 20 kb. Transmission electron microscopy indicated that the phages belong to Siphoviridae, Leviviridae, and Podoviridae families.

Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems.

CRISPR-Cas-mediated defense utilizes information stored as spacers in CRISPR arrays to defend against genetic invaders. We define the mode of target interference and role in antiviral defense for two CRISPR-Cas systems in Marinomonas mediterranea. One system (type I-F) targets DNA. A second system (type III-B) is broadly capable of acquiring spacers in either orientation from RNA and DNA, and exhibits transcription-dependent DNA interference. Examining resistance to phages isolated from Mediterranean seagrass meadows, we found that the type III-B machinery co-opts type I-F CRISPR-RNAs. Sequencing and infectivity assessments of related bacterial and phage strains suggests an 'arms race' in which phage escape from the type I-F system can be overcome through use of type I-F spacers by a horizontally-acquired type III-B system. We propose that the phage-host arms race can drive selection for horizontal uptake and maintenance of promiscuous type III interference modules that supplement existing host type I CRISPR-Cas systems.

Development of a novel and highly efficient method of isolating bacteriophages from water

Bacteriophages are widely used to the treatment of drug-resistant bacteria and the improvement of food safety through bacterial lysis. However, the limited investigations on bacteriophage restrict their further application. In this study, a novel and highly efficient method was developed for isolating bacteriophage from water based on the electropositive silica gel particles (ESPs) method. To optimize the ESPs method, we evaluated the eluent type, flow rate, pH, temperature, and inoculation concentration of bacteriophage using bacteriophage f2. The quantitative detection reported that the recovery of the ESPs method reached over 90%. The qualitative detection demonstrated that the ESPs method effectively isolated 70% of extremely low-concentration bacteriophage (100 PFU/100L). Based on the host bacteria composed of 33 standard strains and 10 isolated strains, the bacteriophages in 18 water samples collected from the three sites in the Tianjin Haihe River Basin were isolated by the ESPs and traditional methods. Results showed that the ESPs method was significantly superior to the traditional method. The ESPs method isolated 32 strains of bacteriophage, whereas the traditional method isolated 15 strains. The sample isolation efficiency and bacteriophage isolation efficiency of the ESPs method were 3.28 and 2.13 times higher than those of the traditional method. The developed ESPs method was characterized by high isolation efficiency, efficient handling of large water sample size and low requirement on water quality.

Phage Abp1 Rescues Human Cells and Mice from Infection by Pan-Drug Resistant Acinetobacter Baumannii

Background/Aims: As an “ESKAPE” pathogen, Acinetobacter baumannii is one of the leading causes of drug-resistant infections in humans. Phage therapy may be a useful strategy in treating infections caused by drug-resistant A. baumannii. Among 21 phage strains that were isolated and described earlier, we investigated the therapeutic efficacy of Abp1 because of its relatively wide host range. Methods: Phage stability assays were used to evaluate thermal and pH stability of Abp1. Abp1 was co-cultured with A. baumannii (AB1) over a range of multiplicities of infection to determine its bactericidal efficacy. HeLa or THP-1 cells were used in the cytotoxicity and protection assays. Finally, the therapeutic effects of Abp1 on local and systemic A. baumannii infection in mice were determined. Results: We found that Abp1 exhibits high thermal and pH stability and has a low frequency of lysogeny. Bacteriophage resistance also occurs at a very low frequency (3.51±0.46×10^-8), and Abp1 can lyse almost all host cells at a MOI as low as 0.1. Abp1 has no detectable cytotoxicity to HeLa or THP-1 cells as determined by LDH release assay. Abp1 can rescue HeLa cells from A. baumannii infection, even if introduced 2 hours post infection. In both local and systemic A. baumannii infection mouse models, Abp1 treatment exhibits good therapeutic effects. Conclusion: Abp1 is an excellent candidate for phage therapy against drug-resistant A. baumannii infections.

Isolation, Characterization, and Bioinformatic Analyses of Lytic Salmonella Enteritidis Phages and Tests of Their Antibacterial Activity in Food.

Salmonella Enteritidis remains a major threat for food safety. To take efforts to develop phage-based biocontrol for S. Enteritidis contamination in food, in this study, the phages against S. Enteritidis were isolated from sewage samples, characterized by host range assays, DNA restriction enzyme pattern analyses, and transmission electron microscope observations, and tested for antibacterial activity in food; some potent phages were further characterized by bioinformatic analyses. Results showed that based on the plaque quality and host range, seven lytic phages targeting S. Enteritidis were selected, considered as seven distinct phages through DNA physical maps, and classified as Myoviridae or Siphoviridae family by morphologic observations; the combined use of such seven strain phages as a "food additive" could succeed in controlling the artificial S. Enteritidis contamination in the different physical forms of food at a range of temperatures; by bioinformatic analyses, both selected phage BPS11Q3 and BPS15Q2 seemed to be newfound obligate lytic phage strains with no indications for any potentially harmful genes in their genomes. In conclusion, our results showed a potential of isolated phages as food additives for controlling S. Enteritidis contamination in some salmonellosis outbreak-associated food vehicles, and there could be minimized potential risk associated with using BPS11Q3 and BPS15Q2 in food.

Interactions of infectious F-specific RNA bacteriophages with suspended matter and sediment: Towards an understanding of FRNAPH distribution in a river water system

The association of viruses with settling particles is certainly a major process controlling the spread of viral pollution in surface water and sediment. To better understand the viral distribution in a river system, the behavior of F-specific RNA bacteriophages (FRNAPHs) was investigated in relationship with the suspended solids and sediment. The partitioning of phage particles (free or associated with solids) in surface water and the attachment capabilities of eight distinct strains of phages to sediment were studied in lab experiments. In situ observations were also performed with the genotyping of 166 individual plaques of FRNAPHs isolated from surface water and sediment. The results reported here demonstrate a variation of the status of infectious phages as a function of the hydro-climatological conditions. Phage-solid association seems to mainly occur during the peak of rainfall-runoff events but also to a certain extent during the recession phase compared to low flow conditions. The transfer of phages from the water column to sediment may occur at this time. Furthermore, the ability of FRNAPHs to interact with sediment was established for six strains out of eight, belonging to genogroups II, III and IV. A similar dynamic was observed for strains within a same genogroup despite different intensity of attachment and inactivation rates for strains of genogroups III and IV. The latter results match the in situ observations in the water and sediment compartments of the studied area. Infectious FRNAPH genogroup II was more abundant in sediment than in surface water. Its capability to sorb to sediment and its higher persistence in the environment compared to genogroups III and IV were the two main explanations. Together, lab and in situ experiments produce an overall vision of the mechanisms governing FRNAPH distribution among the water column and riverbed sediment.

Inventory building of phages against extensively drug-resistant Acinetobacter baumannii isolated from wounds of patients with severe burn and related characteristic analysis

To build inventory of phages against extensively drug-resistant Acinetobacter Baumannii isolated from wounds of inpatients of burn ICU and analyze related characteristics. In 2014 and 2015, 131 strains of extensively drug-resistant Acinetobacter Baumannii were isolated from wounds of inpatients of burn ICU from one hospital in Chongqing. In 2015, 98 strains of extensively drug-resistant Acinetobacter Baumannii were isolated from wounds of inpatients of burn ICU from 6 hospitals in Guangdong province. Above-mentioned 229 strains were collected for conducting experiments as follows: (1) Multilocus sequence typing (MLST) of strains isolated from Chongqing and Guangdong province was analyzed. (2) Sewage co-culture method was applied for isolation of phages with above-mentioned strains and sewage from Chongqing and Guangdong province. Numbers of isolated phages and times of successful isolation and unsuccessful isolation were recorded. (3) The most prevalent subtypes of strains from Chongqing and Guangdong province in 2015 were collected, and their phages respectively underwent cross infection with all strains from Chongqing and those from Guangdong province. The lysis ability of phage was observed when phage underwent cross infection with the same subtype of strain or not the same, and the lytic ratio was calculated. (4) Fluid of phage in one type was randomly selected and equally divided into 3 parts, and its titer was determined by double dilution method. Then each part of phage fluid was subdivided into 3 small parts, which were cultured with LB fluid medium and respectively stored under the condition of -20 ℃, 4 ℃, and room temperature. After being stored for 1 month and 2 months, the titer of phage was determined for evaluating stability of phage. Data were processed with Fisher's exact test, chi-square test, and one-way analysis of variance. (1) The major type of strains from Chongqing in 2014 was ST368 (45%, 31/69), and major types of strains from Chongqing in 2015 were ST75 (26%, 16/62) and ST195 (24%, 15/62), while that from Guangdong province in 2015 was ST977 (46%, 45/98). (2) For strains from Chongqing, isolation effect of phage with sewage of Chongqing (8 times of successful isolation with 9 strains of phages and 1 time of unsuccessful isolation) was better than that with sewage of Guangdong province (1 time of successful isolation with 1 strain of phage and 7 times of unsuccessful isolation). For strains from Guangdong province, isolation effect of phage with sewage of Guangdong province (8 times of successful isolation with 6 strains of phages) was better than that with sewage of Chongqing (7 times of unsuccessful isolation with no phage). These differences were statistically significant (P<0.05 or P<0.01). There was no obvious difference in isolation effect of phage between strains from Chongqing with sewage of Chongqing and strains from Guangdong province with sewage of Guangdong province (P>0.05). (3) The ratios of phages of ST75 and ST977 extensively drug-resistant Acinetobacter Baumannii strains lysing the strains with the same type were respectively 13/16 and 8/9, which were obviously higher than those lysing the strains with different type (respectively 11/115 and 3/53, with χ(2) values respectively 48.23 and 68.46, P values below 0.001). (4) Compared with that before storage, titer of phage under storage condition of -20 ℃, 4 ℃, and room temperature for 1 month decreased by approximately 1 order of magnitude, and that for 2 months decreased by approximately 2 orders of magnitude. After being stored for 1 month and 2 months, there were no statistically significant differences in titer of phage among 3 storage conditions (with F values respectively 1.29 and 1.07, P values above 0.05). This study has successfully built an inventory covering 229 strains of phages of extensively drug-resistant Acinetobacter Baumannii. MLST of extensively drug-resistant Acinetobacter baumannii varies in different area and different time. Phage can be well isolated using sewage with the same source as that of strain. The lysis ability of phage is closely related to the MLST of strains. Inventory of phages should be built according to regional division. Moreover, phage cultured with LB fluid medium shows good stability without special requirements for storage conditions.

Чувствительность условно-патогенных энтеробактерий к антибиотикам и производственным штаммам бактериофагов

Чувствительность условно-патогенных энтеробактерий к антибиотикам и производственным штаммам бактериофагов

Specificity of Multi-Modal Aphid Defenses against Two Rival Parasitoids.

Insects are often attacked by multiple natural enemies, imposing dynamic selective pressures for the development and maintenance of enemy-specific resistance. Pea aphids (Acyrthosiphon pisum) have emerged as models for the study of variation in resistance against natural enemies, including parasitoid wasps. Internal defenses against their most common parasitoid wasp, Aphidius ervi, are sourced through two known mechanisms– 1) endogenously encoded resistance or 2) infection with the heritable bacterial symbiont, Hamiltonella defensa. Levels of resistance can range from nearly 0–100% against A. ervi but varies based on aphid genotype and the strain of toxin-encoding bacteriophage (called APSE) carried by Hamiltonella. Previously, other parasitoid wasps were found to commonly attack this host, but North American introductions of A. ervi have apparently displaced all other parasitoids except Praon pequodorum, a related aphidiine braconid wasp, which is still found attacking this host in natural populations. To explain P. pequodorum’s persistence, multiple studies have compared direct competition between both wasps, but have not examined specificity of host defenses as an indirectly mediating factor. Using an array of experimental aphid lines, we first examined whether aphid defenses varied in effectiveness toward either wasp species. Expectedly, both types of aphid defenses were effective against A. ervi, but unexpectedly, were completely ineffective against P. pequodorum. Further examination showed that P. pequodorum wasps suffered no consistent fitness costs from developing in even highly ‘resistant’ aphids. Comparison of both wasps’ egg-larval development revealed that P. pequodorum’s eggs have thicker chorions and hatch two days later than A. ervi’s, likely explaining their differing abilities to overcome aphid defenses. Overall, our results indicate that aphids resistant to A. ervi may serve as reservoirs for P. pequodorum, hence contributing to its persistence in field populations. We find that specificity of host defenses and defensive symbiont infections, may have important roles in influencing enemy compositions by indirectly mediating the interactions and abundance of rival natural enemies.

POSSIBILITIES OF APPLICATION OF MALDI-TOF MASS-SPECTROMETRY FOR STUDY OF CARBOHYDRATE-SPECIFIC RECEPTORS FOR DIAGNOSTIC BACTERIOPHAGE EL TOR

Study mechanisms of interaction of diagnostic bacteriophage El Tor with sensitive strain Vibrio cholerae El Tor 18507 using direct protein profiling, identification of constant and variable proteins, taking part in interaction of the phage and cell, as well as carbohydrate-specific phage receptors. . A commercial preparation of cholera diagnostic bacteriophage El Tor, strain V. cholerae El Tor 18507 were used. Effect of carbohydrates on bacteriophage activity was determined in experiments with phage by a classic and modified by us method. Protein profiles of the studied objects were studied using MSP-analysis method. Sucrose was shown to inhibit lytic activity of bacteriophage. Proteome profiles of El Tor bacteriophage and sensitive indicator strains were studied, identification of constant and variable proteins of the studied objects by MSP Peak-list program was carried out. Analysis of changes of profiles of phage and microbial cell during interaction with sucrose gave a basis for assuming, that sucrose in the mixture of culture-phage enters interaction namely with phage protein receptors, blocking receptors specific for cholera vibrio, that subsequently manifests in a sharp decrease of phage activity against the sensitive strain.

Bioengineering bacteriophages to enhance the sensitivity of phage amplification-based paper fluidic detection of bacteria

Bacteriophage (phage) amplification is an attractive method for the detection of bacteria due to a narrow phage-host specificity, short amplification times, and the phages’ ability to differentiate between viable and non-viable bacterial cells. The next step in phage-based bacteria detection is leveraging bioengineered phages to create low-cost, rapid, and easy-to-use detection platforms such as lateral flow assays. Our work establishes the proof-of-concept for the use of bioengineered T7 phage strains to increase the sensitivity of phage amplification-based lateral flow assays. We have demonstrated a greater than 10-fold increase in sensitivity using a phage-based protein reporter, maltose-binding protein, over the detection of replicated T7 phage viron itself, and a greater then 100-fold increase in sensitivity using a phage-based enzymatic reporter, alkaline phosphatase. This increase in sensitivity enabled us to detect 103CFU/mL of Escherichia coli in broth after 7h, and by adding a filter concentration step, the ability to detect a regulatory relevant E. coli concentration of 100CFU/100mL in inoculated river water after 9h, where the current standard requires days for results. The combination of the paper fluidic format with phage-based detection provides a platform for the development of novel diagnostics that are sensitive, rapid, and easy to use.

Aligning the unalignable: bacteriophage whole genome alignments.

BackgroundIn recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences.ResultsIn this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressiveMauve aligner – which implements a partial order strategy, but whose alignments are linearized – shows a greatly improved interactive graphic display, while avoiding misalignments.ConclusionsMultiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains.A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0869-5) contains supplementary material, which is available to authorized users.

Pre‐adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates

Recent years have seen renewed interest in phage therapy--the use of viruses to specifically kill disease-causing bacteria--because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here, we determined whether in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung isolates to four different phages. We first pre-adapted all phage strains against all bacterial strains and then compared the efficacy of pre-adapted and nonadapted phages against ancestral bacterial strains. We found that evolved phages were more efficient in reducing bacterial densities than ancestral phages. This was primarily because only 50% of bacterial strains were able to evolve resistance to evolved phages, whereas all bacteria were able to evolve some level of resistance to ancestral phages. Although the rate of resistance evolution did not differ between intermittent and chronic isolates, it incurred a relatively higher growth cost for chronic isolates when measured in the absence of phages. This is likely to explain why evolved phages were more effective in reducing the densities of chronic isolates. Our data show that pathogen genotypes respond differently to phage pre-adaptation, and as a result, phage therapies might need to be individually adjusted for different patients.

Penetration and translocation of Erwinia amylovora-specific bacteriophages in apple - a possibility of enhanced control of fire blight

We have investigated the uptake and delivery of Erwinia amylovora-specific bacteriophages in apple plants. The main aim of this study was to assess the potential of phage application as a means for improving phage persistence and thereby the control of fire blight, the disease caused by E. amylovora. Both phage strains tested (ΦEa104 and H5K) were able to translocate in apple seedlings and were detectable by a modified Adams’ drop test and real-time qPCR in plant parts above ground level following their application to the roots. Conversely, phages were detectable in roots after spraying them onto the stem and leaves. A water suspension of phages effectively decreased symptom severity of E. amylovora infection in apple seedlings following treatment of roots or aerial plant parts and application to the cotyledon, as judged by symptom bonitation. A similar effect was achieved by spraying a phage suspension onto flowering firethorn shoots. Interestingly no significant differences in controlling E. amylovora infection were found among the two phage strains tested. It seems that phages specific to E. amylovora can penetrate plants and exhibit a decrease in severity of symptoms caused by the phytopathogen. Demonstrating in planta translocation of E. amylovora-specific bacteriophages and their effect of reducing fire blight symptoms may significantly contribute to a better control of E. amylovora and promote further investigations on penetration and translocation of phages into plants.

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin.

The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.

The capability of non-native strains of Bacteroides bacteria to detect bacteriophages as faecal indicators in a tropical area.

To evaluate the use of nonlocal, already-available strains of phages to indicate faecal contamination in Thailand waters. Phages of Bacteroides fragilis strains ATCC 700786 (RYC2056PH) and ATCC 51477 (HSP40PH) were measured in 71 human and animal wastewater samples in Thailand using a double-layer agar assay. Bacteriophage RYC2056PH was detected at concentrations comparable to representative human and animal wastewater samples from European and Mediterranean countries, with 61·7 and 33·3% above the threshold value of 100 PFU 100ml(-1) in wastewater samples of human and animal origins, respectively. On the other hand, HSP40PH was detected at low concentrations in both human- and animal-polluted wastewaters. Moreover, RYC2056PH was found in 12 canal waters with human-influenced pollution and was not detected in 6 nonpolluted river waters being tested in this study. The presence of RYC2056PH could indicate nonsource-specific faecal contamination in Thailand. This study provided the first evidence that bacteriophages of the European-isolated B. fragilis strain RYC2056 could be used as nonsource-specific faecal indicators in the Southeast Asian region. The results of this study support the worldwide use of Bacteroides phages as faecal indicators.

Phage-bacteria network analysis and its implication for the understanding of coral disease.

Multiple studies have explored microbial shifts in diseased or stressed corals; however, little is known about bacteriophage interactions with microbes in this context. This study characterized microbial 16S rRNA amplicons and phage metagenomes associated with Montastraea annularis corals during a concurrent white plague disease outbreak and bleaching event. Phage consortia differed between bleached and diseased tissues. Phages in the family Inoviridae were elevated in diseased or healthy tissues compared with bleached portions of diseased tissues. Microbial communities also differed between diseased and bleached corals. Bacteria in the orders Rhodobacterales and Campylobacterales were increased while Kiloniellales was decreased in diseased compared with other tissues. A network of phage-bacteria interactions was constructed of all phage strains and 11 bacterial genera that differed across health states. Phage-bacteria interactions varied in specificity: phages interacted with one to eight bacterial hosts while bacteria interacted with up to 59 phages. Six phages were identified that interacted exclusively with Rhodobacterales and Campylobacterales. These results suggest that phages have a role in controlling stress-associated bacteria, and that networks can be utilized to select potential phages for mitigating detrimental bacterial growth in phage therapy applications.