Browsing by Subject "HOST-RANGE"

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  • Laanto, Elina; Mäkelä, Kati; Hoikkala, Ville; Ravantti, Janne; Sundberg, Lotta-Riina (2020)
    Phage therapy is becoming a widely recognized alternative for fighting pathogenic bacteria due to increasing antibiotic resistance problems. However, one of the common concerns related to the use of phages is the evolution of bacterial resistance against the phages, putatively disabling the treatment. Experimental adaptation of the phage (phage training) to infect a resistant host has been used to combat this problem. Yet, there is very little information on the trade-offs of phage infectivity and host range. Here we co-cultured a myophage FCV-1 with its host, the fish pathogenFlavobacterium columnare, in lake water and monitored the interaction for a one-month period. Phage resistance was detected within one day of co-culture in the majority of the bacterial isolates (16 out of the 18 co-evolved clones). The primary phage resistance mechanism suggests defense via surface modifications, as the phage numbers rose in the first two days of the experiment and remained stable thereafter. However, one bacterial isolate had acquired a spacer in its CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas locus, indicating that also CRISPR-Cas defense was employed in the phage-host interactions. After a week of co-culture, a phage isolate was obtained that was able to infect 18 out of the 32 otherwise resistant clones isolated during the experiment. Phage genome sequencing revealed several mutations in two open reading frames (ORFs) likely to be involved in the regained infectivity of the evolved phage. Their location in the genome suggests that they encode tail genes. Characterization of this evolved phage, however, showed a direct cost for the ability to infect several otherwise resistant clones-adsorption was significantly lower than in the ancestral phage. This work describes a method for adapting the phage to overcome phage resistance in a fish pathogenic system.
  • Leskinen, Katarzyna; Tuomala, Henni; Wicklund, Anu; Horsma-Heikkinen, Jenni; Kuusela, Pentti; Skurnik, Mikael; Kiljunen, Saija (2017)
    Staphylococcus aureus is a commensal and pathogenic bacterium that causes infections in humans and animals. It is a major cause of nosocomial infections worldwide. Due to increasing prevalence of multidrug resistance, alternative methods to eradicate the pathogen are necessary. In this respect, polyvalent staphylococcal myoviruses have been demonstrated to be excellent candidates for phage therapy. Here we present the characterization of the bacteriophage vB_SauM-fRuSau02 (fRuSau02) that was isolated from a commercial Staphylococcus bacteriophage cocktail produced by Microgen (Moscow, Russia). The genomic analysis revealed that fRuSau02 is very closely related to the phage MSA6, and possesses a large genome (148,464 bp), with typical modular organization and a low G+ C (30.22%) content. It can therefore be classified as a new virus among the genus Twortlikevirus. The genome contains 236 predicted genes, 4 of which were interrupted by insertion sequences. Altogether, 78 different structural and virion-associated proteins were identified from purified phage particles by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The host range of fRuSau02 was tested with 135 strains, including 51 and 54 Staphylococcus aureus isolates from humans and pigs, respectively, and 30 coagulase-negative Staphylococcus strains of human origin. All clinical S. aureus strains were at least moderately sensitive to the phage, while only 39% of the pig strains were infected. Also, some strains of Staphylococcus intermedius, Staphylococcus lugdunensis, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus saprophyticus and Staphylococcus pseudointer were sensitive. We conclude that fRuSau02, a phage therapy agent in Russia, can serve as an alternative to antibiotic therapy against S. aureus.
  • Odeh, Issam; Arar, Sharif; Al-Hunaiti, Afnan; Sa'aydeh, Hiyam; Hammad, Ghada; Duplissy, Jonathan; Vuollekoski, Henri; Korpela, Antti; Petäjä, Tuukka; Kulmala, Markku; Hussein, Tareq (2017)
    The quality and chemical composition of urban dew collections with dust precipitates without pre-cleaning of the collecting surface WSF (white standard foil) were investigated for 16 out of 20 collected samples with collected volumes ranging from 22 to 230 ml. The collection period was from March to July 2015 at an urban area, Jubaiha, which is located in the northern part of the capital city Amman, Jordan. The obtained results indicated the predominance of Ca2+ and SO42- ions (ratio 2.2: 1) that originated from Saharan soil dust; where the collected samples were alkaline (mean pH = 7.35) with high mineralization (429.22 mg/L) exceeding the previously reported dew values in Amman-Jordan. A relocation of NaCl and to a less extent Mg2+ from sea to land by Saharan wind is indicated by the percent sea-salt fraction calculations (over 100 and 52, respectively). The collected samples exhibited high total organic carbon (TOC) values ranging from 11.86 to 74.60 mg/L, presence of particulate settled material with turbidity ranging from 20.10 to 520.00 NTU, and presence of undesired elements like boron (mean = 1.48 mg/L) that made it different in properties from other dew water collections at clean surfaces, and exceeding the standard limits for drinking water for these parameters set by Jordanian Drinking Water standards (JS286/2015)/WHO standard. The quality of this water is more close to that for raw or agricultural water but if it is meant to be used as potable source of water, at least sand and activated charcoal filters are needed to purify it.
  • Sadeghi, Mohammadreza; Popov, Vsevolod; Guzman, Hilda; Phan, Tung Gia; Vasilakis, Nikos; Tesh, Robert; Delwart, Eric (2017)
    Eleven viral isolates derived mostly in albopictus C6/36 cells from mosquito pools collected in Southeast Asia and the Americas between 1966 and 2014 contained particles with electron microscopy morphology typical of reoviruses. Metagenomics analysis yielded the near complete genomes of three novel reoviruses, Big Cypress orbivirus, Ninarumi virus, and High Island virus and a new tetravirus, Sarawak virus. Strains of previously characterized Sathuvarachi, Yunnan, Banna and Parry's Lagoon viruses (Reoviridae), Bontang virus (Mesoniviridae), and Culex theileri flavivirus (Flaviviridae) were also characterized. The availability of these mosquito virus genomes will facilitate their detection by metagenomics or PCR to better determine their geographic range, extent of host tropism, and possible association with arthropod or vertebrate disease.
  • Mäntynen, Sari; Sundberg , Lotta-Riina; Oksanen, Hanna Maarit; Poranen, Minna Marjetta (2019)
    Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of viral lineages, postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (similar to 1 x 10(31)) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
  • Rajamäki, Minna-Liisa; Lemmetty, Anne; Laamanen, Jaana; Roininen, Elina; Vishwakarma, Archana; Streng, Janne; Latvala, Satu; Valkonen, Jari P. T. (2019)
    Pathogen-free stocks of vegetatively propagated plants are crucial in certified plant production. They require regular monitoring of the plant germplasm for pathogens, especially of the stocks maintained in the field. Here we tested pre-basic mother plants of Fragaria, Rubus and Ribes spp., and conserved accessions of the plant genetic resources of Rubus spp. maintained at research stations in Finland, for the presence of viruses using small interfering RNA (siRNA) -based diagnostics (VirusDetect). The advance of the method is that unrelated viruses can be detected simultaneously without resumptions of the viruses present. While no virus was detected in pre-basic mother plants of Fragaria and Ribes species, rubus yellow net virus (RYNV) was detected in pre-basic mother plants of Rubus. Raspberry bushy dwarf virus (RBDV), black raspberry necrosis virus (BRNV), raspberry vein chlorosis virus (RVCV) and RYNV were detected in the Rubus genetic resource collection. The L polymerase encoding sequence characterized from seven RVCV isolates showed considerable genetic variation. The data provide the first molecular biological evidence for the presence of RYNV in Finland. RYNV was not revealed in virus indexing by indicator plants, which suggests that it may be endogenously present in some raspberry cultivars. In addition, a putative new RYNV-like badnavirus was detected in Rubus spp. Blackcurrant reversion virus (BRV) and gooseberry vein banding associated virus (GVBaV) were detected in symptomatic Ribes plants grown in the field. Results were consistent with those obtained using PCR or reverse transcription PCR and suggest that the current virus indexing methods of pre-basic mother plants work as expected. Furthermore, many new viruses were identified in the collections of plant genetic resources not previously tested for viruses. In the future, siRNA-based diagnostics could be a useful supplement for the currently used virus detection methods in certified plant production and thus rationalize and simplify the current testing system.
  • Carlson, Colin J.; Farrell, Maxwell J.; Grange, Zoe; Han, Barbara A.; Mollentze, Nardus; Phelan, Alexandra L.; Rasmussen, Angela L.; Albery, Gregory F.; Bett, Bernard; Brett-Major, David M.; Cohen, Lily E.; Dallas, Tad; Eskew, Evan A.; Fagre, Anna C.; Forbes, Kristian M.; Gibb, Rory; Halabi, Sam; Hammer, Charlotte C.; Katz, Rebecca; Kindrachuk, Jason; Muylaert, Renata L.; Nutter, Felicia B.; Ogola, Joseph; Olival, Kevin J.; Rourke, Michelle; Ryan, Sadie J.; Ross, Noam; Seifert, Stephanie N.; Sironen, Tarja; Standley, Claire J.; Taylor, Kishana; Venter, Marietjie; Webala, Paul W. (2021)
    In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.