Browsing by Subject "virulence"

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  • Qiu, Yachen (Helsingin yliopisto, 2021)
    Onion (Allium cepa L.) is an important vegetable, which provides major nutritional benefits. In Finland, basal rot caused by Fusarium fungal species (FBR) has become the most destructive disease of onion in recent years. It causes damping off and stunted growth on onion seedlings and root death and abscission and bulb rot on mature onions. The average onion crop loss caused by basal rot has been up to 10% in conventional farming and as high as 30% in organic farming. In this study, a seedling assay was conducted to test the virulence of different Fusarium isolates on a commercial onion cultivar. The study goals were, primarily, to find out which of the Fusarium isolates, originating from onion and crop rotation plants grown in Finland, are pathogenic, and secondly, to compare the virulence of different isolates. Altogether 115 Fusarium isolates were tested for virulence on onion seedlings in a greenhouse. Fifty-five of the tested isolates of F. oxysporum, F. proliferatum and F. redolens were more or less virulent. 19.4% of F. oxysporum isolates, 35.3% of F. proliferatum isolates and 18.2% of F. redolens isolates showed high virulence. Among the aggressive pathogens isolated from onion samples, F. oxysporum f.sp. cepae is still the dominant onion pathogen, F. proliferatum is a new pathogen on onion in Finland, and relatively more aggressive than F. oxysporum. The F. solani and F. tricinctum isolates tested did not have any detrimental effects on the onion seedling health or growth. In order to control FBR in Finland, avoiding planting onion in the infested soils, growing onions from local seedlings to avoid new contamination and storing onions at cold temperatures are recommended.
  • Ghimire, Sadikshya (Helsingin yliopisto, 2021)
    Fusarium proliferatum has recently become a major threat to onion, which is an important food crop for food security and has a significant role in the agricultural sector. This fungus is found causing rots and producing mycotoxin fumonisin that, if ingested, can cause carcinogenic effects in humans and fatal diseases in animals. F. proliferatum has been identified as a pathogen causing rots and wilts in many plants in several countries, and recently some isolates of this pathogen were also found in Finland causing basal rot in onion. Though F. proliferatum has wide adaptability and pathogenicity, there are research gaps on this newly emerging pathogen, which is mostly limited to some specific hosts such as maize. There is a lack of knowledge of its infection mechanisms and mycotoxin production dynamics in onion. This experimental work was conducted at the University of Helsinki, Finland, to study the nature of pathogenicity and toxin gene expression of F. proliferatum in laboratory conditions as a function of time. Spore suspensions of three isolates of F. proliferatum, Fpr047, Fpr049, and Fpr919, were prepared and used as inoculums that were injected into healthy organically grown onions, which were then stored in dark for five weeks. Control bulbs were inoculated with sterile water. Pathogen virulence, based on symptom development, and fungal colonization in the onion tissues were determined at five different time points and the toxin gene expression was determined at three time points. Colonization levels were determined by real-time PCR using primers binding to the intergenic spacer (IGS) region of F. proliferatum. A part of the IGS region of the three isolates was sequenced to study the diversity between the isolates. All the tested isolates were found to be virulent, and they colonized the onions after one week from inoculation. However, the isolate Fpr919 appeared different from the other two in terms of symptom severity. It was more aggressive than the other two, causing disease symptoms earlier and causing more severe rot symptoms in the infected bulbs. It also had nucleotide sequence variations in the IGS region in comparison with the other two isolates, suggesting genetic diversity. No significant differences were observed between the isolates in the fungal colonization levels. Expression of FUM1 gene and a putative virulence gene SIX2-1 was detected by RT-RT-PCR in most of the infected tissue samples. The results obtained signify that F. proliferatum is a pathogen with the potential of producing fumonisin toxin in onion, suggesting the need for further molecular study on this fungus to control the disease and prevent mycotoxin contamination in plant products.
  • Prieto, Ana M. Guzman; van Schaik, Willem; Rogers, Malbert R. C.; Coque, Teresa M.; Baquero, Fernando; Corander, Jukka; Willems, Rob J. L. (2016)
    Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus. Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E faecalls.
  • Townsend, Eleanor M; Kelly, Lucy; Gannon, Lucy; Muscatt, George; Dunstan, Rhys; Michniewski, Slawomir; Sapkota, Hari; Kiljunen, Saija J; Kolsi, Anna; Skurnik, Mikael; Lithgow, Trevor; Millard, Andrew D; Jameson, Eleanor (2021)
    Introduction: Klebsiella is a clinically important pathogen causing a variety of antimicrobial resistant infections in both community and nosocomial settings, particularly pneumonia, urinary tract infection, and sepsis. Bacteriophage (phage) therapy is being considered a primary option for the treatment of drug-resistant infections of these types. Methods: We report the successful isolation and characterization of 30 novel, genetically diverse Klebsiella phages. Results: The isolated phages span six different phage families and nine genera, representing both lysogenic and lytic lifestyles. Individual Klebsiella phage isolates infected up to 11 of the 18 Klebsiella capsule types tested, and all 18 capsule-types were infected by at least one of the phages. Conclusions: Of the Klebsiella-infecting phages presented in this study, the lytic phages are most suitable for phage therapy, based on their broad host range, high virulence, short lysis period and given that they encode no known toxin or antimicrobial resistance genes. Phage isolates belonging to the Sugarlandvirus and Slopekvirus genera were deemed most suitable for phage therapy based on our characterization. Importantly, when applied alone, none of the characterized phages were able to suppress the growth of Klebsiella for more than 12 h, likely due to the inherent ease of Klebsiella to generate spontaneous phage-resistant mutants. This indicates that for successful phage therapy, a cocktail of multiple phages would be necessary to treat Klebsiella infections.
  • Laine, Anna-Liisa; Makinen, Hannu (2018)
    The ability of a parasite strain to establish and grow on its host may be drastically altered by simultaneous infection by other parasite strains. However, we still lack an understanding of how life-history allocations may change under coinfection, although life-history correlations are a critical mechanism restricting the evolutionary potential and epidemiological dynamics of pathogens. Here, we study how life-history stages and their correlations change in the obligate fungal pathogen Podosphaera plantaginis under single infection and coinfection scenarios. We find increased pathogen loads under coinfection, but this is not explained by an enhanced performance at any of the life-history stages that constitute infections. Instead, we show that under coinfection the correlation between timing of sporulation and final pathogen load becomes positive. The changes in pathogen life-history allocations leading to more severe infections under coinfection can have far-reaching epidemiological consequences, as well as implication for our understanding of the evolution of virulence.
  • Markkanen, Melina (Helsingin yliopisto, 2020)
    Constantly increasing level of bacteria becoming resistant to clinically relevant antibiotics challenges the modern medical achievements made over the past century. In global scale, one of the most significant information gaps concerning the occurrence of resistant bacteria is located in West African countries. Klebsiella pneumoniae and Escherichia coli strains resistant to 3rd generation cephalosporins and carbapenems are a major risk to public health through infections with limited or no available treatment options. The resistance to these antibiotics among Enterobacteriaceae is mainly mediated by hydrolyzing enzymes such as extended-spectrum beta-lactamases (ESBL). The focus of this thesis is to study the genes encoding these enzymes and other resistance factors found in K. pneumoniae and E. coli isolated from human stool and waste water samples in Burkina Faso and Mali. Tree Enterobacteriaceae isolates were selected for whole genome sequence (WGS) analysis based on their phenotypic resistance profiles defined by disk diffusion method. Reads were assembled to draft genomes and the genomes were studied for their antibiotic resistance genes, virulence genes and their associations to mobile genetic elements found in these isolates’ genomes. Additionally a pan-genome was created to investigate species specific features of K. pneumoniae and their role in heavy load of antibiotic resistance genes among these isolates. Pan-genome consisted of two genomes sequenced in this study and 12 genomes from the publically available database. 16-month old Burkinabe child was a carrier of one ESBL-producing K. pneumoniae (isolate Burkina_1) and one ESBL-positive E. coli along with the resistance to multiple other antibiotics. With genome wide analysis the K. pneumoniae strain could be described as sequence type (ST) 45 representing, multidrug resistant and ESBL-gene CTX-M-15 carrying strain with highly similar virulence gene profile to strains previously described as pathogenic K. pneumoniae causing neonatal sepsis. K. pneumoniae isolated from the stool sample of an adult living in Burkina Faso was found to be multidrug resistant, though non-ESBL-producer strain (isolate Burkina_2). The isolate showed no similarity to any previously described sequence type. CTX-M-15 encoding E. coli of ST38 (isolate Mali_1) carried by Malian child showed resistance to five different classes of antibiotics in addition to the 3rd generation cephalosporins. At the same time the isolate showed hybrid virulence gene profile with virulence genes associated to many different E. coli pathotypes including neonatal meningitis causing E. coli (NMEC). The exceptional plasticity of K. pneumoniae genome could be recognized as one of the putative explanations for the high number of resistance genes found among the isolates studied in this work. Antibiotic resistance genes were found to be associated to mobile genetic elements (MGE) and as the genetic plasticity is caused by the acquisition of external genetic material via MGEs such as plasmids, this can lead to indirect accumulation of resistance genes in these genomes. The results in this thesis work show alarming examples of pathogens that potentially cause severe infections, have extremely narrow or no treatment options and are carried by infants. These findings are in line with the few data about the level of faecal carriage of ESBL-producing strains by people in Burkina Faso and Mali reported previously.
  • Zakham, Fathiah; Sironen, Tarja; Vapalahti, Olli; Kant, Ravi (2021)
    Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG ("Bacillus Calmette-Guerin") vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain "M. canettii". Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity. Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development.
  • Pasanen, Miia; Waleron, Malgorzata; Schott, Thomas; Cleenwerck, Ilse; Misztak, Agnieszka; Waleron, Krzysztof; Pritchard, Leighton; Bakr, Ramadan; Degefu, Yeshitila; van der Wolf, Jan; Vandamme, Peter; Pirhonen, Minna (2020)
    Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second Glade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421(T) (CFBP 8630(T)=LMG 30828(T)) is suggested as a type strain.
  • Karvonen, Anssi; Lindström, Kai (2018)
    Parasitism is considered a major selective force in natural host populations. Infections can decrease host condition and vigour, and potentially influence, for example, host population dynamics and behavior such as mate choice. We studied parasite infections of two common marine fish species, the sand goby (Pomatoschistus minutus) and the common goby (Pomatoschistus microps), in the brackish water Northern Baltic Sea. We were particularly interested in the occurrence of parasite taxa located in central sensory organs, such as eyes, potentially affecting fish behavior and mate choice. We found that both fish species harbored parasite communities dominated by taxa transmitted to fish through aquatic invertebrates. Infections also showed significant spatiotemporal variation. Trematodes in the eyes were very few in some locations, but infection levels were higher among females than males, suggesting differences in exposure or resistance between the sexes. To test between these hypotheses, we experimentally exposed male and female sand gobies to infection with the eye fluke Diplostomum pseudospathaceum. These trials showed that the fish became readily infected and females had higher parasite numbers, supporting higher susceptibility of females. Eye fluke infections also caused high cataract intensities among the fish in the wild. Our results demonstrate the potential of these parasites to influence host condition and visual abilities, which may have significant implications for survival and mate choice in goby populations.
  • Gatta, Viviana; Ilina, Polina; Porter, Alison; McElroy, Stuart; Tammela, Päivi (2019)
    Since quorum sensing (QS) is linked to the establishment of bacterial infection, its inactivation represents one of the newest strategies to fight bacterial pathogens. LsrK is a kinase playing a key role in the processing of autoinducer-2 (AI-2), a quorum-sensing mediator in gut enteric bacteria. Inhibition of LsrK might thus impair the quorum-sensing cascade and consequently reduce bacterial pathogenicity. Aiming for the development of a target-based assay for the discovery of LsrK inhibitors, we evaluated different assay set-ups based on ATP detection and optimized an automation-compatible method for the high-throughput screening of chemical libraries. The assay was then used to perform the screening of a 2000-compound library, which provided 12 active compounds with an IC50