Browsing by Subject "PATHOGENS"

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  • Gonzalez-Ortiz, Gemma; Bronsoms, Silvia; Van Ufford, H. C. Quarles; Halkes, S. Bart A.; Virkola, Ritva; Liskamp, Rob M. J.; Beukelman, Cees J.; Pieters, Roland J.; Francisco Perez, Jose; Maria Martin-Orue, Susana (2014)
  • Vitt, Anton; Babenka, Andrei; Bostrom, Elisabeth A.; Gustafsson, Anders; Lira, Ronaldo; Slizen, Veronica; Sorsa, Timo; Tervahartiala, Taina; Buhlin, Kåre (2020)
    To evaluate the effect of adjunctive antiseptic irrigation of periodontal pockets on microbial and cytokine profiles. Fifty-nine patients with severe periodontitis were allocated to one of three groups for scaling and root planing facilitated with different adjunctive antiseptics: 1% polyhexamethyleneguanidine phosphate (PHMG-P) (n = 19), 0.2% chlorhexidine (CHX) (n = 21) or distilled water (n = 19). Gingival crevicular fluid and subgingival bacterial samples were collected at baseline, and at 2 weeks, and 1 and 4 months. The levels of interleukin (IL)-1 beta, IL-8, IL-10, and IL-17A, matrix metalloproteinase (MMP)-8, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum,Aggregatibacter actinomycetemcomitans, and Prevotella intermedia were determined. There were no intergroup differences in cytokine concentrations and bacterial counts at any follow-up, however, varying patterns were observed. In the PHMG-P and water groups IL-1 beta expression peaked at 2 weeks and then gradually declined. In all three groups, the dynamics of MMP-8 concentration were non-linear, increasing by 2 weeks and then declining to below baseline (p > 0.05). P. gingivalis and T. forsythia declined within the first month and increased thereafter, not regaining the baseline level. Adjunctive antiseptic treatment was associated with changes in biomarkers and bacterial counts in the course of the study. The effects of adjunctive antiseptic irrigation were limited in the applied protocol.
  • Mgbeahuruike, Eunice Ego; Holm, Yvonne; Vuorela, Heikki; Amandikwa, Chinyere; Fyhrquist, Pia (2019)
    Ethnobotanical relevance: Piper guineense occurs commonly in West Africa where it is used for fungal infections instead of the costly and not always accessible conventional antifungals. Fungal, yeast-based diseases are common in West-Africa especially among those living with HIV/AIDS, and thus this study was performed in Imo state, South-Eastern Nigeria, where P. guineense is predominantly used for the treatment of fungal diseases, such as skin rashes, oral thrush and vaginosis. Aim of study: The scarce number of previous studies on the documentation of the traditional uses of P. guineense extracts for the treatment of fungal infections in Nigeria prompted this survey. The investigation focused on how traditional healers recognize and diagnose fungal infections, how P. guineense is collected, on the various parts used for the treatments, methods of preparations, administrations and treatments. In addition, an in vitro anti fungal screening of P. guineense fruit and leaf extracts of various polarities, and piperine and piperlongumine, representing the main constituents in these extracts, were performed. Methods: A house to house ethnobotanical survey was conducted using questionnaires. Twenty traditional medical practitioners (TMP) and herb sellers from ten villages were interviewed. Four human pathogenic strains of yeast and Cryptococcus neoformans, a yeast-like basidiomycete causing meningitis in immunocompromised individuals, were used for the antifungal screening. Results: The traditional medical practitioners (TMP) and herb sellers explained that the leaves and fruits are the most commonly used plant parts for the treatments. The oral intake of the extracts in locally produced bamboo alcohol (Kai-kai) is the most common method of administration. In accordance with these recorded traditional uses, we found that extracts of P. guineense were growth inhibitory against the fungal strains with MIC values ranging from 39 to 2500 g/mL. The lowest MIC value of 39 g/mL was recorded for a methanol fruit extract against Candida albicans, C. glabrata and C. tropicalis. In addition, ethanol and hexane fruit extracts were effective against the growth of C. albicans and C. glabrata, respectively, with a MIC of 78 g/mL. Piperlongumine and piperine were active against C. albicans with MIC values of 39 and 78 g/mL respectively. Conclusion: P. guineense fruit and leaf extracts, as well as their piperamide alkaloid constituents piperine and piperlongumine, have interesting antifungal properties and could have potential as new antifungal scaffolds. Our results warrant further in-depth investigations to isolate and characterize piperamide alkaloids and other compounds responsible for the antifungal activity in the extracts.
  • Loikkanen, Emil; Oristo, Satu; Hämäläinen, Natalia; Jokelainen, Pikka; Kantala, Tuija; Sukura, Antti; Maunula, Leena (2020)
    The main animal reservoirs of zoonotic hepatitis E virus (HEV) are domestic pigs and wild boars, but HEV also infects cervids. In this study, we estimated the prevalence of HEV in Finnish cervid species that are commonly hunted for human consumption. We investigated sera from 342 European moose (Alces alces), 70 white-tailed deer (Odocoileus virginianus), and 12 European roe deer (Capreolus capreolus). The samples had been collected from legally hunted animals from different districts of Finland during 2008–2009. We analysed the samples for total anti-HEV antibodies using a double-sandwich ELISA assay. Seropositive sera were analysed with RT-qPCR for HEV RNA. HEV seroprevalence was 9.1% (31/342) in moose and 1.4% (1/70) in white-tailed deer. None of the European roe deer were HEV seropositive (0/12). No HEV RNA was detected from samples of seropositive animals. HEV seropositive moose were detected in all districts. Statistically, HEV seroprevalence in moose was significantly higher (p 
  • Colston, Josh M.; Zaitchik, Benjamin F.; Badr, Hamada S.; Burnett, Eleanor; Ali, Syed Asad; Rayamajhi, Ajit; Satter, Syed M.; Eibach, Daniel; Krumkamp, Ralf; May, Jurgen; Chilengi, Roma; Howard, Leigh M.; Sow, Samba O.; Hossain, M. Jahangir; Saha, Debasish; Nisar, M. Imran; Zaidi, Anita K. M.; Kanungo, Suman; Mandomando, Inacio; Faruque, Abu S. G.; Kotloff, Karen L.; Levine, Myron M.; Breiman, Robert F.; Omore, Richard; Page, Nicola; Platts-Mills, James A.; Ashorn, Ulla; Fan, Yue-Mei; Shrestha, Prakash Sunder; Ahmed, Tahmeed; Mduma, Estomih; Yori, Pablo Penatero; Bhutta, Zulfiqar; Bessong, Pascal; Olortegui, Maribel P.; Lima, Aldo A. M.; Kang, Gagandeep; Humphrey, Jean; Prendergast, Andrew J.; Ntozini, Robert; Okada, Kazuhisa; Wongboot, Warawan; Gaensbauer, James; Melgar, Mario T.; Pelkonen, Tuula; Freitas, Cesar Mavacala; Kosek, Margaret N. (2022)
    Diarrheal disease, still a major cause of childhood illness, is caused by numerous, diverse infectious microorganisms, which are differentially sensitive to environmental conditions. Enteropathogen-specific impacts of climate remain underexplored. Results from 15 studies that diagnosed enteropathogens in 64,788 stool samples from 20,760 children in 19 countries were combined. Infection status for 10 common enteropathogens-adenovirus, astrovirus, norovirus, rotavirus, sapovirus, Campylobacter, ETEC, Shigella, Cryptosporidium and Giardia-was matched by date with hydrometeorological variables from a global Earth observation dataset-precipitation and runoff volume, humidity, soil moisture, solar radiation, air pressure, temperature, and wind speed. Models were fitted for each pathogen, accounting for lags, nonlinearity, confounders, and threshold effects. Different variables showed complex, non-linear associations with infection risk varying in magnitude and direction depending on pathogen species. Rotavirus infection decreased markedly following increasing 7-day average temperatures-a relative risk of 0.76 (95% confidence interval: 0.69-0.85) above 28 degrees C-while ETEC risk increased by almost half, 1.43 (1.36-1.50), in the 20-35 degrees C range. Risk for all pathogens was highest following soil moistures in the upper range. Humidity was associated with increases in bacterial infections and decreases in most viral infections. Several virus species' risk increased following lower-than-average rainfall, while rotavirus and ETEC increased with heavier runoff. Temperature, soil moisture, and humidity are particularly influential parameters across all enteropathogens, likely impacting pathogen survival outside the host. Precipitation and runoff have divergent associations with different enteric viruses. These effects may engender shifts in the relative burden of diarrhea-causing agents as the global climate changes. Plain Language Summary Diarrheal disease is a big health problem for children. It can be caused by different bugs, which can be caught more easily in certain weather conditions, though not much is understood about this because the climate varies so much from one place to the next. This study combined data from many different countries where diarrhea-causing bugs were diagnosed in children's stool. Satellites recorded what the weather was like on the day each sample was collected. Rotavirus is easiest to catch in cold weather and when water washes over the ground after rain. Dry weather also makes it and other viruses easy to catch. Bacteria spread best when the air is warm and humid, and the soil moist, though one type of E. coli can also be spread in rainwater. Climate change will make dry places drier, wet places wetter and everywhere warmer. This might lead to more diarrhea caused by bacteria and less by viruses in some places, though places with moist soil might see more of every kind of bug.
  • Tiwari, Ananda; Hokajärvi, Anna Maria; Domingo, Jorge Santo; Elk, Michael; Jayaprakash, Balamuralikrishna; Ryu, Hodon; Siponen, Sallamaari; Vepsäläinen, Asko; Kauppinen, Ari; Puurunen, Osmo; Artimo, Aki; Perkola, Noora; Huttula, Timo; Miettinen, Ilkka T.; Pitkänen, Tarja (2021)
    Background Rivers and lakes are used for multiple purposes such as for drinking water (DW) production, recreation, and as recipients of wastewater from various sources. The deterioration of surface water quality with wastewater is well-known, but less is known about the bacterial community dynamics in the affected surface waters. Understanding the bacterial community characteristics -from the source of contamination, through the watershed to the DW production process-may help safeguard human health and the environment. Results The spatial and seasonal dynamics of bacterial communities, their predicted functions, and potential health-related bacterial (PHRB) reads within the Kokemaenjoki River watershed in southwest Finland were analyzed with the 16S rRNA-gene amplicon sequencing method. Water samples were collected from various sampling points of the watershed, from its major pollution sources (sewage influent and effluent, industrial effluent, mine runoff) and different stages of the DW treatment process (pre-treatment, groundwater observation well, DW production well) by using the river water as raw water with an artificial groundwater recharge (AGR). The beta-diversity analysis revealed that bacterial communities were highly varied among sample groups (R = 0.92, p <0.001, ANOSIM). The species richness and evenness indices were highest in surface water (Chao1; 920 +/- 10) among sample groups and gradually decreased during the DW treatment process (DW production well; Chao1: 320 +/- 20). Although the phylum Proteobacteria was omnipresent, its relative abundance was higher in sewage and industrial effluents (66-80%) than in surface water (55%). Phyla Firmicutes and Fusobacteria were only detected in sewage samples. Actinobacteria was more abundant in the surface water (>= 13%) than in other groups (= 13%) than in others (
  • Rene-Martellet, Magalie; Minard, Guillaume; Massot, Raphael; Van Tran Van; Moro, Claire Valiente; Chabanne, Luc; Mavingui, Patrick (2017)
    Background: Ticks of the group Rhipicephalus sanguineus (sensu lato) are distributed worldwide and are major pathogen vectors of both dogs and humans. Previous phylogenetic reconstructions have suggested the existence of two main lineages within this group, "Tropical" and "Temperate". Symbiotic interactions contribute to vector development, survival, reproduction and competence. The diversity of microbial communities associated with different populations of R. sanguineus (s.l.) remains poorly characterized, however, this knowledge will aid in future studies of hosts-microbiota-pathogen interactions. To gain insight into the bacterial communities associated with R. sanguineus (s.l.) ticks, 40 specimens from France, Senegal and Arizona were analyzed by high-throughput 16S amplicon sequencing. All tick specimens were taxonomically classified using the mitochondrial 12S rDNA gene, which provides sufficient phylogenetic resolution to discriminate different lineages of R. sanguineus. Results: Rhipicephalus sanguineus (s.l.) samples from Senegal belonged to the "Tropical" lineage, samples from France belonged to the "Temperate" lineage, whereas both lineages were identified in samples from Arizona. Regardless of origin, each bacterial microbiota was dominated by three genera: Coxiella, Rickettsia and Bacillus. Rickettsia and Coxiella were the two main genera found in females whereas males had a higher proportion of Bacillus. Significant differences of relative abundances were evidenced between specimens from different geographical origins. Conclusions: This study highlights differences in the microbiota composition within R. sanguineus (s.l.) specimens from different genotypes, genders and geographical origins. This knowledge will help in future studies of the symbiotic interactions, biology and vector competence of the R. sanguineus (s.l.) complex.
  • Lienemann, Taru; Kyyhkynen, Aino; Halkilahti, Jani; Haukka, Kaisa; Siitonen, Anja (2015)
    Background: Salmonella enterica spp. enterica serotype Typhimurium (STM) is the most common agent of domestically acquired salmonellosis in Finland. Subtyping methods which allow the characterization of STM are essential for effective laboratory-based STM surveillance and for recognition of outbreaks. This study describes the diversity of Finnish STM isolates using phage typing, antimicrobial susceptible testing, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA), and compares the discriminatory power and the concordance of these methods. Results: A total of 375 sporadic STM isolates were analysed. The isolates were divided into 31 definite phage (DT) types, dominated by DT1 (47 % of the isolates), U277 (9 % of the isolates) and DT104 (8 % of the isolates). Of all the isolates, 62 % were susceptible to all the 12 antimicrobials tested and 11 % were multidrug resistant. Subtyping resulted in 83 different XbaI-PFGE profiles and 111 MLVA types. The three most common XbaI-PFGE profiles (STYM1, STYM7 and STYM8) and one MLVA profile with three single locus variants accounted for 56 % and 49 % of the STM isolates, respectively. The studied isolates showed a genetic similarity of more than 70 % by XbaI-PFGE. In MLVA, 71 % of the isolates lacked STTR6 and 77 % missed STTR10p loci. Nevertheless, the calculated Simpson's diversity index for XbaI-PFGE was 0.829 (95 % CI 0.792-0.865) and for MLVA 0.867 (95 % CI 0.835-0.898). However, the discriminatory power of the 5-loci MLVA varied among the phage types. The highest concordance of the results was found between XbaI-PFGE and phage typing (adjusted Wallace coefficient was 0.833 and adjusted Rand coefficient was 0.627). Conclusions: In general, the calculated discriminatory power was higher for genotyping methods (MLVA and XbaI-PFGE) than for phenotyping methods (phage typing). Overall, comparable diversity indices were calculated for PFGE and MLVA (both DI > 0.8). However, MLVA was phage type dependent providing better discrimination of the most common phage types. Furthermore, 5-loci MLVA was a less laborious method and easier to interpret than XbaI-PFGE. Thus, the laboratory-based surveillance of the Finnish human STM infections has been conducted with a combination of phage typing, antimicrobial susceptibility testing and 5-loci MLVA since January 2014.
  • Turunen, Katri; Antikainen, Jenni; Lääveri, Tinja; Kirveskari, Juha; Svennerholm, Ann-Mari; Kantele, Anu (2020)
    Background: Enterotoxigenic Escherichia coli (ETEC) is a major pathogen causing travellers' diarrhoea (TD) among visitors to low- and middle-income countries (LMIC). Scant data are available on rates of travel-acquired ETEC producing heat-labile (LT) and/or heat-stable (ST) toxin or its subtypes, STh (human) and STp (porcine) in various geographic regions, and on clinical pictures associated with each toxin. Methods: Using qPCR, we analysed LT, STh, and STp in stools positive for ETEC in a prospective study among 103 Finnish travellers visiting LMIC. They filled in questionnaires and provided stool samples before and after travel. We scrutinized geographic distribution of LT, STh, and STp ETEC findings, and association between these different ETEC subtypes and moderate/severe TD. Results: Among the 103 stool samples positive for ETEC toxins, the rate for LT was 76%, for STh 26%, and STp 41%. The rate for LT-only was 44%, for 5Th-only 6%, STp-only 16%, LT + STh 10%, LT + STp 15%, STh + STp 3%, and LT + STh + STp 8%. Findings varied by destination; the rates of LT, STh, and STp were 79%, 21%, and 57%, respectively, in Southern Asia (n = 14); 85%, 10%, and 20% in South-eastern Asia (n = 20); 84%, 13%, and 29% in Eastern Africa (n = 31); and 56%, 50%, and 63% in Western Africa (n = 32), respectively. Of travellers positive for LT, STh, and STp, 83%, 100%, and 88%, encountered TD; 35%, 55%, and 41% reported moderate/severe TD. STh was associated with moderate/severe TD. Conclusions: Toxin findings varied by destination; multiple toxins were commonly detected. Moderate/severe TD was reported most frequently by subjects with STh-ETEC.
  • Larsson, D. G. Joakim; Andremont, Antoine; Bengtsson-Palme, Johan; Brandt, Kristian Koefoed; Husman, Ana Maria de Roda; Fagerstedt, Patriq; Fick, Jerker; Flach, Carl-Fredrik; Gaze, William H.; Kuroda, Makoto; Kvint, Kristian; Laxminarayan, Ramanan; Manaia, Celia M.; Nielsen, Kaare Magne; Plant, Laura; Ploy, Marie-Cecile; Segovia, Carlos; Simonet, Pascal; Smalla, Kornelia; Snape, Jason; Topp, Edward; van Hengel, Arjon J.; Verner-Jeffreys, David W.; Virta, Marko P. J.; Wellington, Elizabeth M.; Wernersson, Ann-Sofie (2018)
    There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.(1)
  • Sheppard, Samuel K.; Cheng, Lu; Meric, Guillaume; De Haan, Caroline P. A.; Llarena, Ann-Katrin; Marttinen, Pekka; Vidal, Ana; Ridley, Anne; Clifton-Hadley, Felicity; Connor, Thomas R.; Strachan, Norval J. C.; Forbes, Ken; Colles, Frances M.; Jolley, Keith A.; Bentley, Stephen D.; Maiden, Martin C. J.; Hänninen, Marja-Liisa; Parkhill, Julian; Hanage, William P.; Corander, Jukka (2014)
  • Kantele, Anu; Lääveri, Tinja; Mero, Sointu; Häkkinen, Inka M. K.; Kirveskari, Juha; Johnston, Brian D.; Johnson, James R. (2020)
    Background. One-third of the 100 million travelers to the tropics annually acquire extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-PE), with undefined clinical consequences. Methods. Symptoms suggesting Enterobacteriaceae infections were recorded prospectively among 430 Finnish travelers, 90 (21%) of whom acquired ESBL-PE abroad. ESBL-PE isolates underwent polymerase chain reaction-based detection of diarrheagenic Escherichia coli (DEC) pathotypes (enteroaggregative E. coli [EAEC], enteropathogenic E. coli [EPEC], enterotoxigenic E. coli [ETEC], enteroinvasive E. coli, and Shiga toxin-producing E. coli), and extraintestinal pathogenic/uropathogenic E. coli (ExPEC/UPEC). Laboratory-confirmed ESBL-PE infections were surveyed 5 years before and after travel. Results. Among the 90 ESBL-PE carriers, manifestations of Enterobacteriaceae infection included travelers' diarrhea (TD) (75/90 subjects) and urinary tract infection (UTI) (3/90). The carriers had 96 ESBL-producing E. coli isolates, 51% exhibiting a molecular pathotype: 13 (14%) were DEC (10 EAEC, 2 EPEC, 1 ETEC) (12 associated with TD) and 39 (41%) ExPEC/UPEC (none associated with UTI). Of ESBL-PE, 3 (3%) were ExPEC/UPEC-EAEC hybrids (2 associated with diarrhea, none with UTI). Potential ESBL-PE infections were detected in 15 of 90 subjects (17%). The 10-year medical record survey identified 4 laboratory-confirmed ESBL-PE infections among the 430 travelers, all in subjects who screened ESBL-PE negative after returning home from their index journeys but had traveled abroad before their infection episodes. Conclusions. Half of all travel-acquired ESBL-producing E. coli strains qualified molecularly as pathogens. Extraintestinal and uropathogenic pathotypes outnumbered enteric pathotypes (41% vs 14%), yet the latter correlated more closely with symptomatic infection (0% vs 92%). Despite more ESBL-PE strains qualifying as ExPEC/UPEC than DEC, travel-acquired ESBL-PE are more often associated with TD than UTI.
  • Silva, Ximena; Roux, Jolanda; Asiegbu, Fred O. (2020)
    Background and objectives: The global forest economy is threatened by eucalypt pathogens which are often latent or cryptic species that escape common quarantine and detection methods. Plantation forestry using eucalypts is of considerable importance to Paraguay, but knowledge regarding the pests and diseases affecting these plantations is limited. This study identified fungal diseases present in these plantations. Materials and Methods: We surveyed eucalypt plantations in four provinces in Paraguay and collected material from diseased trees for identification of the causal agents. The samples were analyzed using a combination of morphological and molecular methods. Results: Diseases encountered included Botryosphaeria stem canker, Calonectria leaf blight, Chrysoporthe stem canker, myrtle/eucalypt rust, Coniella leaf spot, heartwood rot and Teratosphaeria stem canker. Contrary to expectations, the causal agent of Teratosphaeria stem canker was identified as Teratosphaeria zuluensis (M.J. Wingf., Crous & T.A. Cout.) M.J. Wingf. & Crous and not Teratosphaeria gauchensis (M.-N. Cortinas, Crous & M.J. Wingf.) M.J. Wingf. & Crous, that is commonly documented for the South American region. Conclusions: This study updates the knowledge on forest fungal pathogens in Paraguayan eucalypt plantations and is the first report of T. zuluensis in Paraguay and in South America.
  • Linnakoski, Riikka; Sugano, Junko; Junttila, Samuli; Pulkkinen, Pertti; Asiegbu, Fred O.; Forbes, Kristian M. (2017)
    Norway spruce is one of the most important commercial forestry species in Europe, and is commonly infected by the bark beetle-vectored necrotrophic fungus, Endoconidiophora polonica. Spruce trees display a restricted capacity to respond to environmental perturbations, and we hypothesized that water limitation will increase disease severity in this pathosystem. To test this prediction, 737 seedlings were randomized to high (W+) or low (W-) water availability treatment groups, and experimentally inoculated with one of three E. polonica strains or mock-inoculated. Seedling mortality was monitored throughout an annual growing season, and total seedling growth and lesion length indices were measured at the experiment conclusion. Seedling growth was greater in the W+ than W- treatment group, demonstrating limitation due to water availability. For seedlings infected with two of the fungal strains, no differences in disease severity occurred in response to water availability. For the third fungal strain, however, greater disease severity (mortality and lesion lengths) occurred in W- than W+ seedlings. While the co-circulation in nature of multiple E. polonica strains of varying virulence is known, this is the first experimental evidence that water availability can alter strain-specific disease severity.
  • Sormunen, Jani Jukka; Kulha, Niko; Klemola, Tero; Makela, Satu; Vesilahti, Ella-Maria; Vesterinen, Eero Juhani (2020)
    Most tick-related studies in Europe have been conducted in nonurban areas, but ticks and tick-borne pathogens also occur in urban green spaces. From a public health perspective, risks regarding tick-borne infections should be studied in these urban areas, where contacts between infected ticks and humans may be more frequent than elsewhere, due to high human activity. We examined the risk of encountering an infected tick in urban green spaces in Helsinki, Finland. We collected ticks at nine sites throughout Helsinki, recorded the prevalence of several pathogens and identified areas with a high potential for contacts between infected ticks and humans. Moreover, we explored the relationship between the density ofBorrelia burgdorferisensu lato-infected ticks and locally diagnosed cases of borreliosis and compared the potential for human-tick encounters in Helsinki to those in nonurban areas in south-western Finland. During 34.8 km of cloth dragging, 2,417Ixodes ricinuswere caught (402 adults, 1,399 nymphs and 616 larvae). From analysed nymphs, we found 11 distinct tick-borne pathogens, with 31.5% of nymphs carrying at least one pathogen. Tick activity was highest in August and September, leading to the density of nymphs infected withB. burgdorferis.l., and concurrently infection risk, to also be highest during this time. Nymph densities varied between the sampling sites, with obvious implications to spatial variation in infection risk. While ticks and tick-borne pathogens were found in both Helsinki and nonurban areas in south-western Finland, the estimates of human activity were generally higher in urban green spaces, leading to a higher potential for human-tick contacts therein. The presence of ticks and tick-borne pathogens and high local human activity in urban green spaces suggest that they form potential foci regarding the acquisition of tick-borne infections. Risk areas within cities should be identified and knowledge regarding urban ticks increased.
  • Sandelin, Atte; Härtel, Heidi; Seppä-Lassila, Leena; Kaartinen, Liisa; Rautala, Helena; Soveri, Timo; Simojoki, Heli (2020)
    BackgroundBovine respiratory disease (BRD) continues to be great challenge in calf rearing units. The urgent need to decrease the use of antibiotics and increase animal welfare in beef production has forced us to introduce new preventive methods. Vaccinations could contribute to the solution, but the high incidence of BRD already at an early age has made it difficult to introduce suitable vaccination programs. Challenge studies have shown promising results in 3-14day old calves vaccinated with intranasal BRD vaccine, but very few field trials are available to assess the efficacy of the intranasal vaccines in field conditions. We evaluated the effect of one dose of commercial intranasal vaccination on calf mortality, daily gain, and treatment incidence for BRD in one calf rearing unit. In total, 497 calves (mean age 19days) were included in our study, 247 of which were vaccinated at the time of arrival to the unit and 250 served as negative controls (unvaccinated). Vaccinated and unvaccinated calves were situated in separate compartments until weaning. Daily gain, treatment incidence, and mortality were recorded until the calves were transported to the finishing unit, which averaged 154.5days from arrival.ResultsAverage daily gain over the complete study period was 1151.9g/day (SD 137.9) for the vaccinated calves and 1139.5g/day (SD 135.9) for the unvaccinated calves. Intranasal vaccination combined with older arrival age (17days or older) resulted in a higher daily gain (47.8g/day) compared with unvaccinated calves (coef. 0.0478, p=0.003). This association was not recorded in calves that were younger than 17days upon arrival. Intranasal vaccination was not significantly associated either with mortality (OR 0.976, p=0.968) or treatment incidence for BRD (OR 1.341, p=0.120). In total, six vaccinated calves (2.43%) and six unvaccinated calves (2.40%) died during the study period.ConclusionsVaccinating arriving calves with intranasal vaccine in the calf rearing unit did not decrease the mortality or treatment incidence for BRD, but it significantly improved the weight gain in calves transported to the unit at the age of 17days or older.
  • Turzhanova, Ainur; Khapilina, Oxana; Tumenbayeva, A; Shevtsov, Vladislav; Raiser, Olesya; Kalendar, Ruslan (2020)
    The genus Alternaria is a widely distributed major plant pathogen that can act as a saprophyte in plant debris. Fungi of this genus frequently infect cereal crops and cause such diseases as black point and wheat leaf blight, which decrease the yield and quality of cereal products. A total of 25 Alternaria sp. isolates were collected from germ grains of various wheat cultivars from different geographic regions in Kazakhstan. We investigated the genetic relationships of the main Alternaria species related to black point disease of wheat in Kazakhstan, using the inter-primer binding site (iPBS) DNA profiling technique. We used 25 retrotransposon-based iPBS primers to identify the differences among and within Alternaria species populations, and analyzed the variation using clustering (UPGMA) and statistical approaches (AMOVA). Isolates of Alternaria species clustered into two main genetic groups, with species of A.alternata and A.tennuissima forming one cluster, and isolates of A. infectoria forming another. The genetic diversity found using retrotransposon profiles was strongly correlated with geographic data. Overall, the iPBS fingerprinting technique is highly informative and useful for the evaluation of genetic diversity and relationships of Alternaria species.
  • Pensar, Johan; Puranen, Santeri; Arnold, Brian; MacAlasdair, Neil; Kuronen, Juri; Tonkin-Hill, Gerry; Pesonen, Maiju; Xu, Yingying; Sipola, Aleksi; Sanchez-Buso, Leonor; Lees, John A.; Chewapreechi, Claire; Bentley, Stephen D.; Harris, Simon R.; Parkhill, Julian; Croucher, Nicholas J.; Corander, Jukka (2019)
    Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles across the chromosome and model-free testing of dependencies between pairs of polymorphisms have been shown to successfully uncover patterns of selection in bacterial populations. Here we introduce a model-free method, SpydrPick, whose computational efficiency enables analysis at the scale of pan-genomes of many bacteria. SpydrPick incorporates an efficient correction for population structure, which adjusts for the phylogenetic signal in the data without requiring an explicit phylogenetic tree. We also introduce a new type of visualization of the results similar to the Manhattan plots used in genome-wide association studies, which enables rapid exploration of the identified signals of co-evolution. Simulations demonstrate the usefulness of our method and give some insight to when this type of analysis is most likely to be successful. Application of the method to large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, revealed both previously identified and novel putative targets of co-selection related to virulence and antibiotic resistance, highlighting the potential of this approach to drive molecular discoveries, even in the absence of phenotypic data.
  • Lääveri, Tinja; Pakkanen, Sari H.; Antikainen, Jenni; Riutta, Jukka; Mero, Sointu; Kirveskari, Juha; Kantele, Anu (2014)
  • Kaitala, Veijo; Koivu-Jolma, Mikko; Laakso, Jouni (2021)
    An infective prey has the potential to infect, kill and consume its predator. Such a prey-predator relationship fundamentally differs from the predator-prey interaction because the prey can directly profit from the predator as a growth resource. Here we present a population dynamics model of partial role reversal in the predator-prey interaction of two species, the bottom dwelling marine deposit feeder sea cucumber Apostichopus japonicus and an important food source for the sea cucumber but potentially infective bacterium Vibrio splendidus. We analyse the effects of different parameters, e.g. infectivity and grazing rate, on the population sizes. We show that relative population sizes of the sea cucumber and V. Splendidus may switch with increasing infectivity. We also show that in the partial role reversal interaction the infective prey may benefit from the presence of the predator such that the population size may exceed the value of the carrying capacity of the prey in the absence of the predator. We also analysed the conditions for species extinction. The extinction of the prey, V. splendidus, may occur when its growth rate is low, or in the absence of infectivity. The extinction of the predator, A. japonicus, may follow if either the infectivity of the prey is high or a moderately infective prey is abundant. We conclude that partial role reversal is an undervalued subject in predator-prey studies.