Browsing by Subject "SPREAD"

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  • Raerinne, Jani (2018)
    In addition to their core explanatory and predictive assumptions, scientific models include simplifying assumptions, which function as idealizations, approximations, and abstractions. There are methods to investigate whether simplifying assumptions bias the results of models, such as robustness analyses. However, the equally important issue - the focus of this paper - has received less attention, namely, what are the methodological and epistemic strengths and limitations associated with different simplifying assumptions. I concentrate on one type of simplifying assumption, the use of mega parameters as abstractions in ecological models. First, I argue that there are two kinds of mega parameters qua abstractions, sufficient parameters and aggregative parameters, which have gone unnoticed in the literature. The two are associated with different heuristics, holism and reductionism, which many view as incompatible. Second, I will provide a different analysis of abstractions and the associated heuristics than previous authors. Reductionism and holism and the accompanying abstractions have different methodological and epistemic functions, strengths, and limitations, and the heuristics should be viewed as providing complementary research perspectives of cognitively limited beings. This is then, third, used as a premise to argue for epistemic and methodological pluralism in theoretical ecology. Finally, the presented taxonomy of abstractions is used to comment on the current debate whether mechanistic accounts of explanation are compatible with the use of abstractions. This debate has suffered from an abstract discussion of abstractions. With a better taxonomy of abstractions the debate can be resolved.
  • Becker, Daniel J.; Hall, Richard J.; Forbes, Kristian M.; Plowright, Raina K.; Altizer, Sonia (2018)
  • Kantele, Anu; Laaveri, Tinja; Mero, Sointu; Vilkman, Katri; Pakkanen, Sari H.; Ollgren, Jukka; Antikainen, Jenni; Kirveskari, Juha (2015)
    Background. More than 300 million travelers visit regions with poor hygiene annually. A significant percentage of them become colonized by resistant intestinal bacteria such as extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) and may transmit the strains to others and to medical care settings when they return home. Despite the threats to global healthcare caused by an upsurge in antimicrobial resistance, no effort has been centered on prevention of colonization while traveling. Methods. Stool samples were collected from 430 Finns before and after traveling outside Scandinavia. All specimens were analyzed for ESBL-and carbapenemase-producing Enterobacteriaceae (CPE). Questionnaires were used to survey volunteers about use of antimicrobials as well as other potential risk factors. The results were subjected to multivariable analysis. Results. Twenty-one percent (90/430) of the travelers became colonized by ESBL-PE and none by CPE. Geographic region, occurrence of travelers' diarrhea (TD), age, and use of antimicrobial (AB) for TD were identified as independent risk factors predisposing to contracting ESBL-PE. Eleven percent of those in subgroup TD-AB-, 21% in TD+AB-, and 37% in TD+AB+ acquired ESBL-PE. The risk proved to be highest in South Asia (46%); 23% became colonized in subgroup TD-AB-, 47% in TD+AB-, and 80% in TD+AB+. In Southeast Asia, the rates were 14%, 37%, and 69%, respectively. Conclusions. TDand antimicrobials for TD proved to be independent risk factors, with up to 80% of TD+AB+ travelers contracting ESBL-PE. Inmodernpre-travel counseling for those visiting high-risk regions, travelers should be advised against taking antibiotics for mild or moderate TD.
  • Kanerva, M.; Skogberg, K.; Ryynanen, K.; Pahkamaki, A.; Jalava, J.; Ollgren, J.; Tarkka, E.; Lyytikainen, O. (2015)
    In Finland, occurrence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) has previously been sporadic and related to travel. We describe the first outbreak of colonisation with KPC-KP strain ST512; it affected nine patients in a 137-bed primary care hospital. The index case was detected by chance when a non-prescribed urine culture was taken from an asymptomatic patient with suprapubic urinary catheter in June 2013. Thereafter, all patients on the 38-bed ward were screened until two screening rounds were negative and extensive control measures were performed. Eight additional KPC-KP-carriers were found, and the highest prevalence of carriers on the ward was nine of 38. All other patients hospitalised on the outbreak ward between 1 May and 10 June and 101 former roommates of KPC-KP carriers since January had negative screening results. Two screening rounds on the hospital's other wards were negative. No link to travel abroad was detected. Compared with non-carriers, but without statistical significance, KPC-KP carriers were older (83 vs 76 years) and had more often received antimicrobial treatment within the three months before screening (9/9 vs 90/133). No clinical infections occurred during the six-month follow-up. Early detection, prompt control measures and repetitive screening were crucial in controlling the outbreak.
  • Hagens, Eliza R. C.; Henegouwen, Mark I. van Berge; van Sandick, Johanna W.; Cuesta, Miguel A.; van der Peet, Donald L.; Heisterkamp, Joos; Nieuwenhuijzen, Grard A. P.; Rosman, Camiel; Scheepers, Joris J. G.; Sosef, Meindert N.; van Hillegersberg, Richard; Lagarde, Sjoerd M.; Nilsson, Magnus; Räsänen, Jari; Nafteux, Philippe; Pattyn, Piet; Hoelscher, Arnulf H.; Schroeder, Wolfgang; Schneider, Paul M.; Mariette, Christophe; Castoro, Carlo; Bonavina, Luigi; Rosati, Riccardo; de Manzoni, Giovanni; Mattioli, Sandro; Roig Garcia, Josep; Pera, Manuel; Griffin, Michael; Wilkerson, Paul; Chaudry, M. Asif; Sgromo, Bruno; Tucker, Olga; Cheong, Edward; Moorthy, Krishna; Walsh, Thomas N.; Reynolds, John; Tachimori, Yuji; Inoue, Haruhiro; Matsubara, Hisahiro; Kosugi, Shin-ichi; Chen, Haiquan; Law, Simon Y. K.; Pramesh, C. S.; Puntambekar, Shailesh P.; Murthy, Sudish; Linden, Philip; Hofstetter, Wayne L.; Kuppusamy, Madhan K.; Shen, K. Robert; Darling, Gail E.; Sabino, Flavio D.; Grimminger, Peter P.; Meijer, Sybren L.; Bergman, Jacques J. G. H. M.; Hulshof, Maarten C. C. M.; van Laarhoven, Hanneke W. M.; Mearadji, Banafsche; Bennink, Roel J.; Annema, Jouke T.; Dijkgraaf, Marcel G. W.; Gisbertz, Suzanne S. (2019)
    BackgroundAn important parameter for survival in patients with esophageal carcinoma is lymph node status. The distribution of lymph node metastases depends on tumor characteristics such as tumor location, histology, invasion depth, and on neoadjuvant treatment. The exact distribution is unknown. Neoadjuvant treatment and surgical strategy depends on the distribution pattern of nodal metastases but consensus on the extent of lymphadenectomy has not been reached. The aim of this study is to determine the distribution of lymph node metastases in patients with resectable esophageal or gastro-esophageal junction carcinoma in whom a transthoracic esophagectomy with a 2- or 3-field lymphadenectomy is performed. This can be the foundation for a uniform worldwide staging system and establishment of the optimal surgical strategy for esophageal cancer patients.MethodsThe TIGER study is an international observational cohort study with 50 participating centers. Patients with a resectable esophageal or gastro-esophageal junction carcinoma in whom a transthoracic esophagectomy with a 2- or 3-field lymphadenectomy is performed in participating centers will be included. All lymph node stations will be excised and separately individually analyzed by pathological examination. The aim is to include 5000 patients. The primary endpoint is the distribution of lymph node metastases in esophageal and esophago-gastric junction carcinoma specimens following transthoracic esophagectomy with at least 2-field lymphadenectomy in relation to tumor histology, tumor location, invasion depth, number of lymph nodes and lymph node metastases, pre-operative diagnostics, neo-adjuvant therapy and (disease free) survival.DiscussionThe TIGER study will provide a roadmap of the location of lymph node metastases in relation to tumor histology, tumor location, invasion depth, number of lymph nodes and lymph node metastases, pre-operative diagnostics, neo-adjuvant therapy and survival. Patient-tailored treatment can be developed based on these results, such as the optimal radiation field and extent of lymphadenectomy based on the primary tumor characteristics.Trial registrationNCT03222895, date of registration: July 19th, 2017.
  • Escamez, Sacha; Stael, Simon; Vainonen, Julia; Willems, Patrick; Jin, Huiting; Kimura, Sachie; Van Breusegem, Frank; Gevaert, Kris; Wrzaczek, Michael Alois; Tuominen, Hannele (2019)
    During plant vascular development, xylem tracheary elements (TEs) form water-conducting, empty pipes by genetically regulated cell death. Cell death is prevented from spreading to non-TEs by unidentified intercellular mechanisms, downstream of METACASPASE9 (MC9)-mediated regulation of autophagy in TEs. Here, we identified differentially abundant extracellular peptides in vascular-differentiating wild-type and MC9-down-regulated Arabidopsis cell suspensions. A peptide named Kratos rescued the abnormally high ectopic non-TE death resulting from either MC9 knockout or TE-specific overexpression of the ATG5 autophagy protein during experimentally induced vascular differentiation in Arabidopsis cotyledons. Kratos also reduced cell death following mechanical damage and extracellular ROS production in Arabidopsis leaves. Stress-induced but not vascular non-TE cell death was enhanced by another identified peptide, named Bia. Bia is therefore reminiscent of several known plant cell death-inducing peptides acting as damage-associated molecular patterns. In contrast, Kratos plays a novel extracellular cell survival role in the context of development and during stress response.
  • Kantele, Anu; Mero, Sointu; Kirveskari, Juha; Laaveri, Tinja (2017)
    Background: One third of travellers to the poor regions of the (sub) tropics become colonized by extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE). Co-resistance to non-betalactam antibiotics complicates the treatment of potential ESBL-PE infections. Methods: We analysed co-resistance to non-beta-lactams among travel-acquired ESBL-PE isolates of 90 visitors to the (sub) tropics with respect to major risk factors of colonization: destination, age, travellers' diarrhoea (TD) and antibiotic (AB) use. Results: Of the ESBL-PE isolates, 53%, 52%, 73%, and 2% proved co-resistant to ciprofloxacin, tobramycin, co-trimoxazole, and nitrofurantoin, respectively. The rates were similar among those with (TD+) or without (TD-) travellers' diarrhoea. Among fluoroquinolone-users vs. AB non-users, the co-resistance rates for ciprofloxacin were 95% versus 37% (p = 0.001), for tobramycin 85% versus 43% (p = 0.005), co-trimoxazole 85% versus 68% (p = 0.146), and nitrofurantoin 5% versus 2% (p = 0.147). In multivariable analysis co-resistance to ciprofloxacin was associated with increasing age, fluoroquinolone use, and tobramycin resistance. Conlusions: While TD predisposes to ESBL-PE non-selectively, antimicrobial use favours strains resistant to drug taken and, simultaneously, any drug with resistance genetically linked to the drug used. Antibiotics taken during travel predispose to ESBL-PE with a high co-resistance rate. (C) 2017 The Author(s). Published by Elsevier Ltd.
  • Lanne, Markku; Nyberg, Henri (2016)
    We propose a new generalized forecast error variance decomposition with the attractive property that the proportions of the impact accounted for by innovations in each variable sum to unity. Our decomposition is based on the generalized impulse response function, and it can easily be obtained by simulation. The new decomposition is illustrated in an empirical application to US output growth and interest rate spread data.
  • Lilley, Thomas M.; Wilson, Ian W.; Field, Kenneth A.; Reeder, DeeAnn M.; Vodzak, Megan E.; Turner, Gregory G.; Kurta, Allen; Blomberg, Anna S.; Hoff, Samantha; Herzog, Carl; Sewall, Brent J.; Paterson, Steve (2020)
    Novel pathogens can cause massive declines in populations, and even extirpation of hosts. But disease can also act as a selective pressure on survivors, driving the evolution of resistance or tolerance. Bat white-nose syndrome (WNS) is a rapidly spreading wildlife disease in North America. The fungus causing the disease invades skin tissues of hibernating bats, resulting in disruption of hibernation behavior, premature energy depletion, and subsequent death. We used whole-genome sequencing to investigate changes in allele frequencies within a population of Myotis lucifugus in eastern North America to search for genetic resistance to WNS. Our results show low F-ST values within the population across time, i.e., prior to WNS (Pre-WNS) compared to the population that has survived WNS (Post-WNS). However, when dividing the population with a geographical cut-off between the states of Pennsylvania and New York, a sharp increase in values on scaffold GL429776 is evident in the Post-WNS samples. Genes present in the diverged area are associated with thermoregulation and promotion of brown fat production. Thus, although WNS may not have subjected the entire M. lucifugus population to selective pressure, it may have selected for specific alleles in Pennsylvania through decreased gene flow within the population. However, the persistence of remnant sub-populations in the aftermath of WNS is likely due to multiple factors in bat life history.
  • Shepheard, Marcus A.; Fleming, Vicki M.; Connor, Thomas R.; Corander, Jukka; Feil, Edward J.; Fraser, Christophe; Hanage, William P. (2013)
  • StaphTrav Network; Nurjadi, D.; Fleck, R.; Kantele, A.; Zanger, P. (2019)
    Objectives: Recently, following import by travel and migration, epidemic community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has caused nosocomial outbreaks in Europe, sometimes with a fatal outcome. We describe clinico-epidemiological characteristics of CA-MRSA detected by the European Network for the Surveillance of imported S. aureus ( from May 2011 to November 2016. Methods: Sentinel surveillance at 13 travel clinics enrolling patients with travel-associated skin and soft-tissue infection (SSTI) and analysing lesion and nose swabs at one central laboratory. Results: A total of 564 independent case-patients with SSTI were enrolled and had 374 (67%) S. aureus-positive lesions, of which 14% (51/374) were MRSA. The majority of CA-MRSA isolates from SSTI were Panton-Valentine leucocidin (PVL)-positive (43/51, 84%). The risk of methicillin-resistance in imported S. aureus varied by travel region (p Conclusions: Travel-associated CA-MRSA SSTI is a transmissible condition that leads to medical consultations and colonization of the infected host. (c) 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
  • Munsch-Alatossava, Patricia; Jääskeläinen, Susanna; Alatossava, Tapani; Gauchi, Jean-Pierrre (2017)
    Antibiotic resistance has been noted to be a major and increasing human health issue. Cold storage of raw milk promotes the thriving of psychrotrophic/psychrotolerant bacteria, which are well known for their ability to produce enzymes that are frequently heat stable. However, these bacteria also carry antibiotic resistance (AR) features. In places, where no cold chain facilities are available and despite existing recommendations numerous adulterants, including antibiotics, are added to raw milk. Previously, N-2 gas flushing showed real potential for hindering bacterial growth in raw milk at a storage temperature ranging from 6 to 25 degrees C. Here, the ability of N-2 gas (N) to tackle antibiotic-resistant bacteria was tested and compared to that of the activated lactoperoxidase system (HT) for three raw milk samples that were stored at 6 degrees C for 7 days. To that end, the mesophiles and psychrotrophs that were resistant to gentamycin (G), ceftazidime (Ce), levofloxacin (L), and trimethoprim-sulfamethoxazole (TS) were enumerated. For the log(10) ratio (which is defined as the bacterial counts from a certain condition divided by the counts on the corresponding control), classical Analyses of Variance (ANOVA) was performed, followed by a mean comparison with the Ryan-Einot-Gabriel-Welsch multiple range test (REGWQ). If the storage "time" factor was the major determinant of the recorded effects, cold storage alone or in combination with HT or with N promoted a sample-dependent response in consideration of the AR levels. The efficiency of N in limiting the increase in AR was highest for fresh raw milk and was judged to be equivalent to that of HT for one sample and superior to that of HT for the two other samples; moreover, compared to HT, N seemed to favor a more diverse community at 6 degrees C that was less heavily loaded with antibiotic multi-resistance features. Our results imply that N-2 gas flushing could strengthen cold storage of raw milk by tackling the bacterial spoilage potential while simultaneously hindering the increase of bacteria carrying antibiotic resistance/multi-resistance features.
  • NordicAST CPE Study Grp; Haldorsen, Bjorg; Kärpänoja, Pauliina (2018)
    Objectives: To examine performance of EUCAST disc diffusion and supplementary MIC methods for detection of Enterobacteriaceae with reduced susceptibility to meropenem using EUCAST screening recommendations. Methods: Sixty-one Nordic laboratories delivered data on EUCAST disc diffusion (n = 61), semi-automated meropenem MIC (n = 23; VITEK2, n = 20 and Phoenix, n = 3) and gradient meropenem MIC (n = 58) methods: The strains (n - 27) included the major carbapenemase classes (A, n - 4; B, n - 9; D, n - 6) involved in the global spread of carbapenemase-producing Enterobacteriaceae (CPE) and non-CPE strains (n = 8) covering a range of broth microdilution (BMD) meropenem MICs. Results: A triplicate Klebsiella vanicola (meropenem MIC >= 0,5 mg/L) harbouring OXA-48 and Escherichia coli ATCC 25922 showed an overall good precision. Meropenem zone diameters below the EUCAST screening cut-off (= 1 mg/L (n = 21), irrespective of resistance mechanism. For three strains (MIC - 0.5 mg/L) with OXA-481-181, eight laboratories provided meropenem zone diameters above the screening cut-off, Very major errors (VMEs) were not observed. The overall distributions of major errors (MEs) and minor errors (mEs) were 9% and 36% (disc diffusion), 26% and 18% (VITEK2) and 7% and 20% (gradient MIC), respectively, Differences in ME and mE distributions between disc diffusion and MIC gradient tests compared with semi-automated methods were significant (P <0,0001), using BMD MICs as a reference for categorization, Conclusions: The EUCAST disc diffusion method is a robust method to screen for CPE but isolates with meropenem MICs
  • Lilley, Thomas M.; Sävilammi, Tiina; Ossa, Gonzalo; Blomberg, Anna S.; Vasemägi, Anti; Yung, Veronica; Vendrami, David L. J.; Johnson, Joseph S. (2020)
    Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here.
  • Darch, Sophie E.; McNally, Alan; Harrison, Freya; Corander, Jukka; Barr, Helen L.; Paszkiewicz, Konrad; Holden, Stephen; Fogarty, Andrew; Crusz, Shanika A.; Diggle, Stephen P. (2015)
  • Meierhofer, Melissa; Lilley, Thomas M.; Ruokolainen, Lasse; Johnson, Joseph; Parratt, Steven; Morrison, Michael; Pearce, Brian; Evans, Jonah; Anttila, Jani (2021)
    Predicting the emergence and spread of infectious diseases is critical for the effective conservation of biodiversity. White-nose syndrome (WNS), an emerging infectious disease of bats, has resulted in high mortality in eastern North America. Because the fungal causative agent Pseudogymnoascus destructans is constrained by temperature and humidity, spread dynamics may vary by geography. Environmental conditions in the southern part of the continent are different than the northeast, where disease dynamics are typically studied, making it difficult to predict how the disease will manifest. Herein, we modelled WNS pathogen spread in Texas based on cave densities and average dispersal distances of hosts, projecting these results out to 10 years. We parameterized a predictive model of WNS epidemiology and its effects on bat populations with observed cave environmental data. Our model suggests that bat populations in northern Texas will be more affected by WNS mortality than southern Texas. As such, we recommend prioritizing the preservation of large overwintering colonies of bats in north Texas through management actions. Our model illustrates that infectious disease spread and infectious disease severity can become uncoupled over a gradient of environmental variation and highlight the importance of understanding host, pathogen and environmental conditions across a breadth of environments.
  • Jaric, Ivan; Courchamp, Franck; Correia, Ricardo A.; Crowley, Sarah L.; Essl, Franz; Fischer, Anke; Gonzalez-Moreno, Pablo; Kalinkat, Gregor; Lambin, Xavier; Lenzner, Bernd; Meinard, Yves; Mill, Aileen; Musseau, Camille; Novoa, Ana; Pergl, Jan; Pysek, Petr; Pyskova, Klara; Robertson, Peter; von Schmalensee, Menja; Shackleton, Ross T.; Stefansson, Robert A.; Stajerova, Katerina; Verissimo, Diogo; Jeschke, Jonathan M. (2020)
    Commonly used in the literature to refer to the "attractiveness", "appeal", or "beauty" of a species, charisma can be defined as a set of characteristics - and the perception thereof - that affect people's attitudes and behaviors toward a species. It is a highly relevant concept for invasion science, with implications across all stages of the invasion process. However, the concept of invasive alien species (IAS) charisma has not yet been systematically investigated. We discuss this concept in detail, provide a set of recommendations for further research, and highlight management implications. We review how charisma affects the processes associated with biological invasions andIASmanagement, including species introductions and spread, media portrayals, public perceptions of species management, research attention, and active public involvement in research and management. Explicit consideration ofIAScharisma is critical for understanding the factors that shape people's attitudes toward particular species, planning management measures and strategies, and implementing a combination of education programs, awareness raising, and public involvement campaigns.
  • Kagambéga, Asséta; Lienemann, Taru; Frye, Jonathan G.; Barro, Nicolas; Haukka, Kaisa (2018)
    Background: Multidrug-resistant Salmonella is an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistant Salmonella enterica serovar Typhimurium isolates from patients and poultry feces. Methods: Salmonella strains were isolated from poultry and patients using standard bacteriological methods described in previous studies. The strains were serotype according to Kaufmann-White scheme and tested for antibiotic susceptibility to 12 different antimicrobial agents using the disk diffusion method. The whole genome of the S. Typhimurium isolates was analyzed using Illumina technology and compared with 20 isolates of S. Typhimurium for which the ST has been deposited in a global MLST database. The ResFinder Web server was used to find the antibiotic resistance genes from whole genome sequencing (WGS) data. For comparative genomics, publicly available complete and draft genomes of different S. Typhimurium laboratory-adapted strains were downloaded from GenBank. Results: All the tested Salmonella serotype Typhimurium were multiresistant to five commonly used antibiotics (ampicillin, chloramphenicol, streptomycin, sulfonamide, and trimethoprim). The multilocus sequence type ST313 was detected from all the strains. Our sequences were very similar to S. Typhimurium ST313 strain D23580 isolated from a patient with invasive non-typhoid Salmonella (NTS) infection in Malawi, also located in sub-Saharan Africa. The use of ResFinder web server on the whole genome of the strains showed a resistance to aminoglycoside associated with carriage of the following resistances genes: strA, strB, and aadA1; resistance to beta-lactams associated with carriage of a bla(TEM-1B) genes; resistance to phenicol associated with carriage of catA1 gene; resistance to sulfonamide associated with carriage of sul1 and sul2 genes; resistance to tetracycline associated with carriage of tet B gene; and resistance to trimethoprim associated to dfrA1 gene for all the isolates. Conclusion: The poultry and human isolates were genetically similar showing a potential food safety risk for consumers. Our finding of multidrug-resistant S. Typhimurium ST313 in poultry feces calls for further studies to clarify the potential reservoirs of this emerging pathogen.