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  • Obst, Matthias; Exter, Katrina; Allcock, A. Louise; Arvanitidis, Christos; Axberg, Alizz; Bustamante, Maria; Cancio, Ibon; Carreira-Flores, Diego; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Chrismas, Nathan; Clark, Melody S.; Comtet, Thierry; Dailianis, Thanos; Davies, Neil; Deneudt, Klaas; de Cerio, Oihane Diaz; Fortic, Ana; Gerovasileiou, Vasilis; Hablutzel, Pascal; Keklikoglou, Kleoniki; Kotoulas, Georgios; Lasota, Rafal; Leite, Barbara R.; Loisel, Stephane; Leveque, Laurent; Levy, Liraz; Malachowicz, Magdalena; Mavria, Borut; Meyer, Christopher; Mortelmans, Jonas; Norkko, Joanna; Pade, Nicolas; Power, Anne Marie; Ramsak, Andreja; Reiss, Henning; Solbakken, Jostein; Stoehr, Peter A.; Sundberg, Per; Thyrring, Jakob; Troncoso, Jesus S.; Viard, Frederique; Wenne, Roman; Yperifanou, Eleni Loanna; Zbawicka, Malgorzata; Pavloudi, Christina (2020)
    Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre (
  • Li, Xiaodong; Meng, Shuo; Puhakka, Eini; Ikonen, Jussi; Liu, Longcheng; Siitari-Kauppi, Marja (2020)
    To determine the diffusion and sorption properties of radionuclides in intact crystalline rocks, a new electromigration device was built and tested by running with I- and Se(IV) ions. By introducing a potentiostat to impose a constant voltage over the studied rock sample, the electromigration device can give more stable and accurate experimental results than those from the traditional electromigration devices. In addition, the variation in the pH of the background electrolytes was minimised by adding a small amount of NaHCO3 as buffers. To interpret the experimental results with more confidence, an advection-dispersion model was also developed in this study, which accounts for the most important mechanisms governing ionic transport in the electromigration experiments. Data analysis of the breakthrough curves by the advection-dispersion model, instead of the traditional ideal plug-flow model, suggest that the effective diffusivities of I- and Se(IV) are (1.15 +/- 0.06) x 10(-13) m(2)/s and (3.50 +/- 0.86) x 10(-14) m(2)/s, respectively. The results also show that I- is more mobile than Se(IV) ions when migrating through the same intact rock sample and that their sorption properties are almost identical.
  • Jääskeläinen, Tiina; Kärkkäinen, Olli; Jokkala, Jenna; Klåvus, Anton; Heinonen, Seppo; Auriola, Seppo; Lehtonen, Marko; FINNPEC Core Invest Grp; Hanhineva, Kati; Laivuori, Hannele (2021)
    IntroductionMaternal metabolism changes substantially during pregnancy. However, few studies have used metabolomics technologies to characterize changes across gestation.Objectives and methodsWe applied liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics to determine whether the metabolic profile of serum differs throughout the pregnancy between pre-eclamptic and healthy women in the FINNPEC (Finnish Genetics of Preeclampsia Consortium) Study. Serum samples were available from early and late pregnancy.ResultsProgression of pregnancy had large-scale effects to the serum metabolite profile. Altogether 50 identified metabolites increased and 49 metabolites decreased when samples of early pregnancy were compared to samples of late pregnancy. The metabolic signatures of pregnancy were largely shared in pre-eclamptic and healthy women, only urea, monoacylglyceride 18:1 and glycerophosphocholine were identified to be increased in the pre-eclamptic women when compared to healthy controls.ConclusionsOur study highlights the need of large-scale longitudinal metabolomic studies in non-complicated pregnancies before more detailed understanding of metabolism in adverse outcomes could be provided. Our findings are one of the first steps for a broader metabolic understanding of the physiological changes caused by pregnancy per se.
  • El-Khoury, Riyad; Dufour, Eric; Rak, Malgorzata; Ramanantsoa, Nelina; Grandchamp, Nicolas; Csaba, Zsolt; Duvillie, Bertrand; Benit, Paule; Gallego, Jorge; Gressens, Pierre; Sarkis, Chamsy; Jacobs, Howard T.; Rustin, Pierre (2013)
  • Smura, Teemu; Blomqvist, Soile; Kolehmainen, Pekka; Schuffenecker, Isabelle; Lina, Bruno; Boettcher, Sindy; Diedrich, Sabine; Love, Arthur; Brytting, Mia; Hauzenberger, Elenor; Dudman, Susanne; Ivanova, Olga; Lukasev, Alexander; Fischer, Thea Kolsen; Midgley, Sofie; Susi, Petri; Savolainen-Kopra, Carita; Lappalainen, Maija; Jääskeläinen, Anne J. (2020)
    Picornaviruses (family Picornaviridae) are small, nonenveloped, positive-sense, single-stranded RNA viruses. The members of this family are currently classified into 47 genera and 110 species. Of picornaviruses, entero-and parechoviruses are associated with aseptic meningitis. They are transmitted via fecal-oral and respiratory routes, and occasionally, these viruses may cause a brief viremia and gain access to central nervous system (CNS). During the diagnostic screening of entero-and parechovirus types in Finland in year 2013-14, we detected a cluster of echovirus 4 (E4) infections in young adults and adolescents. As E4 is infrequently detected in Finland, we contacted several Northern and Central European laboratories that conduct routine surveillance for enteroviruses and, for those who have had E4 cases, we send a query for E4 sequences and data. Here we report CNS infections caused by E4 in Finland, Sweden, Norway, Denmark, Iceland and Germany in 2013 and 2014, and show that the E4 detected in these countries form a single lineage. In contrast, E4 strains circulating in these countries preceding the year 2013, and those circulating elsewhere in Europe during 2013-2014, formed several independent clusters.
  • Fischer, Daniel; Mosler, Karl; Mottonen, Jyrki; Nordhausen, Klaus; Pokotylo, Oleksii; Vogel, Daniel (2020)
    The Oja median is one of several extensions of the univariate median to the multivariate case. It has many desirable properties, but is computationally demanding. In this paper, we first review the properties of the Oja median and compare it to other multivariate medians. Then, we discuss four algorithms to compute the Oja median, which are implemented in our R package OjaNP. Besides these algorithms, the package contains also functions to compute Oja signs, Oja signed ranks, Oja ranks, and the related scatter concepts. To illustrate their use, the corresponding multivariate one- and C-sample location tests are implemented.
  • Petersen, Anders Ø.; Julienne, Hanna; Hyötyläinen, Tuulia; Sen, Partho; Fan, Yong; Pedersen, Helle Krogh; Jäntti, Sirkku; Hansen, Tue H.; Nielsen, Trine; Jørgensen, Torben; Hansen, Torben; Myers, Pernille Neve; Nielsen, H. Bjørn; Ehrlich, S. Dusko; Orešič, Matej; Pedersen, Oluf (2021)
    Knowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.
  • Kauhanen, Dimple; Sysi-Aho, Marko; Koistinen, Kaisa M.; Laaksonen, Reijo; Sinisalo, Juha; Ekroos, Kim (2016)
    Monitoring the levels of the ceramides (Cer) d18:1/16:0, Cer d18:1/18:0, Cer d18:1/24:0, and Cer d18:1/24:1 and ratios thereof in human plasma empowers the prediction of fatal outcome of coronary artery disease (CAD). We describe a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology for clinical-scaled measurement of the four distinct ceramides. Rapid plasma precipitation was accomplished in 96-well format. Excellent extraction recoveries in the range of 98-109 % were achieved for each ceramide. Addition of corresponding D-7-labeled ceramide standards facilitated precise quantification of each plasma ceramide species utilizing a novel short 5-min LC-MS/MS method. Neither matrix interference nor carryover was observed. Robust intra- and inter-assay accuracy and precision <15 % at five different concentrations were obtained. Linear calibration lines with regressions, R (2) > 0.99, were achieved for all analytes. Short-term bench top, long-term plasma, and extract stability demonstrated that the distinct ceramides were stable in the conditions evaluated. The validity of the methodology was demonstrated by determining the precise ceramide concentrations in a small CAD case-control study. Thus, our LC-MS/MS methodology features simple sample preparation and short analysis time for accurate quantification of Cer d18:1/16:0, Cer d18:1/18:0, Cer d18:1/24:0, and Cer d18:1/24:1, designed for routine analysis.
  • COST Action GENIEURI BM1106 Microb; Vork, Lisa; Penders, John; Jalanka, Jonna; Salonen, Anne; de Vos, Willem M.; Jonkers, Daisy M. A. E. (2021)
    Introduction Stool consistency has been associated with fecal microbial composition. Stool consistency often varies over time, in subjects with and without gastrointestinal disorders, raising the question whether variability in the microbial composition should be considered in microbiota studies. We evaluated within-subject day-to-day variability in stool consistency and the association with the fecal microbiota in irritable bowel syndrome (IBS) and healthy subjects, over seven days. Methods Twelve IBS patients and 12 healthy subjects collected fecal samples during seven consecutive days. Stool consistency was determined by the patient-reported Bristol Stool Scale (BSS) and fecal dry weight percentage. 16S rRNA V4 gene sequencing was performed and microbial richness (alpha diversity; Chao1 index, observed number of species, effective Shannon index) and microbial community structure (beta diversity; Bray-Curtis distance, generalized UniFrac, and taxa abundance on family level) were determined. Results Linear mixed-effects models showed significant associations between stool consistency and microbial richness, but no time effect. This implies that between-subject but not within-subject variation in microbiota over time can partially be explained by variation in stool consistency. Redundancy analysis showed a significant association between stool consistency and microbial community structure, but additional linear mixed-effects models did not demonstrate a time effect on this. Conclusion This study supports an association between stool consistency and fecal microbiota, but no effect of day-to-day fluctuations in stool consistency within seven days. This consolidates the importance of considering stool consistency in gut microbiota research, though confirms the validity of single fecal sampling to represent an individual's microbiota at a given time point. NCT00775060.
  • Witjes, Julia J.; Smits, Loek P.; Pekmez, Ceyda T.; Prodan, Andrei; Meijnikman, Abraham S.; Troelstra, Marian A.; Bouter, Kristien E. C.; Herrema, Hilde; Levin, Evgeni; Holleboom, Adriaan G.; Winkelmeijer, Maaike; Beuers, Ulrich H.; van Lienden, Krijn; Aron-Wisnewky, Judith; Mannisto, Ville; Bergman, Jacques J.; Runge, Jurgen H.; Nederveen, Aart J.; Dragsted, Lars O.; Konstanti, Prokopis; Zoetendal, Erwin G.; de Vos, Willem; Verheij, Joanne; Groen, Albert K.; Nieuwdorp, Max (2020)
    The intestinal microbiota has been linked to the development and prevalence of steatohepatitis in humans. Interestingly, steatohepatitis is significantly lower in individuals taking a plant-based, low-animal-protein diet, which is thought to be mediated by gut microbiota. However, data on causality between these observations in humans is scarce. In this regard, fecal microbiota transplantation (FMT) using healthy donors is safe and is capable of changing microbial composition in human disease. We therefore performed a double-blind randomized controlled proof-of-principle study in which individuals with hepatic steatosis on ultrasound were randomized to two study arms: lean vegan donor (allogenic n = 10) or own (autologous n = 11) FMT. Both were performed three times at 8-week intervals. A liver biopsy was performed at baseline and after 24 weeks in every subject to determine histopathology (Nonalcoholic Steatohepatitis Clinical Research Network) classification and changes in hepatic gene expression based on RNA sequencing. Secondary outcome parameters were changes in intestinal microbiota composition and fasting plasma metabolomics. We observed a trend toward improved necro-inflammatory histology, and found significant changes in expression of hepatic genes involved in inflammation and lipid metabolism following allogenic FMT. Intestinal microbial community structure changed following allogenic FMT, which was associated with changes in plasma metabolites as well as markers of .Conclusion:Allogenic FMT using lean vegan donors in individuals with hepatic steatosis shows an effect on intestinal microbiota composition, which is associated with beneficial changes in plasma metabolites and markers of steatohepatitis.
  • Mostowy, Rafal; Croucher, Nicholas J.; Andam, Cheryl P.; Corander, Jukka; Hanage, William P.; Marttinen, Pekka (2017)
    Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at to pemartti/fastGEAR/ (last accessed February 6, 2017).
  • Puukko, Esa; Lehto, Jukka; Lindberg, Antero; Voutilainen, Mikko (2018)
    This study aims to determine upscaling factors for the radionuclides' distribution coefficients (Kd) on crushed rocks to intact rock for the safety analysis of radionuclide migration from spent nuclear fuel in bedrock towards biosphere. Here we report the distribution coefficients for intact rock determined by electromigration sorption experiments and compare the results with those from recently performed batch sorption experiments. In total 34 rock samples, representing three typical rock types from Olkiluoto Finland, were studied in order to determine distribution coefficients, effective diffusion coefficients and porosities using the electromigration sorption experiments, formation factor experiments and porosity measurement. The parameters determined represent the three main parameters of geosphere used in the safety assessment of spent nuclear fuel disposal. The distribution coefficients of cesium and strontium on intact rock varied between (0.12–26.2) × 10−3 m3/kg and (1.4–13.3) × 10−3 m3/kg, respectively, whereas recent results for crushed rock varied between (2–57) × 10−3 m3/kg and (17–40) × 10−3 m3/kg, respectively. This implies that crushing increases the distribution coefficient significantly and upscaling factors from 3 to 33 were determined for scaling the distribution coefficients of crushed rock to ones of intact rock. The determined distribution coefficients of cesium and strontium for intact rock can be directly applied in the safety assessment whereas the upscaling factors can be used to convert distribution coefficients determined for crushed rock into ones for intact rock. Based on the results for porosities and effective diffusion coefficients it was concluded that they do not seem to correlate with sorption parameters. However, an alteration state, heterogeneity and mineral content seem to be important factors affecting the distribution coefficients and upscaling factors.
  • Haiko, Johanna; Savolainen, Laura E.; Hilla, Risto; Patari-Sampo, Anu (2016)
    Complicated urinary tract infections, such as pyelonephritis, may lead to sepsis. Rapid diagnosis is needed to identify the causative urinary pathogen and to verify the appropriate empirical antimicrobial therapy. We describe here a rapid identification method for urinary pathogens: urine is incubated on chocolate agar for 3 h at 35 degrees C with 5%CO2 and subjected to MALDI-TOF MS analysis by VITEK MS. Overall 207 screened clinical urine samples were tested in parallel with conventional urine culture. The method, called U-si-MALDI-TOF (urine short incubation MALDI-TOF), showed correct identification for 86% of Gram-negative urinary tract pathogens (Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae), when present at >10(5) cfu/ml in culture (n = 107), compared with conventional culture method. However, Gram-positive bacteria (n = 28) were not successfully identified by U-si-MALDI-TOF. This method is especially suitable for rapid identification of E. coli, the most common cause of urinary tract infections and urosepsis. Turnaround time for identification using U-si-MALDI-TOF compared with conventional urine culture was improved from 24 h to 4-6 h. (C) 2016 Elsevier B.V. All rights reserved.
  • Mitt, Mario; Kals, Mart; Parn, Kalle; Gabriel, Stacey B.; Lander, Eric S.; Palotie, Aarno; Ripatti, Samuli; Morris, Andrew P.; Metspalu, Andres; Esko, Tonu; Magi, Reedik; Palta, Priit (2017)
    Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF) >= 5% and low-frequency variants (0.5
  • Ambers, Angie; Votrubova, Jitka; Vanek, Daniel; Sajantila, Antti; Budowle, Bruce (2018)
    Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies. In this comparative study, Y-STR typing with both Yfiler and Yfiler Plus (Thermo Fisher Scientific, Waltham, MA, USA) was performed on a variety of human skeletal remains, including samples from the American Civil War (1861-1865), the late nineteenth century gold rush era in Deadwood, SD, USA (1874-1877), the Seven Years' War (1756-1763), a seventeenth-century archaeological site in Raspenava, Bohemia (Czech Republic), and World War II (1939-1945). The skeletal remains used for this study were recovered from a wide range of environmental conditions and were extracted using several common methods. Regardless of the DNA extraction method used and the age/condition of the remains, 22 out of 24 bone samples yielded a greater number of alleles using the Yfiler Plus kit compared to the Yfiler kit using the same quantity of input DNA. There was no discernable correlation with the degradation index values for these samples. Overall, the efficacy of the Yfiler Plus assay was demonstrated on degraded DNA from skeletal remains. Yfiler Plus increases the discriminatory power over the previous generation multiplex due to the larger set of Y-STR markers available for analysis and buffer modifications with the newer version kit. Increased haplotype resolution is provided to infer or refute putative genetic relationships.
  • Leskinen, Anumaija; Gautier, Celine; Räty, Antti; Kekki, Tommi; Laporte, Elodie; Giuliani, Margaux; Bubendorff, Jacques; Laurila, Julia Pauliina; Kurhela, Kristian Otto Aleksi; Fichet, Pascal; Salminen-Paatero, Susanna (2021)
    This paper reports the results obtained in a Nordic Nuclear Safety Research project during the second intercomparison exercise for the determination of difficult to measure radionuclides in decommissioning waste. Eight laboratories participated by carrying out radiochemical analysis of H-3, C-14, Cl-36, Ca-41, Fe-55 and Ni-63 in an activated concrete. In addition, gamma emitters, namely Eu-152 and Co-60, were analysed. The assigned values were derived from the submitted results according to ISO 13,528 standard and the performance assessments were determined using z scores. The measured results were compared with activation calculation result showing varying degree of comparability.
  • Svensson, Urban; Voutilainen, Mikko; Muuri, Eveliina; Ferry, Michel; Gylling, Björn (2019)
    A numerical reactive transport model for crystalline rocks is developed and evaluated. The model is based on mineral maps generated by X-ray micro computed tomography (X-μCT); the maps used have a resolution of approximately 30 μm and the rock samples are on the cm scale. A computational grid for the intergranular space is generated and a micro-DFN (Discrete Fracture Network) model governs the grid properties. A particle tracking method (Time Domain Random Walk) is used for transport simulations. The basic concept of the model can now be formulated as follows; “when a particle is close to a reactive mineral surface it has a certain probability to get sorbed during a certain time span. Once sorbed it will remain so a certain time”. The model requires a number of input parameters that represent the sorption properties of the reactive minerals. Attempts are made to relate the parameters to traditional distribution parameters. The model is evaluated by comparisons with recent laboratory experimental data. These experiments consider two rock types (veined gneiss and pegmatitic granite) and two radionuclides (cesium and barium). It is concluded that the new reactive transport model can simulate the experimental data in a consistent and realistic way.
  • Ambers, Angie; Turnbough, Meredith; Benjamin, Robert; Gill-King, Harrell; King, Jonathan; Sajantila, Antti; Budowle, Bruce (2016)
    Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors. Published by Elsevier Ireland Ltd.
  • Falgenhauer, Linda; Schwengers, Oliver; Schmiedel, Judith; Baars, Christian; Lambrecht, Oda; Hess, Stefanie; Berendonk, Thomas U.; Falgenhauer, Jane; Chakraborty, Trinad; Imirzalioglu, Can (2019)
    Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate the role of water for their spread in more detail, we characterized ESBL/Carbapenemase-producing bacteria from surface water and sediment samples using phenotypic and genotypic approaches. ESBL/Carbapenemase-producing isolates were obtained from water/sediment samples. Species and antibiotic resistance were determined. A subset of these isolates (n = 33) was whole-genome-sequenced and analyzed for the presence of antibiotic resistance genes and virulence determinants. Their relatedness to isolates associated with human infections was investigated using multilocus sequence type and cgMLST-based analysis. Eighty-nine percent of the isolates comprised of clinically relevant species. Fifty-eight percent exhibited a multidrug-resistance phenotype. Two isolates harbored the mobile colistin resistance gene mcr-1. One carbapenemase-producing isolate identified as Enterobacter kobei harbored bla(VIM-)(1). Two Escherichia coli isolates had sequence types (ST) associated with human infections (ST131 and ST1485) and a Klebsiella pneumoniae isolate was classified as hypervirulent. A multidrug-resistant (MDR) Pseudomonas aeruginosa isolate encoding known virulence genes associated with severe lung infections in cystic fibrosis patients was also detected. The presence of MDR and clinically relevant isolates in recreational and surface water underlines the role of aquatic environments as both reservoirs and hot spots for MDR bacteria. Future assessment of water quality should include the examination of the multidrug resistance of clinically relevant bacterial species and thus provide an important link regarding the spread of MDR bacteria in a One Health context.