Publications

2026

  1. Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communities
    Melina Markkanen, Heidi Putkuri, Dovydas Kičiatovas, and 3 more authors
    Feb 2026
    DOI
  2. Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts
    Melina Markkanen, Denise Pezzutto, Marko Virta, and 1 more author
    Microbiology Spectrum, Jan 2026
    DOI
  3. Towards One Health action for addressing antimicrobial resistance in the age of polycrisis
    Ishi Keenum, Thomas U. Berendonk, Jonas Bonnedahl, and 36 more authors
    Nature Sustainability, Jan 2026
    DOI

2025

  1. Complete genome sequences of Lacticaseibacillus paracasei strains E and E11.5 isolated from dairy products
    Nina Zhang, Guesh Mulaw, Antti Karkman, and 2 more authors
    Microbiology Resource Announcements, Jul 2025
    DOI
  2. Global health risk assessment of antibiotic resistance in agricultural soils
    Yanzheng Gao, Zekai Li, Sean Fettrow, and 8 more authors
    Oct 2025
    DOI
  3. Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community
    Veera Partanen, Svjetlana Dekić Rozman, Antti Karkman, and 3 more authors
    ISME Communications, Jan 2025
    DOI
  4. Comparative genomics and characterization of highly adhesive and stress resistant Lacticaseibacillus paracasei strain E
    Nina Zhang, Antti Karkman, Kaisa Hiippala, and 3 more authors
    Current Research in Food Science, Jan 2025
    DOI

2024

  1. Alkali-Activated Foams Coated with Colloidal Ag for Point-of-Use Water Disinfection
    Mohammad Amzad Hossain Bhuyan, Antti Karkman, Hanna Prokkola, and 3 more authors
    ACS ES&T Water, Jan 2024
    DOI
  2. Bacterial hosts of clinically significant beta-lactamase genes in Croatian wastewaters
    Svjetlana Dekić Rozman, Ana Puljko, Antti Karkman, and 2 more authors
    FEMS Microbiology Ecology, May 2024
    DOI
  3. Metagenomic assemblies tend to break around antibiotic resistance genes
    Anna Abramova, Antti Karkman, and Johan Bengtsson-Palme
    BMC Genomics, Oct 2024
    DOI

2023

  1. Metagenomic assemblies tend to break around antibiotic resistance genes
    Anna Abramova, Antti Karkman, and Johan Bengtsson-Palme
    Dec 2023
    DOI
  2. Metagenomic Analysis of the Abundance and Composition of Antibiotic Resistance Genes in Hospital Wastewater in Benin, Burkina Faso, and Finland
    Melina A. Markkanen, Kaisa Haukka, Katariina M. M. Pärnänen, and 8 more authors
    mSphere, Feb 2023
    DOI

2021

  1. Metagenomic analysis of the abundance and composition of antibiotic resistance genes in hospital wastewater in Benin, Burkina Faso, and Finland
    Melina A. Markkanen, Kaisa Haukka, Katariina M. M. Pärnänen, and 8 more authors
    Oct 2021
    DOI
  2. Interplay between skin microbiota and immunity in atopic individuals
    Matilda Riskumäki, Ioannis Tessas, Noora Ottman, and 11 more authors
    Allergy, Feb 2021
    DOI

2020

  1. Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome
    Carolin Rutgersson, Stefan Ebmeyer, Simon Bo Lassen, and 6 more authors
    Environment International, Apr 2020
    DOI
  2. Immune‐microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence
    Lasse Ruokolainen, Nanna Fyhrquist, Tiina Laatikainen, and 19 more authors
    Clinical & Experimental Allergy, Sep 2020
    DOI
  3. Predicting clinical resistance prevalence using sewage metagenomic data
    Antti Karkman, Fanny Berglund, Carl-Fredrik Flach, and 2 more authors
    Communications Biology, Nov 2020
    DOI
  4. Community-led, integrated, reproducible multi-omics with anvi’o
    A. Murat Eren, Evan Kiefl, Alon Shaiber, and 31 more authors
    Nature Microbiology, Dec 2020
    DOI
  5. Contrasting microbiotas between Finnish and Estonian infants: Exposure to Acinetobacter may contribute to the allergy gap
    Lasse Ruokolainen, Anna Parkkola, Antti Karkman, and 10 more authors
    Allergy, Mar 2020
    DOI

2019

  1. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments
    Antti Karkman, Katariina Pärnänen, and D. G. Joakim Larsson
    Nature Communications, Jan 2019
    DOI
  2. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence
    Katariina M. M. Pärnänen, Carlos Narciso-da-Rocha, David Kneis, and 23 more authors
    Science Advances, Mar 2019
    DOI

2018

  1. Nature‐oriented daycare diversifies skin microbiota in children—No robust association with allergies
    Jenni Lehtimäki, Tiina Laatikainen, Antti Karkman, and 4 more authors
    Pediatric Allergy and Immunology, Feb 2018
    DOI
  2. Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent
    Jenni Hultman, Manu Tamminen, Katariina Pärnänen, and 3 more authors
    FEMS Microbiology Ecology, Mar 2018
    DOI
  3. Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements
    Katariina Pärnänen, Antti Karkman, Jenni Hultman, and 9 more authors
    Nature Communications, Sep 2018
    DOI
  4. Antibiotic-Resistance Genes in Waste Water
    Antti Karkman, Thi Thuy Do, Fiona Walsh, and 1 more author
    Trends in Microbiology, Mar 2018
    DOI
  5. Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments
    Karkman Antti, Pärnänen Katariina, and Larsson D.G. Joakim
    Jun 2018
    DOI

2017

  1. Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia
    L. Ruokolainen, L. Paalanen, A. Karkman, and 15 more authors
    Clinical & Experimental Allergy, Mar 2017
    DOI
  2. The ecology of human microbiota: dynamics and diversity in health and disease
    Antti Karkman, Jenni Lehtimäki, and Lasse Ruokolainen
    Annals of the New York Academy of Sciences, Mar 2017
    DOI
  3. Patterns in the skin microbiota differ in children and teenagers between rural and urban environments
    Jenni Lehtimäki, Antti Karkman, Tiina Laatikainen, and 5 more authors
    Scientific Reports, Mar 2017
    DOI
  4. High Throughput Method for Analyzing Antibiotic Resistance Genes in Wastewater Treatment Plants
    Johanna Muurinen, Antti Karkman, and Marko Virta
    Sep 2017
    DOI
  5. Holistic View on Health: Two Protective Layers of Biodiversity
    Lasse Ruokolainen, Jenni Lehtimäki, Antti Karkman, and 3 more authors
    Annales Zoologici Fennici, Apr 2017
    DOI
  6. An active bacterial community linked to high chl-a concentrations in Antarctic winter-pack ice and evidence for the development of an anaerobic sea-ice bacterial community
    Eeva Eronen-Rasimus, Anne-Mari Luhtanen, Janne-Markus Rintala, and 4 more authors
    The ISME Journal, Jul 2017
    DOI
  7. Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use
    Johanna Muurinen, Robert Stedtfeld, Antti Karkman, and 3 more authors
    Environmental Science & Technology, May 2017
    DOI

2016

  1. Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow
    Serena Caucci, Antti Karkman, Damiano Cacace, and 6 more authors
    FEMS Microbiology Ecology, Apr 2016
    DOI
  2. Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics
    Katariina Pärnänen, Antti Karkman, Manu Tamminen, and 4 more authors
    Scientific Reports, Oct 2016
    DOI
  3. Bacterial communities in Arctic first‐year drift ice during the winter/spring transition
    Eeva Eronen‐Rasimus, Jonna Piiparinen, Antti Karkman, and 3 more authors
    Environmental Microbiology Reports, Jun 2016
    DOI
  4. “Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
    Marco Fondi, Antti Karkman, Manu V. Tamminen, and 5 more authors
    Genome Biology and Evolution, Apr 2016
    DOI
  5. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant
    Antti Karkman, Timothy A. Johnson, Christina Lyra, and 4 more authors
    FEMS Microbiology Ecology, Jan 2016
    DOI
  6. Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments
    Windi I. Muziasari, Katariina Pärnänen, Timothy A. Johnson, and 6 more authors
    FEMS Microbiology Ecology, Mar 2016
    DOI

2015

  1. Cyanobacteria as a Source for Novel Anti-Leukemic Compounds
    Anu Humisto, Lars Herfindal, Jouni Jokela, and 4 more authors
    Current Pharmaceutical Biotechnology, Oct 2015
    DOI

2014

  1. Sulphonamide and Trimethoprim Resistance Genes Persist in Sediments at Baltic Sea Aquaculture Farms but Are Not Detected in the Surrounding Environment
    Windi Indra Muziasari, Satoshi Managaki, Katariina Pärnänen, and 5 more authors
    PLoS ONE, Mar 2014
    DOI
  2. Discovery of bacterial polyhydroxyalkanoate synthase (PhaC)-encoding genes from seasonal Baltic Sea ice and cold estuarine waters
    Katariina Pärnänen, Antti Karkman, Marko Virta, and 2 more authors
    Extremophiles, Oct 2014
    DOI
  3. Abundances of Tetracycline, Sulphonamide and Beta-Lactam Antibiotic Resistance Genes in Conventional Wastewater Treatment Plants (WWTPs) with Different Waste Load
    Mailis Laht, Antti Karkman, Veiko Voolaid, and 4 more authors
    PLoS ONE, Aug 2014
    DOI

2012

  1. Enterococcus rivorum sp. nov., from water of pristine brooks
    R. Maarit Niemi, Tuula Ollinkangas, Lars Paulin, and 5 more authors
    International Journal of Systematic and Evolutionary Microbiology, Sep 2012
    DOI

2011

  1. Fish Farming Affects the Abundance and Diversity of the Mercury Resistance Gene merA in Marine Sediments
    Leena K. Pitkänen, Manu Tamminen, Anu Hynninen, and 4 more authors
    Microbes and Environments, Sep 2011
    DOI
  2. Cold temperature decreases bacterial species richness in nitrogen‐removing bioreactors treating inorganic mine waters
    A. Karkman, K. Mattila, M. Tamminen, and 1 more author
    Biotechnology and Bioengineering, Aug 2011
    DOI
  3. Differences in bacterial community composition in Baltic Sea sediment in response to fish farming
    Manu Tamminen, Antti Karkman, Jukka Corander, and 2 more authors
    Aquaculture, Mar 2011
    DOI

2010

  1. Tetracycline Resistance Genes Persist at Aquaculture Farms in the Absence of Selection Pressure
    Manu Tamminen, Antti Karkman, Andres Lõhmus, and 5 more authors
    Environmental Science & Technology, Dec 2010
    DOI