References
Arosenius, H, A Backhans, et al. 2025.
“Bacteriological Investigations of Suspected NNPD Cases in
Sweden.” In Proceedings: 15th European Symposium
of Porcine Health Management, Bern, Switzerland, May 21-23.
Backhans, A, E Hurri, et al. 2023.
“Nytt Från SvarmPat: Få Behandlingsalternativ Mot Mycoplasma
Bovis [News from SvarmPat: Limited Treatment Options
for Mycoplasma Bovis].” Svensk Veterinärtidning
3: 53.
Backhans, A, and M Lindberg. 2020. “Spåren Av Svindysenteri Kan
Följas Med Genteknik [The Traces of Swine Dysentery Can Be
Followed Using Genetic Techniques].” Grisföretagaren 2:
18–19.
Been, M de, VF Lanza, et al. 2014.
“Dissemination of Cephalosporin Resistance Genes Between
Escherichia Coli Strains from Farm Animals and Humans by
Specific Plasmid Lineages.” PLoS Genetics 10: e1004776.
Bengtsson, B, L Persson, et al. 2017.
“High Occurrence of mecC-MRSA in Wild Hedgehogs (Erinaceus
Europaeus) in Sweden.” Veterinary
Microbiology 207: 103–7.
Bharat, A, A Petkau, et al. 2022.
“Correlation Between Phenotypic and in Silico Detection of
Antimicrobial Resistance in Salmonella Enterica in
Canada Using Staramr.”
Microorganisms 10: 292.
Bolinger, H, and S Kathariou. 2017. “The Current State of
Macrolide Resistance in Campylobacter Spp.: Trends and Impact
of Resistance Mechanisms.” Applied and Environmental
Microbiology 83: e00416–17.
Börjesson, S, L Gunnarsson, et al. 2020.
“Low Occurrence of Extended-Spectrum Cephalosporinase Producing
Enterobacteriaceae and No Detection of
Methicillin-Resistant Coagulase-Positive Staphylococci in Healthy Dogs
in Sweden.” Acta Veterinaria Scandinavica
62 (1): 18.
Börjesson, S, S Ny, et al. 2016.
“Limited Dissemination of Extended-Spectrum Beta-Lactamase- and
Plasmid-Encoded AmpC-Producing Escherichia Coli from Food and
Farm Animals, Sweden.” Emerging Infectious
Diseases 22: 634–40.
Chen, S. 2025. “Fastp 1.0: An Ultra-Fast All-Round Tool for FASTQ
Data Quality Control and Preprocessing.” iMeta 4
(e70078).
Clinical and Laboratory Standards Institute (CLSI). 2015. Methods
for Antimicrobial Dilution and Susceptibility Testing of Infrequently
Isolated or Fastidious Bacteria; Approved Guideline - Third Edition CLSI
Guideline M45 Ed3. Wayne, PA, USA.
Clinical and Laboratory Standards Institute (CLSI). 2020a. Methods
for Antimicrobial Broth Dilution and Disk Diffusion Susceptibility
Testing of Bacteria Isolated from Aquatic Animals; Second Edition VET03
Ed2. Wayne, PA, USA.
Clinical and Laboratory Standards Institute (CLSI). 2020b.
Performance Standards for Antimicrobial Susceptibility Testing of
Bacteria Isolated from Aquatic Animals; Third Edition VET04 Ed3.
Wayne, PA, USA.
Clinical and Laboratory Standards Institute (CLSI). 2024a.
Performance Standards for Antimicrobial Disk and Dilution
Susceptibility Tests for Bacteria Isolated from Animals; Seventh Edition
CLSI Supplement VET01S Ed7. Wayne, PA, USA.
Clinical and Laboratory Standards Institute (CLSI). 2024b.
Performance Standards for Antimicrobial Disk and Dilution
Susceptibility Tests for Bacteria Isolated from Animals; Sixth Edition
CLSI Standard VET01 Ed6. Wayne, PA, USA.
Committee for medicinal products for veterinary use (CVMP). 2009.
Reflection Paper on MRSA in Food Producing and Companion Animals in
the European Union: Epidemiology and Control Options for
Human and Animal Health. https://www.ema.europa.eu/en/documents/scientific-guideline/reflection-paper-mrsa-food-producing-and-companion-animals-european-union-epidemiology-and-control-options-human-and-animal-health_en.pdf.
Council of the European Union. 2023. Council Recommendation on
Stepping up EU Actions to Combat Antimicrobial Resistance
in a One Health Approach. Recommendation. https://data.consilium.europa.eu/doc/document/ST-9581-2023-INIT/en/pdf.
European Centre for Disease Prevention and Control (ECDC). 2023.
Antimicrobial Consumption in the EU/EEA
(ESAC-Net) – Annual Epidemiological Report 2022. https://www.ecdc.europa.eu/sites/default/files/documents/AER-antimicrobial-consumption.pdf.
European Centre for Disease Prevention and Control (ECDC). 2025.
Communicable Disease Threats Report, 29 November - 5
December 2025, Week 49. Weekly Report. https://www.ecdc.europa.eu/en/publications-data/communicable-disease-threats-report-29-november-5-december-2025-week-49.
European Commission. 2021. Commission Delegated Regulation (EU)
2021/578 of 29 January 2021 Supplementing Regulation (EU) 2019/6 of the European Parliament and of
the Council with Regard to Requirements for the Collection of
Data on the Volume of Sales and on the Use of Antimicrobial Medicinal
Products in Animals. https://eur-lex.europa.eu/eli/reg_del/2021/578/oj.
European Committee on Antimicrobial Susceptibility Testing (EUCAST).
2025. Breakpoint Tables for Interpretation of MICs and
Zone Diameters. Version 15.0. https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_15.0_Breakpoint_Tables.pdf.
European Food Safety Authority (EFSA). 2009. “Scientific Opinion
of the Panel on Biological Hazards on a Request from the European
Commission on Assessment of the Public Health Significance of
Meticillin Resistant Staphylococcus Aureus (MRSA) in Animals
and Foods.” EFSA Journal 993: 1–73.
European Food Safety Authority (EFSA). 2011. “Scientific Opinion
on the Public Health Risks of Bacterial Strains Producing
Extended-Spectrum Beta-Lactamases and/or AmpC Beta-Lactamases in Food
and Food-Producing Animals.” EFSA Journal 9: 2322.
European Medicines Agency (EMA). 2011. Trends in the Sales of
Veterinary Antimicrobial Agents in Nine European Countries
(2005–2009). Surveillance Report. https://www.ema.europa.eu/en/documents/report/trends-sales-veterinary-antimicrobial-agents-nine-european-countries_en.pdf.
European Medicines Agency (EMA). 2019. Disabling and Potentially
Permanent Side Effects Lead to Suspension or Restrictions of Quinolone
and Fluoroquinolone Antibiotics. Referral. https://www.ema.europa.eu/en/medicines/human/referrals/quinolone-fluoroquinolone-containing-medicinal-products.
European Medicines Agency (EMA). 2025a. Categorisation of
Antibiotics in the European Union: Answer to the Request
from the European Commission for Updating the Scientific
Advice on the Impact on Public Health and Animal Health of the Use of
Antibiotics in Animals. Scientific Advice. https://www.ema.europa.eu/en/documents/report/categorisation-antibiotics-european-union-answer-request-european-commission-updating-scientific-advice-impact-public-health-animal-health-use-antibiotics-animals_en.pdf.
European Medicines Agency (EMA). 2025b. European Sales and Use of
Antimicrobials for Veterinary Medicine (ESUAvet). Annual Surveillance
Report for 2024. https://www.ema.europa.eu/en/documents/report/european-sales-use-antimicrobials-veterinary-medicine-annual-surveillance-report-2024_en.pdf.
European Parliament and Council of the European Union. 2019.
Regulation (EU) 2019/6 of the European
Parliament and of the Council of 11 December 2018 on Veterinary
Medicinal Products and Repealing Directive 2001/82/EC. http://data.europa.eu/eli/reg/2019/6/oj.
Fang, H, F Ataker, et al. 2008.
“Molecular Epidemiology of Extended-Spectrum Beta-Lactamases Among
Escherichia Coli Isolates Collected in a Swedish
Hospital and Its Associated Health Care Facilities from 2001 to
2006.” Journal of Clinical Microbiology 46: 707–12.
Feldgarden, M, V Brover, et al. 2021.
“AMRFinderPlus and the Reference Gene Catalog Facilitate
Examination of the Genomic Links Among Antimicrobial Resistance, Stress
Response, and Virulence.” Scientific Reports 11: 12728.
García-Álvarez, L, MT Holden, et al. 2011.
“Meticillin-Resistant Staphylococcus Aureus with a Novel
mecA Homologue in Human and Bovine Populations in the UK and
Denmark: A Descriptive Study.” The Lancet
Infectious Diseases 11: 595–603.
Gohel, David. 2023. Ggiraph: Interactive Graphics for ggplot2. https://cran.r-project.org/package=ggiraph.
Government Offices of Sweden. 2026. Sveriges Strategi För Att
Begränsa Antibiotikaresistens 2026–2035 [Sweden’s Strategy to Curb Antimicrobial Resistance
2026–2035]. Strategy Document. https://www.government.se/contentassets/efa443680a8b48b79ddc24932e277e27/eng-amr_strategi-webb.pdf.
Ito, T, K Hiramatsu, et al. 2012.
“Guidelines for Reporting Novel mecA Gene Homologues.”
Antimicrobial Agents and Chemotherapy 56: 4997–99.
Jolley, KA, JE Bray, et al. 2018.
“Open-Access Bacterial Population Genomics: BIGSdb Software, the
PubMLST.org Website and Their Applications.” Wellcome Open
Research 3 (124).
Karlsson, M, C Fellström, et al. 2003.
“Antimicrobial Susceptibility Testing of Porcine Brachyspira
(Serpulina) Species Isolates.” Journal of Clinical
Microbiology 41: 2596–604.
Kizerwetter-Świda, M, D Chrobak-Chmiel, et
al. 2017. “Changes in the Population Structure of Canine
Methicillin-Resistant Staphylococcus Pseudintermedius in
Poland.” Veterinary Microbiology 208:
106–9.
Kizerwetter-Świda, M, D Chrobak-Chmiel, et
al. 2026. “Tetracycline Resistance Among Canine
Methicillin-Resistant Staphylococcus Pseudintermedius (MRSP)
Clinical Isolates: Is Minocycline a Viable Treatment Option?”
Antibiotics 15 (9).
Kuusela, J. 2025. “Nytt Från SvarmPat: Antibiotikaanvändning Vid
Lunginflammation Orsakad Av Mycoplasma Bovis [News
from SvarmPat: Antimicrobial Use in Pneumonia Caused by Mycoplasma
Bovis].” Svensk Veterinärtidning 2: 43.
Kyhlsgard, J. 2025. “Pathogens from Pneumonic Lesions in
Swedish Pigs at Slaughter - Antibiotic Susceptibility of
Bacteria Associated with the Porcine Respiratory Disease
Complex.” Master’s thesis, Swedish university of agricultural
sciences, Uppsala, Sweden. https://stud.epsilon.slu.se/20905/1/kyhlsgard_j_250128.pdf.
Larsen, J, CL Raisen, et al. 2022.
“Emergence of Methicillin Resistance Predates the Clinical Use of
Antibiotics.” Nature 602: 135–41.
Moses, IB, F Fernandes Santos, et al. 2023.
“Human Colonization and Infection by Staphylococcus
Pseudintermedius: An Emerging and Underestimated Zoonotic
Pathogen.” Microorganisms 11 (581).
Myrenås, M, K Pedersen, et al. 2024.
“Genomic Analyses of Methicillin-Resistant Staphylococcus
Pseudintermedius from Companion Animals Reveal Changing Clonal
Populations, Multidrug Resistance, and Virulence.”
Antibiotics 13 (962).
Nettersjö, Oscar, and Markus Öst. 2023. Pxweb: Retrieve Data from
the PX-WEB API. https://github.com/rOpenGov/pxweb.
Nilsson, O, S Börjesson, et al. 2020.
“Decreased Detection of ESBL- or pAmpC-Producing Escherichia
Coli in Broiler Breeders Imported into Sweden.”
Acta Veterinaria Scandinavica 62: 33.
Papić, B, M Golob, et al. 2021.
“Genomic Insights into the Emergence and Spread of
Methicillin-Resistant Staphylococcus Pseudintermedius in
Veterinary Clinics.” Veterinary Microbiology 258:
109–19.
Perez-Perez, FJ, and ND Hanson. 2002. “Detection of
Plasmid-Mediated AmpC Beta-Lactamase Genes in Clinical Isolates by Using
Multiplex PCR.” Journal of Clinical Microbiology 40:
2153–62.
Persson, Y, S Börjesson, et al. 2021.
“No Detection of Methicillin-Resistant Staphylococcus
Aureus in Dairy Goats.” Dairy 2: 65–70.
Pettersson, L. 2007. Försäljning Av Antibiotika För Hund Och Katt i
Sverige Under 2005 Och 2006 [Sales of
Antibiotics for Dogs and Cats in Sweden During 2005 and
2006]. Department of pharmacy, Uppsala university, Uppsala, Sweden.
Pichon, B, R Hill, et al. 2012.
“Development of a Real-Time Quadruplex PCR Assay for Simultaneous
Detection of Nuc, Panton-Valentine Leucocidin (PVL), mecA and Homologue
mecALGA251.” Journal of Antimicrobial Chemotherapy 67:
2338–41.
Posit Software, PBC. 2026. Quarto. https://quarto.org/.
Pringle, M, A Landén, et al. 2012.
“Antimicrobial Susceptibility of Porcine Brachyspira
Hyodysenteriae and Brachyspira Pilosicoli Isolated in
Sweden Between 1990 and 2010.” Acta Veterinaria
Scandinavica 54: 54.
Public Health Agency of Sweden. 2025. Smittsamma Sjukdomar –
Statistik [Communicable Diseases - Statistics]. https://www.folkhalsomyndigheten.se/statistik-och-data/hitta-statistik-och-data/smittsamma-sjukdomar-statistik/.
Public Health Agency of Sweden, Swedish Medical Products Agency, and
Strama. 2014. Behandlingsrekommendation För Vanliga Infektioner i
Öppenvård [Recommendations for Treatment of Common
Infections in Outpatient Care]. Behandlingsrekommendation. https://www.folkhalsomyndigheten.se/contentassets/246aa17721b44c5380a0117f6d0aba40/behandlingsrekommendationer-oppenvard.pdf.
Rasmussen, SL, J Larsen, et al. 2019.
“European Hedgehogs (Erinaceus Europaeus) as a Natural
Reservoir of Methicillin-Resistant Staphylococcus Aureus
Carrying mecC in Denmark.” PLoS One,
e0222031.
Rincón Gracia, M, A Backhans, et al. 2026.
“Antibiotic Susceptibility of Enterococcus Hirae from
Piglets with NNPD.” In Proceedings: 16th European Symposium
of Porcine Health Management, Florence, Italy, May 13-15.
Seemann, T. n.d. Mlst Github. https://github.com/tseemann/mlst.
Seligsohn, D, K Gustafsson, et al. 2026.
“Nytt Från SvarmPat: Virus Sannolikt Av Underordnad Betydelse Vid
Lunginflammation Hos Får [News from SvarmPat: Viruses Are
Likely of Minor Importance in Pneumonia in Sheep].” Svensk
Veterinärtidning 5: 48–49.
Shore, AC, EC Deasy, et al. 2011.
“Detection of Staphylococcal Cassette Chromosome Mec Type XI
Carrying Highly Divergent mecA, mecI, mecR1, blaZ, and Ccr Genes in
Human Clinical Isolates of Clonal Complex 130 Methicillin-Resistant
Staphylococcus Aureus.” Antimicrobial Agents and
Chemotherapy 55: 3765–73.
Sjölund, M, A Backhans, et al. 2015.
“Antimicrobial Usage in 60 Swedish Farrow-to-Finish
Pig Herds.” Preventive Veterinary Medicine 121: 257–64.
Söderlund, R, M Hakhverdyan, et al. 2018.
“Genome Analysis Provides Insights into the Epidemiology of
Infection with Flavobacterium Psychrophilum Among Farmed
Salmonid Fish in Sweden.” Microbial Genomics 4 (12):
e000241.
Söderlund, R, C Jernberg, et al. 2019.
“Linked Seasonal Outbreaks of Salmonella Typhimurium
Among Passerine Birds, Domestic Cats and Humans, Sweden,
2009 to 2016.” Eurosurveillance 24 (34): 1900074.
Solvang, A, M Tråvén, et al. 2025.
“Nytt Från SvarmPat: Ct-Värden Och Luftvägssmitta Hos Kalv
[News from SvarmPat: Ct Values and Respiratory Tract
Infections in Calves].” Svensk Veterinärtidning 10: 33.
Souvorov, A, R Agarwala, et al. 2018.
“SKESA: Strategic k-Mer Extension for Scrupulous
Assemblies.” Genome Biology 19: 153.
Strama. 2025. Stramas Mål För Antibiotikaanvändning Inom Öppen Vård
[Strama Targets for Antibiotic Use in Primary Care].
Report. https://strama.se/wp-content/uploads/2025/04/stramas-mal-for-antibiotikaanvandningen-beskrivning.pdf.
Strama. 2026. Bristsituationer [Medicine
Shortages]. Behandlingsrekommendation. https://strama.se/behandlingsrekommendationer/bristsituationer/.
Swedish Medical Products Agency. 2015. “Dosering Av Antibiotika
till Häst - Behandlingsrekommendation [Dosage of
Antibiotics for Horses – Treatment Recommendations].”
Information Från Läkemedelsverket 26 (supplement): 4–16. https://www.lakemedelsverket.se/globalassets/dokument/behandling-och-forskrivning/behandlingsrekommendationer/behandlingsrekommendation/behandlingsrekommendation-antibiotika-till-hast.pdf.
Swedish Medical Products Agency. 2022. Dosering Av Antibiotika till
Gris - Behandlingsrekommendation [Dosage of Antibiotics for
Pigs – Treatment Recommendations]. https://www.lakemedelsverket.se/globalassets/dokument/behandling-och-forskrivning/behandlingsrekommendationer/behandlingsrekommendation/behandlingsrekommendation-antibiotika-till-gris.pdf.
The Swedish Veterinary Association. 2025. Sveriges Veterinärförbunds
Riktlinjer [the Swedish Veterinary Association’s Guidelines]. https://www.svf.se/veterinaermedicin/svfs-riktlinjer/.
Unnerstad, HE, K Mieziewska, et al. 2018.
“Suspected Transmission and Subsequent Spread of MRSA from Farmer
to Dairy Cows.” Veterinary Microbiology 225: 114–19.
Werinder, A, A Backhans, et al. 2026.
“Nytt Från SvarmPat: Neomycinresistens Hos e. Coli Från
Grisar Med Avvänjningsdiarré [News from SvarmPat: Neomycin Resistance in
e. Coli from Pigs with Post-Weaning Diarrhoea].”
Svensk Veterinärtidning 2: 51–52.
Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data
Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
Wickham, Hadley, Mara Averick, Jennifer Bryan, et al. 2019.
“Welcome to the tidyverse.”
Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.
Wilson, Edwin Bidwell. 1927. “Probable Inference, the Law of
Succession, and Statistical Inference.” Journal of the
American Statistical Association 22 (158): 209–12.
Wood, DE, J Lu, et al. 2019. “Improved
Metagenomic Analysis with Kraken 2.” Genome Biology 20:
257.
Woodford, N, EJ Fagan, et al. 2006.
“Multiplex PCR for Rapid Detection of Genes Encoding CTX-m
Extended-Spectrum (Beta)-Lactamases.” Journal of
Antimicrobial Chemotherapy 57: 154–55.
World Health Organization (WHO). 2025. AWaRe Classification.
Report. Geneva. https://www.who.int/publications/i/item/B09489.
Xie, Yihui, Joe Cheng, and Xianying Tan. 2023. DT: A
Wrapper of the JavaScript Library ’DataTables’. https://rstudio.github.io/DT/.
Zankari, E, R Allesøe, et al. 2017.
“PointFinder: A Novel Web Tool for WGS-Based Detection of
Antimicrobial Resistance Associated with Chromosomal Point Mutations in
Bacterial Pathogens.” Journal of Antimicrobial
Chemotherapy 72: 2764–68.
Zankari, E, H Hasman, et al. 2012.
“Identification of Acquired Antimicrobial Resistance
Genes.” Journal of Antimicrobial Chemotherapy 67:
2640–44.