Browsing by Subject "Antimicrobial resistance"

Sort by: Order: Results:

Now showing items 1-17 of 17
  • Mai, The Tien; Turner, Paul; Corander, Jukka (2021)
    Background Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often based on random-effect models, typically for computational reasons. The alternative of using a fixed-effect model has received much more limited attention in the literature. Results In this paper, we propose a generic strategy for heritability inference, termed as "boosting heritability", by combining the advantageous features of different recent methods to produce an estimate of the heritability with a high-dimensional linear model. Boosting heritability uses in particular a multiple sample splitting strategy which leads in general to a stable and accurate estimate. We use both simulated data and real antibiotic resistance data from a major human pathogen, Sptreptococcus pneumoniae, to demonstrate the attractive features of our inference strategy. Conclusions Boosting is shown to offer a reliable and practically useful tool for inference about heritability.
  • Mai, The T; Turner, Paul; Corander, Jukka (BioMed Central, 2021)
    Abstract Background Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often based on random-effect models, typically for computational reasons. The alternative of using a fixed-effect model has received much more limited attention in the literature. Results In this paper, we propose a generic strategy for heritability inference, termed as “boosting heritability”, by combining the advantageous features of different recent methods to produce an estimate of the heritability with a high-dimensional linear model. Boosting heritability uses in particular a multiple sample splitting strategy which leads in general to a stable and accurate estimate. We use both simulated data and real antibiotic resistance data from a major human pathogen, Sptreptococcus pneumoniae, to demonstrate the attractive features of our inference strategy. Conclusions Boosting is shown to offer a reliable and practically useful tool for inference about heritability.
  • Skarp, C. P. A.; Hanninen, M-L; Rautelin, Hilpi I (2016)
    The incidence of human infections caused by Campylobacter jejuni and Campylobacter coil, the main bacterial agents of gastrointestinal disease, has been increasing worldwide. Here, we review the role of poultry as a source and reservoir for Campylobacter. Contamination and subsequent colonization of broiler flocks at the farm level often lead to transmission of Campylobacter along the poultry production chain and contamination of poultry meat at retail. Yet Cainpylobacter prevalence in poultry, as well as the contamination level of poultry products, vary greatly between different countries so there are differences in the intervention strategies that need to be applied. Temporal patterns in poultry do not always coincide with those found in human infections. Studies in rural and urban areas have revealed differences in Campylobacter infections attributed to poultry, as poultry seems to be the predominant reservoir in urban, but not necessarily in rural, settings. Furthermore, foreign travel is considered a major risk factor in acquiring the disease, especially for individuals living in the northern European countries. Intervention strategies aimed at reducing Campylobacter colonization in poultry and focused at the farm level have been successful in reducing the number of Campylobacter cases in several countries. Increasing farm biosecurity and education of consumers are likely to limit the risk of infection. Overall, poultry is an important reservoir and source of human campylobacteriosis, although the contribution of other sources, reservoirs and transmission warrants more research. Clinical Microbiology and Infection (C) 2015 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.
  • 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)
  • Oikarainen, Paula E.; Pohjola, Leena K.; Pietola, Eeva S.; Heikinheimo, Annamari (2019)
    Extended-spectrum beta-lactamase (ESBL) and plasmidic AmpC (pAmpC) producing Escherichia coli are found in the poultry production even without antibiotic use. The spread of these bacteria has been suggested to occur via imported parent birds, enabling transmission to production level broilers vertically via eggs. We studied transmission of ESBL/pAmpC-producing E. coli and E. coli without antibiotic selection by sampling imported parent birds (n = 450), egg surfaces prior to and after the incubation period (n = 300 and n = 428, respectively) and the laying house environment (n = 20). Samples were additionally taken from embryos (n = 422). To study the prevention of transmission, a competitive exclusion (CE) solution was added onto freshly laid eggs prior to incubation period (n = 150). Results showed carriage of ESBL/pAmpC-producing E. coil in parent birds (26.7%), the environment (5%) and egg surfaces before the incubation period (1.3%), but not from egg surfaces or embryos after the incubation period. Whole genome sequencing revealed ESBL/pAmpC-producing E. coil isolates belonging to clonal lineages ST429 and ST2040. However, the finding of E. coli cultured without antibiotic selection in two (2.2%) embryos strengthens the need to study E. coil transmission in poultry production in more depth. Since ESBL/pAmpC-producing E. coli seem not to persist on egg surfaces, there is no need to use CE solution ex ovo as a prevention method. The results indicate that other routes, such as for example transmission through fomites or horizontal gene transfer by other bacterial species, could be more important than vertical transmission in the spread of resistance in broiler production.
  • Nykäsenoja, Suvi; Olkkola, Satu; Pohjanvirta, Tarja; Biström, Mia; Kaartinen, Liisa; Helin-Soilevaara, Henriette; Aarnio, Maria; Raunio-Saarnisto, Mirja; Kivilahti-Mäntylä, Katariina; Nevalainen, Martti; Grönthal, Thomas; Eskola, Katarina; Rantala, Merja (Finnish Food Authority, 2019)
    Finnish Food Authority publications
    Consumption of veterinary antimicrobials in food-producing animal species in Finland is low and in recent years, has decreased further. Drop is noted in sales of almost all antimicrobial classes. Particularly sales of orally administered products have decreased. Sales of tablets intended to companion animals has almost halved during this decade. Majority, two thirds, of all antimicrobial products sold in 2018 was for treatment of individual animals and the remaining third products applicable for group treatment. Narrow spectrum penicillin G was the most used antimicrobial for animals and the proportion of highest priority critically important antimicrobials (HPCIA) was very low. The antimicrobial resistance situation in bacteria from animals and food has remained relatively good in Finland. However, in certain bacteria resistance was detected in moderate or high levels. Therefore, there is a need to further emphasise the preventive measures and prudent use of antimicrobials. It is important to follow the Finnish recommendations for the use of antimicrobials in animals. Among salmonella and campylobacter isolated from Finnish food-producing animals, resistance levels were mainly low. For the first time in Finland, multidrug resistant S. Kentucky was isolated from cattle in 2018. From 2014, the occurrence of fluoroquinolone and tetracycline resistance in campylobacter from broilers have varied. The occurrence of fluoroquinolone resistance in indicator E. coli has increased although the resistance is still low. Among pathogenic bacteria isolated from food-producing animals the most notifiable change was the worsening of resistance in some bovine respiratory disease pathogens. In other pathogens from food-producing animals the resistance situation remained similar as in previous years. The proportion of resistant bacterial isolates from companion animals and horses decreased for nearly all antimicrobials. However, the proportion of resistant isolates is still high for some antimicrobials. ESBL/AmpC-producing bacteria were still encountered in broilers and broiler meat; prevalence of these bacteria in broiler meat was somewhat lower in 2018 compared to 2016.
  • Sartelli, Massimo; Coccolini, Federico; Abu-Zidan, Fikri M.; Ansaloni, Luca; Bartoli, Stefano; Biffl, Walter; Borghi, Felice; Chouillard, Elie; Cui, Yunfeng; Nascimento, Rafael De Oliveira; De Simone, Belinda; Di Saverio, Salomone; Duane, Therese; Eckmann, Christian; Eid, Hani O.; Gomes, Carlos Augusto; Gomes, Felipe Couto; Hecker, Andreas; Hecker, Birgit; Isik, Arda; Itani, Kamal M. F.; Leppäniemi, Ari; Litvin, Andrey; Luppi, Davide; Maier, Ronald; Manzano-Nunez, Ramiro; Marwah, Sanjay; Mazuski, John; Moore, Ernest; Perrone, Gennaro; Rasa, Kemal; Rubio, Ines; Sawyer, Robert; Labricciosa, Francesco M.; Catena, Fausto (2020)
    Appropriate measures of infection prevention and management are integral to optimal clinical practice and standards of care. Among surgeons, these measures are often over-looked. However, surgeons are at the forefront in preventing and managing infections. Surgeons are responsible for many of the processes of healthcare that impact the risk for surgical site infections and play a key role in their prevention. Surgeons are also at the forefront in managing patients with infections, who often need prompt source control and appropriate antibiotic therapy, and are directly responsible for their outcome. In this context, the direct leadership of surgeons in infection prevention and management is of utmost importance. In order to disseminate worldwide this message, the editorial has been translated into 9 different languages (Arabic, Chinese, French, German, Italian, Portuguese, Spanish, Russian, and Turkish).
  • Pezzutto, Denise (Helsingin yliopisto, 2019)
    Antimicrobial resistance is an emerging concern at the global scale, threatening the effectiveness of antibiotics in treating bacterial infections. Among anthropogenically impacted environments, wastewater treatment plants have been indicated as possible reservoirs of antibiotic resistance genes, putative hotspots for their horizontal gene transfer, and a source of their dissemination to the environment. Generally, the abundance of antibiotic resistance genes is reduced during the wastewater treatment process. However, some genes were shown to be enriched in purified effluent water and dried sludge, which are then released to the environment, compared to influent water. Also, the taxonomy of the hosts carrying antibiotic resistance genes could change as a result of horizontal gene transfer events. The aim of this study was to analyse and compare the host range of a series of antibiotic resistance genes in influent water, effluent water and dried sludge collected from the Viikinmäki wastewater treatment plant in Helsinki, Finland, by applying Emulsion, Paired Isolation and Concatenation PCR (epicPCR). EpicPCR is a method that can link a gene of interest to the 16S rRNA gene from the genome of the host bacterium, without any cultivation step. The abundance of the hosts was also evaluated by sequencing the 16S rRNA gene from the whole bacterial community. In several cases, the target antibiotic resistance genes (blaIMP, blaNDM, ermB, ermF, sul1 and strB) were carried in effluent water and dried sludge by taxa that were not hosting them in influent water, suggesting that horizontal gene transfer events might have occurred during the treatment. All the examined genes were detected both in abundant and in rare taxa, including genera that also comprise pathogenic species, such as Arcobacter and Acinetobacter. Some of the detected hosts were not previously known to show resistant phenotypes, namely members of the family Methylophilaceae. These results corroborate the idea that wastewater treatment plants might be hotspots for the horizontal gene transfer of resistance determinants, and potentially disseminate antibiotic resistant pathogens to the environment. However, in order to ensure the accuracy of the results, the limits of epicPCR as a method need to be identified and addressed.
  • Pinto de Magalhães, Joana; Franko, Nina; Raboni, Samanta; Annunziato, Giannamaria; Tammela, Päivi; Bruno, Agostino; Bettati, Stefano; Mozzarelli, Andrea; Pieroni, Marco; Cambanini, Barbara; Costantino, Gabriele (2020)
    In Upsilon-proteobacteria and Actinomycetales, cysteine biosynthetic enzymes are indispensable during persistence and become dispensable during growth or acute infection. The biosynthetic machinery required to convert inorganic sulfur into cysteine is absent in mammals; therefore, it is a suitable drug target. We searched for inhibitors of Salmonella serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of L-cysteine biosynthesis. The virtual screening of three ChemDiv focused libraries containing 91 243 compounds was performed to identify potential SAT inhibitors. Scaffold similarity and the analysis of the overall physicochemical properties allowed the selection of 73 compounds that were purchased and evaluated on the recombinant enzyme. Six compounds displaying an IC50
  • Pyorälä, Satu; Baptiste, Keith Edward; Cary, Boudewijn; van Duijkeren, Engeline; Greko, Christina; Moreno, Miguel A.; Constanca Matias Ferreira Pomba, M.; Rantala, Merja; Ruzauskas, Modestas; Sanders, Pascal; Threlfall, E. John; Torren-Edo, Jordi; Torneke, Karolina (2014)
  • Hassan, Karl A.; Liu, Qi; Elbourne, Liam D.H.; Ahmad, Irshad; Sharples, David; Naidu, Varsha; Chan, Chak Lam; Li, Liping; Harborne, Steven P.D.; Pokhrel, Alaska; Postis, Vincent L.G.; Goldman, Adrian; Henderson, Peter J.F.; Paulsen, Ian T. (2018)
    Abstract The proteobacterial antimicrobial compound efflux (PACE) family of transport proteins was only recently described. PACE family transport proteins can confer resistance to a range of biocides used as disinfectants and antiseptics, and are encoded by many important Gram-negative human pathogens. However, we are only just beginning to appreciate the range of functions and the mechanism(s) of transport operating in these proteins. Genes encoding PACE family proteins are typically conserved in the core genomes of bacterial species rather than on recently acquired mobile genetic elements, suggesting that they confer important core functions in addition to biocide resistance. Three-dimensional structural information is not yet available for PACE family proteins. However, PACE proteins have several very highly conserved amino acid sequence motifs that are likely to be important for substrate transport. PACE proteins also display strong amino acid sequence conservation between their N- and C-terminal halves, suggesting that they evolved by duplication of an ancestral protein comprised of two transmembrane helices. In light of their drug resistance functions in Gram-negative pathogens, PACE proteins should be the subject of detailed future investigation.
  • Lai, Foon Yin; Muziasari, Windi; Virta, Marko; Wiberg, Karin; Ahrens, Lutz (2021)
    Antibiotic resistance in aquatic ecosystems presents an environmental health issue worldwide. Urban recipient water quality is susceptible to effluent discharges with antibiotic resistance contaminants and needs to be protected, particularly for those as sources of drinking water production. Knowledge on aquatic resistome profiles in downstream of wastewater treatment plants allows a better understanding of the extent to which antibiotic resistance contaminants emerge and spread in recipient waters, but such information remains very limited in Sweden. The key objective of this study was to determine the resistome profiles of numerous antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and other genes in urban recipient water systems connected to Sweden's major drinking water reservoir. This was achieved through analysis of surface water samples for 296 genes using high-throughput quantitative PCR arrays. A total of 167 genes were detected in at least one of the samples, including 150 ARGs conferring resistance to 11 classes of antibiotics, 7 integrase MGEs and 9 other genes. There was a spatial difference in the resistome profiles with the greatest average relative abundance of resistance genes observed in the water body of Vasteras followed by Uppsala, Stockholm and Eskilstuna, as similar to the general pattern of the antibiotic sales for these regions. ARGs against beta-lactams and sulfonamides showed the highest average relative abundance in the studied water bodies, while vancomycin resistance genes were only found in the Uppsala water environment. Generally, the recipient water bodies were detected with higher numbers of genes and greater relative abundances as compared to the upstream sites. Anthropogenic pollution, i.e., wastewater discharge, in the recipient water was also reflected by the finding of intI, sul1 and crAssphage. Overall, this study provided the first quantitative assessment of aquatic environmental resistomes in Sweden, highlighting the widespread of antibiotic resistance contaminants in urban recipient waters.
  • Holma, Tanja; Torvikoski, Jukka; Friberg, Nathalie; Nevalainen, Annika; Tarkka, Eveliina; Antikainen, Jenni; Martelin, Jari J. (2022)
    Rapid detection of pathogens causing bloodstream infections (BSI) directly from positive blood cultures is of highest importance in order to enable an adequate and timely antimicrobial therapy. In this study, the utility and performance of a recently launched next-generation fully automated test system, the Biofire FilmArray (R) Blood Culture Identification 2 (BCID2) panel, was evaluated using a set of 103 well-characterized microbial isolates including 29 antimicrobial resistance genes and 80 signal-positive and 23 signal-negative clinical blood culture samples. The results were compared to culture-based reference methods, MALDI-TOF, and/or 16S rDNA sequencing. Of the clinical blood culture samples, 68 were monomicrobial (85.0%) and 12 polymicrobial (15.0%). Six samples contained ESBL (bla(CTX-M)), two MRSA (mecA), and three MRSE (mecA) isolates. In overall, the FilmArray BCID2 panel detected well on-panel targets and resistance markers from mono- and polymicrobial samples. However, one Klebsiella aerogenes and one Bacteroides ovatus were undetected, and the assay falsely reported one Shigella flexneri as Escherichia coli. Hence, the sensitivity and specificity for detecting microbial species were 98.8% (95%CI, 95.8-99.9%) and 99.9% (95%CI, 99.8-99.9%), respectively. The sensitivity and specificity for detecting of resistance gene markers were 100%. The results were available within 70 min from signal-positive blood cultures with minimal hands-on time. In conclusion, the BCID2 test allows reliable and simplified detection of a vast variety of clinically relevant microbes causing BSI and the most common antimicrobial resistance markers present among these isolates.
  • Taponen, Suvi; Nykäsenoja, Suvi; Pohjanvirta, Tarja; Pitkälä, Anna; Pyörälä, Satu (2016)
    Background: Coagulase-negative staphylococci (CoNS) are the most common bovine mastitis causing bacteria in many countries. It is known that resistance for antimicrobials is in general more common in CoNS than in Staphylococcus aureus but little is known about the antimicrobial resistance of specific CoNS species. In this study, 400 CoNS isolates from bovine mastitic milk samples were identified to species level using ribotyping and MALDI-TOF MS, and their antimicrobial susceptibility was determined using a commercially available microdilution system. The results were interpreted according to the epidemiological cut-off values by the European Committee on Antimicrobial Susceptibility testing. Results: The most common CoNS species were S. simulans, S. epidermidis, S. chromogenes and S. haemolyticus. Penicillin resistance was the most common type of antimicrobial resistance. Staphylococcus epidermidis was the most resistant among the four major species. Almost one-third of our S. epidermidis isolates were resistant to >2 antimicrobials and close to 7 % were multidrug resistant. The majority of S. epidermidis isolates were resistant to benzylpenicillin. On the contrary, only few S. simulans isolates were penicillin-resistant. Phenotypic oxacillin resistance was found in all four main species, and 34 % of the isolates were oxacillin resistant. However, only 21 isolates (5 %) were positive for the mecA gene. Of these, 20 were S. epidermidis and one S. sciuri. mecC positive isolates were not found. Conclusion: Staphylococcus epidermidis differed from the three other major CoNS species as resistance to the tested antimicrobials was common, several isolates were multidrug resistant, and 19 % of the isolates carried the mecA gene encoding methicillin resistance.
  • Taponen, Suvi; Nykäsenoja, Suvi; Pohjanvirta, Tarja; Pitkälä, Anna; Pyörälä, Satu (BioMed Central, 2016)
    Background: Coagulase-negative staphylococci (CoNS) are the most common bovine mastitis causing bacteria in many countries. It is known that resistance for antimicrobials is in general more common in CoNS than in Staphylococcus aureus but little is known about the antimicrobial resistance of specific CoNS species. In this study, 400 CoNS isolates from bovine mastitic milk samples were identified to species level using ribotyping and MALDI-TOF MS, and their antimicrobial susceptibility was determined using a commercially available microdilution system. The results were interpreted according to the epidemiological cut-off values by the European Committee on Antimicrobial Susceptibility testing. Results: The most common CoNS species were S. simulans, S. epidermidis, S. chromogenes and S. haemolyticus. Penicillin resistance was the most common type of antimicrobial resistance. Staphylococcus epidermidis was the most resistant among the four major species. Almost one-third of our S. epidermidis isolates were resistant to >2 antimicrobials and close to 7 % were multidrug resistant. The majority of S. epidermidis isolates were resistant to benzylpenicillin. On the contrary, only few S. simulans isolates were penicillin-resistant. Phenotypic oxacillin resistance was found in all four main species, and 34 % of the isolates were oxacillin resistant. However, only 21 isolates (5 %) were positive for the mecA gene. Of these, 20 were S. epidermidis and one S. sciuri. mecC positive isolates were not found. Conclusion: Staphylococcus epidermidis differed from the three other major CoNS species as resistance to the tested antimicrobials was common, several isolates were multidrug resistant, and 19 % of the isolates carried the mecA gene encoding methicillin resistance.
  • Vilkman, Katri; Lääveri, Tinja; Pakkanen, Sari H.; Kantele, Anu (2019)
    Background: As antibiotics predispose travelers to acquiring multidrug-resistant intestinal bacteria, they should no longer be considered a mainstay for treating travelers' diarrhea. It has been claimed that stand-by antibiotics are justified as a means to avoid visits to local healthcare providers which often lead to polypharmacy. Method: We revisited the traveler data of 316 prospectively recruited volunteers with travelers' diarrhea by retrieving from questionnaires and health diaries information on antibiotic use, stand-by antibiotic carriage, and visits with local healthcare. Multivariable analysis was applied to identify factors associated with antibiotic use. Results: Among our 316 volunteers with travelers' diarrhea, however, carrying stand-by antibiotics seemed not to reduce the rate of healthcare-seeking; on the contrary, antibiotic use was more frequent among stand-by antibiotic carriers (34%) than non-carriers (11%). Antibiotics were equally taken for severe and incapacitating travelers' diarrhea, but compared to non-carriers, stand-by antibiotic carriers resorted to medication also for mild/moderate (38% vs. 4%) and non-incapacitating disease (29% vs. 5%). Antibiotic use was associated with stand-by antibiotic carriage (OR 7.2; 95%CI 2.8-18.8), vomiting (OR 3.5; 95%CI 1.3-9.5), incapacitating diarrhea (OR 3.6; 95%CI 1.3-9.8), age (OR 1.03; 95%CI 1.00-1.05), and healthcare visit for diarrhea (OR 465.3; 95%CI 22.5-9633.6). Conclusions: Carriage of stand-by antibiotics encouraged less cautious use of antibiotics. Recommendations involving prescription of antibiotics for all travelers require urgent revision.
  • Päivärinta, M.; Latvio, S.; Fredriksson-Ahomaa, M.; Heikinheimo, A. (2020)
    Plasmid-encoded extended-spectrum β-lactamase and AmpC gene-carrying Escherichia coli (ESBL/AmpC E. coli) is an increasing cause of human infections worldwide. Increasing carbapenem and colistin resistance further complicate treatment of these infections. The aim of this study was to assess the occurrence of ESBL/AmpC E. coli in different broiler flocks and farms, as well as in broiler meat, in a country with no antimicrobial usage in broiler production. An additional goal was to assess the genetic characteristics of ESBL/AmpC E. coli isolates by using whole genome sequencing (WGS). Altogether 520 caecal swabs and 85 vacuum-packed broiler meat samples were investigated at the slaughterhouse level. WGS of the bacterial isolates revealed acquired antimicrobial resistance (AMR) genes, multilocus sequence types (MLST) and plasmid sequences. ESBL/AmpC E. coli was identified in 92 (18%) of the caecum and 27 (32%) of the meat samples. ESBL/AmpC E. coli-carrying birds derived from six (33%) out of 18 farms. Of the two blaESBL/AmpC genes detected by PCR, blaCMY-2 (96%) was predominant over blaCTX-M-1 (4%). Furthermore, WGS revealed an additional AMR gene sul2. Carbapenemase, colistin, and other AMR genes were not detected from the isolates of either the caecal or meat samples. Altogether seven MLSTs (ST101, ST117, ST212, ST351, ST373, ST1594 and an unknown ST) and a variety of different plasmid sequences (IncB/O/K/Z, IncI1, IncFII, IncII, IncFIB, IncFIC, IncX1 and an additional set of Col-plasmids) were detected. This is the first study on genomic epidemiology of ESBL/AmpC E. coli on broiler farms and flocks with no antimicrobial usage, by using WGS analysis. Results show that ESBL/AmpC E. coli occurrence is common both in the caecum and in the packaged meat. However, compared to other European countries, the occurrence is low and the presence of AMR genes other than blaCMY-2 and blaCTX-M-1 is rare. More studies are needed to understand the ESBL/AmpC E. coli occurrence in broiler production to prevent the meat from contamination during slaughter and processing, thereby also preventing zoonotic transmission of ESBL/AmpC E. coli. Additionally, more studies are needed to understand the ecology and fitness cost of Enterobacteriaceae plasmids in animal production in order to prevent their acquisition of plasmid-encoded antimicrobial resistance genes such as carbapenem and colistin resistance genes, as this would pose a great hazard to food safety.