Antimicrobial resistance of zoonotic and commensal bacteria in Europe: the missing link between consumption and resistance in veterinary medicine

Short variable regions flaA gene (SVR-flaA) diversity and virulence profile of multidrug resistant Campylobacter from poultry and poultry meat in India

Human gastrointestinal infections caused by Campylobacter species is the second most important foodborne illness after salmonellosis worldwide. Poultry represent one of the main sources of Campylobacter organisms. In the present study the short variable region of flagellin gene (SVR-flaA) typing was carried out to determine the variation among the circulating strains of Campylobacter jejuni and Campylobacter coli. The C. jejuni and C. coli isolated from poultry and poultry meat were screened for the presence of virulence determinants like cadF, flaA, cdtB, and wlaN gene. The screening for wlaN gene is crucial in view of fact that most patients with Guillian Barre's (GB) syndrome with a preceding history of diarrhoeal illness have been found to harbour wlaN gene positive C jejuni strains. Out of the 200 samples comprising of poultry meat and cloacal swabs, 21.5% of samples were found to harbour Campylobacter spp. of which 2.5% were Campylobacter jejuni, and 19% were confirmed as Campylobacter coli. The cadF, flaA, cdtB virulence genes were detected in all the Campylobacter spp. isolated in the present study. The presence of the wlaN gene in the Campylobacter jejuni isolated in the present study may pose a public health threat with long term human health implications. The SVR-flaA typing of twelve Campylobacter isolates obtained in present study revealed that Campylobacter coli flaA sequence OL471375 is a new strain with a novel allele type 1675 and peptide sequence 5 which stands deposited in pubMLST database for Campylobacter. The other flaA-SVR gene sequences identified in this study were OL471369, OL471370, OL471371, OL471372, OL471373, and OL471374. Among twelve Campylobacter spp. three distinct DdeI-RFLP patterns were observed, each varying in size from 100 to 1000 base pairs. Antimicrobial profiling of the Campylobacter spp. isolated in present study revealed that 50% of the strains were multidrug resistant. All the Campylobacter spp. were resistant to ciprofloxacin (CIP), ampicillin (AMP), penicillin (PEN) and nalidixic acid (NAL) whereas 57.1%, of strains were resistant to tetracycline (TET) and erythromycin (ERY) 28% to amoxicillin (AMX) and enrofloxacin (ENO), 85% to amikacin (AMK). The high degree of resistance to fluoroquinoles observed in present study is crucial in view of fluoroquinolones being drugs of choice for treatment of human Campylobacter infections.

Surveillance of Antimicrobial Resistance of Escherichia coli Isolates from Intestinal Contents of Dairy and Veal Calves in the Veneto Region, Northeaster Italy

This surveillance study aimed to estimate the proportion of antimicrobial resistant strains and antimicrobial resistance (AMR) profiles of E. coli isolates detected from the intestinal contents of veal and dairy calves in the Veneto Region, Northeaster Italy. Additionally, we investigated the differences in AMR profiles between dairy and veal calves over the period 2017-2022. Overall 1150 E. coli isolates were tested from calves exhibiting enteric disease, with 868 from dairy and 282 from veal calves. The percentage of resistant isolates to nine antimicrobials was notably higher in veal calves compared to dairy calves, except for ampicillin. Throughout the study period, we observed a significant increase in the proportion of resistant isolates to florfenicol, gentamycin, paromomycin, tetracycline and trimethoprim/sulfamethoxazole in dairy calves, while we did not detect any significant increase in the proportion of resistant isolates among veal calves. A substantial proportion (75.9%) of the isolated E. coli exhibited multi-drug resistance (MDR). The proportion of multi-drug resistant isolates was significantly higher in veal calves (91.7%) compared to dairy calves (74.3%) all through the surveillance period (2017-2022), with no significant variation in MDR proportion among veal calves between 2017 and 2022 but a significant increase among dairy calves.

Porcine carcasses as an underestimated source of antimicrobial resistant Campylobacter coli

Introduction

Campylobacteriosis is the most common human foodborne bacterial infection worldwide and is caused by bacteria of the Camplylobacter genus. The main source of these bacteria is poultry, but other food-producing animals such as pigs are also responsible for human infections. An increasing number of strains with resistance to fluoroquinolones and other antimicrobials such as macrolides were recently noted. The aim of the study was to investigate Campylobacter contamination of porcine carcasses and determine the antimicrobial resistance of the obtained isolates.

Material and Methods

A total of 534 swabs from carcasses of pigs slaughtered in Poland during 2019-2022 were tested for Campylobacter spp.

Results

Campylobacter was detected in 164 (30.7%) carcasses; among them 149 (90.8%) were classified as C. coli and the remaining 15 (9.2%) samples were C. jejuni-positive. Because a low number of C. jejuni isolates were identified, only the C. coli isolates were subjected to antimicrobial resistance analysis. The majority of these isolates were resistant to streptomycin (94.0%), ciprofloxacin (65.8%) and tetracycline (65.1%). A total of 94 (63.1%) strains displayed antimicrobial multiresistance patterns and were mainly resistant to fluoroquinolones, aminoglycosides and tetracyclines (74; 49.7% of the isolates tested).

Conclusion

The obtained results showed that pig carcasses may be contaminated with antimicrobial-resistant C. coli.

An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

Effects of bovine respiratory disease on the plasma metabolome of beef steers during the receiving period

The study aimed to investigate the impact of Bovine Respiratory Disease (BRD) on the metabolism of beef steers during a 35-d receiving period using plasma metabolomics. In this study, 77 newly weaned crossbred (Angus × Hereford) beef steers (BW = 206 ± 12 kg and age = 180 ± 17 days) were categorized into two groups: Healthy and Sick groups. The Sick group comprised beef steers diagnosed with BRD at any time during the 35-day period (n = 31), while the Healthy group did not show any signs of BRD (n = 46). Blood samples were collected from the coccygeal vessels on day 35, and plasma samples were subjected to targeted metabolomics analysis using Nuclear Magnetic Resonance spectroscopy. Data and statistical analyses, including biomarker and pathway enrichment analyses, were performed using Metaboanalyst 5.0. Results of the growth performance showed that sick steers had lower (p ≤ 0.05) ADG (1.44 vs. 1.64 kg/d) and higher (p = 0.01) feed:gain ratio (3.57 vs. 3.13) compared to healthy steers. A total of 50 metabolites were quantified. The partial least squares discriminant scores plot showed a slight separation between the two groups of steers, indicating some metabolic differences. Furthermore, the plasma concentrations of four metabolites (sarcosine, methionine, dimethyl sulfone, and L-histidine) were greater (p ≤ 0.05) in healthy steers compared to sick steers. Among these metabolites, sarcosine and methionine qualified as candidate biomarkers associated with BRD infection based on an area under the curve >0.70. Additionally, quantitative enrichment analysis revealed that cysteine and methionine metabolism was enriched in healthy steers compared to sick steers. This suggests that these metabolic pathways may play a role in the response to BRD infection. The findings of this study highlight the altered plasma metabolome in steers with BRD during the receiving period. Understanding these metabolic changes can contribute to the development of effective management strategies and nutritional interventions to mitigate the negative impact of BRD on beef cattle health and immune function.

Antimicrobial resistance and its relationship with antimicrobial use on Austrian dairy farms

The aim of this study was to investigate the prevalence of ESBL/AmpC-producing E. coli and the resistance pattern of commensal E. coli, as well as the link between the use of antibiotics (AMU) and the occurrence of resistance in E. coli on Austrian dairy farms. AMU data from 51 farms were collected over a one-year period in 2020. Fecal samples were collected from cows, pre-weaned and weaned calves in 2020 and 2022. Samples were then analyzed using non-selective and selective agar plates, E. coli isolates were confirmed by MALDI-TOF analysis. Broth microdilution was used for antimicrobial susceptibility testing. The AMU of each farm was quantified as the number of Defined Daily Doses (nDDDvet) and Defined Course Doses (nDCDvet) per cow and year. Cephalosporins (mean 1.049; median 0.732 DDDvet/cow/year) and penicillins (mean 0.667; median 0.383 DDDvet/cow/year) were the most frequently used antibiotics on these farms, followed by tetracyclines (mean 0.275; median 0.084 DDDvet/cow/year). In 2020, 26.8% of the E. coli isolated were resistant to at least one antibiotic class and 17.7% of the isolates were classified as multidrug resistant (≥3 antibiotic classes). Out of 198 E. coli isolates, 7.6% were identified as extended-spectrum/AmpC beta-lactamase (ESBL/AmpC) producing E. coli. In 2022, 33.7% of E. coli isolates showed resistance to at least one antibiotic and 20.0% of isolates displayed multidrug resistance. Furthermore, 29.5% of the samples carried ESBL/AmpC-producing E. coli. In 2020 and 2022, the most frequently determined antibiotic resistances among commensal E. coli isolates were to tetracyclines, sulfonamides and penicillins. In addition, pre-weaned calves had the highest resistance rates in both years. Statistical analyses showed a significant association between low and high use AMU classifications for penicillins (in nDDDvet/cow/year) and their respective resistance among commensal E. coli isolates in 2020 (p = 0.044), as well as for sulfonamide/trimethoprim (p = 0.010) and tetracyclines (p = 0.042). A trend was also noted between the total amount of antibiotics used on farm in 2020 (by nDDDvet/cow/year) and multidrug resistances in commensal E. coli isolated on farm that year (p = 0.067). In conclusion, the relationship between AMU and antimicrobial resistance (AMR) on dairy farms continues to be complex and difficult to quantify.

Quarter-wise proportion and beta-lactam resistance rate of bovine mastitis associated- Staphylococcus aureus among infectious episodes in Ethiopia: Systematic review and meta-Analysis

Background

Bovine mastitis, a condition with multifactorial etiology, imposes a significant economic burden on the dairy sector in Ethiopia, with Staphylococcus aureus (S. aureus) being one of the leading etiologic agents. The acquisition of a compiled source of information concerning S. aureus is imperative in order to enhance the control and prevention strategies, as well as to facilitate the successful implementation of the national action plan aimed at curbing antimicrobial resistance by the year 2025. Thus, the primary objective of this meta-analysis was to comprehensively summarize the estimates of the proportion and beta-lactam resistance profile of S. aureus in bovine mastitis in Ethiopia.

Methods

electronic bibliographic data such as PubMed, Web of Science, HINARI, Google Scholar, and other databases were used to search articles and quality assessment was performed using the AMSTAR-2. The pooled proportion, the rate of beta-lactam resistance, and a 95% confidence interval were calculated with a random effects model using STATA 17 statistical software. Funnel plots, and Eggers were used to assess publication bias.

Results

Twenty-six (26) cross-sectional studies were included in this meta-analysis. The overall pooled proportion of S.aureus was 35% (95% CI: 0.31 to 0.41). Considerable heterogeneity was observed in the included studies (I² = 90.75%; P < 0.01). The subgroup analysis of the study region showed significant differences. The highest estimated regional pooled proportion of bovine mastitis-associated S.aureus was 40% in the Amhara and Tigray regions. Funnel plot and Eggers results showed no statistically significant publication bias (Eggers test: p = 0.5656) in estimating the proportion of S.aureus infections in association with bovine mastitis. A total of 14 articles were included to estimate beta-lactam antimicrobial resistance. The estimated pooled beta-lactam antimicrobial resistance rate of S.aureus was resistance to penicillin at 75%, followed by amoxicillin at 67%, ampicillin at 50% and cephalosporin at 57% were evaluated in the treatment of S. aureus. Therefore, the present meta-analysis has revealed that the prevalence of bovine-associated Staphylococcus aureus and its resistance to beta-lactam antibiotics are alarmingly high in the region of Ethiopia. This further emphasizes the vital necessity of implementing effective preventive measures to reduce the incidence and spread of this pathogen across the entire nation.

Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur

Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg^-1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg^-1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and bla_TEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.

Luteolin Attenuates APEC-Induced Oxidative Stress and Inflammation via Inhibiting the HMGB1/TLR4/NF-κB Signal Axis in the Ileum of Chicks

Avian pathogenic E. coli (APEC) is typically the cause of avian colibacillosis, which can result in oxidative stress, inflammation, and intestinal damage (APEC). Luteolin, in the form of glycosylation flavone, has potent anti-inflammatory and anti-oxidative properties. However, its effects on APEC-induced intestinal oxidative stress and NF-κB-mediated inflammation in chicks remains poorly understood. After hatching, one-day-old chicks were stochastically assigned to four groups: a control group (basic diet), an E. coli group (basic diet) and L10 and L20 groups (with a dry matter of luteolin diet 10 mg/kg and 20 mg/kg, respectively), with fifteen chicks in each group and one repeat per group. They were pretreated for thirteen days. The body weight, mortality, histopathological changes in the ileum, antioxidant status, and the mRNA and protein-expression levels of factors associated with the HMGB1/TLR4/NF-κB signal axis of the chicks were measured. The results showed that luteolin treatment decreased the mRNA and protein-expression level of the related factors of HMGB1/TLR4/NF-κB signal axis in the ileum, reduced inflammation, increased antioxidant enzyme activity, and reduced intestinal injury. Collectively, luteolin alleviated APEC-induced intestinal damage by means of hindering the HMGB1/TLR4/NF-κB signal axis, which suggests that luteolin could be a good method for the prevention and treatment of avian colibacillosis.

Phytogenics and encapsulated sodium butyrate can replace antibiotics as growth promoters for lightly weaned piglets

The objective of this study was to evaluate the effect of essential oils plus dry herbs (PHYTO) and encapsulated sodium butyrate (BUT) supplementation compared with enramycin (ENR), as a growth promoter, on the performance, diarrhoea control and intestinal microbiota in lightly weaned piglets. Two hundred weaned piglets, 20 days old, 4.69 ± 0.56 kg, were submitted during the nursery phase (20 to 69 days of age) to four treatments: control (CTR)-without any additive supplementation; ENR (with 8 ppm of enramycin throughout), BUT (with 2000 ppm between 20 to 34 d, 1500 ppm between 34 to 48 d and 1000 ppm between 48 to 69 d), and PHYTO (150 ppm between 20 to 48 d). At 62 days old, forty piglets (10 replicates per treatment) were slaughtered to perform bacterial identification through 16S rRNA (V3-V4) sequencing of the caecal content. During the second phase of the trial (34 to 48 days), the BUT group showed higher DWG (P = 0.023) and BW (P = 0.039) than the CTR group, and all groups that received additives had better FCR than the CTR group (P = 0.001). In the last phase of the trial (48 to 69 days), the ENR group presented a better FCR (P = 0.054) than the CRT and other groups. In the total period (20 to 69 days), ENR and BUT showed better FCR (P = 0.006) than CRT. Diarrhoea incident data showed differences (P<0.05), favouring the BUT treatment compared to the CTR. Only the Megasphaeraceae and Streptococcaceae families showed differences (p<0.05) in relative abundance between CTR and PHYTO and between CTR and BUT, respectively. Differential abundances of the Megasphaera and Streptococcus genera were observed between CTR and PHYTO and CTR and BUT. Phytogenics and encapsulated sodium butyrate are able and effective for modulating the specific caecal microbiota, improving performance and controlling diarrhoea occurrence.

Analysis of Extended Spectrum Beta Lactamase (ESBL) Genes of Non-Invasive ESBL Enterobacterales in Southeast Austria in 2017

Extended spectrum beta lactamases producing Enterobacteriaceae are a major player in the antibiotic resistance challenge. In general, the situation regarding antibiotic resistance in Austria is very good compared to many other countries. Perhaps this is why there is a lack of data on the distribution of ESBL genes in the clinical setting. The aim of this study was to collect data on ESBL genes from a larger sample of human non-invasive clinical isolates from one region in Austria. In total, 468 isolates from different sample materials isolated at the Medical University of Graz from 2017 were examined. The most frequent organisms were Escherichia coli and Klebsiella pneumoniae. Among the enzymes produced, CTX-M-15 was clearly dominant, exotic ESBLs were only represented by three Proteus mirabilis isolates harboring genes for VEB-6 and one P. mirabilis for CTX-M-2, respectively. Compared to other countries, the results are in line with the expectations. The data help to better classify the many studies from the non-clinical field in Austria and to shift the focus slightly away from the exotic results and sample sites.

Effect of Qiling Jiaogulan Powder on Pulmonary Fibrosis and Pulmonary Arteriole Remodeling in Low-Temperature-Exposed Broilers

Chinese herbal medicine plays an important role in regulating the nutritional metabolism of poultry and maintaining or improving normal physiological functions and animal health. The present study investigated the effects of dietary supplementation with Qiling Jiaogulan Powder (QLJP) on pulmonary fibrosis and pulmonary arteriole remodeling in low temperature-exposed broilers. Seven-day-old Ross 308 broilers (n = 240) were reared adaptively to 14 days of age. The broilers were randomly divided into six groups: A control group (basal diet and normal feeding temperature); model group (basal diet); low-, medium- and high-dose QLJP groups (basal diet supplemented with 1 g/kg, 2 g/kg, 4 g/kg QLJP); and L-Arg group (basal diet supplemented with 10 g/kg L-arginine). Additionally, all the broilers, except the broilers in the control group, from the age of 14 days old, had a house temperature continuously lowered by 2 °C each day until it reached 12 °C at 21 days of age, and the low temperature was maintained until the end of the experiment. There were four replicates per group and 10 birds per replicate. The results showed that the structure of the lung tissue was clearer and basically intact in the broilers in the QLJP groups, with a small number of collagen fibers formed, and the content of hydroxyproline (HYP) was significantly reduced. QLJP improved pulmonary arteriole lesions, such as tunica media thickening, intimal hyperplasia, arterial wall hypertrophy, and lumen narrowing. QLJP reduced the relative media thickness (%) and relative medial area (%) of the pulmonary arteriole, and significantly decreased the expression level of the alpha-smooth muscle actin (α-SMA) protein in pulmonary arteriole, which alleviated pulmonary arteriole remodeling. The quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA) results showed that QLJP treatment significantly reduced the gene and protein levels of transforming growth factor-beta l (TGF-β1) and Smad2 in the lung and downregulated the gene and protein levels of collagen type I alpha 1 (COL1A1) and matrix metalloproteinase 2 (MMP2). In conclusion, the results of our study suggested that dietary supplementation with QLJP improved pulmonary fibrosis and pulmonary arteriole remodeling by inhibiting the expression of genes related to the TGF-β1/Smad2 signaling pathway and inhibited the occurrence and development of pulmonary arterial hypertension in low-temperature-exposed broilers.

Evaluation of Garlic Juice Processing Waste Supplementation in Juvenile Black Rockfish (Sebastes schlegelii) Diets on Growth Performance, Antioxidant and Digestive Enzyme Activity, Growth- and Antioxidant-Related Gene Expression, and Disease Resistance against Streptococcus iniae

An 8-week feeding trial was conducted to evaluate the effects of various dietary levels of garlic juice processing waste (GJPW) on the growth, feed utilization, digestive and antioxidant enzyme activity, growth- and antioxidant-related gene expression, and resistance to Streptococcus iniae infection of juvenile black rockfish (Sebastes schlegelii). A total of 450 juvenile rockfish were randomly distributed into 30 L rectangular tanks (30 fish per tank). Five experimental diets were prepared in triplicate. The fish were fed experimental diets supplemented with GJPW at concentrations of 0 (GJPW0, control), 2.5 (GJPW2.5), 5 (GJPW5), 7.5 (GJPW7.5), and 10 g kg^-1 (GJPW10) diet. All of the GJPW-supplemented treatments (2.5, 5, 7.5, and 10 g kg^-1) significantly enhanced weight gain (WG), specific growth rate (SGR), feed efficiency (FE), protein efficiency ratio (PER), and digestive enzyme activity (amylase, trypsin, and lipase). A decreasing trend was seen in plasma aspartate aminotransferase (ALT), alanine aminotransferase (AST), and glucose (GLU) content with increasing dietary levels of GJPW. In contrast, plasma lysozyme and antioxidant enzyme activities were significantly increased with increasing dietary GJPW levels. Furthermore, GJPW administration significantly upregulated the expression of insulin-like growth factor-1 (IGF-1), superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST) in the liver of rockfish. A challenge test with S. iniae showed significantly higher resistance in the GJPW-supplemented treatments than in the control. In short, dietary supplementation GJPW enhanced growth performance and antioxidant response in juvenile black rockfish, with suitable effects in fish fed with 2.5 g kg^-1 GJPW for 8 weeks.

European-wide antimicrobial resistance monitoring in commensal Escherichia coli isolated from healthy food animals between 2004 and 2018

OBJECTIVES

To describe the susceptibility of Escherichia coli to medically important antibiotics, collected over four periods (2004-2006, 2008-2009, 2013-2014, 2017-2018), from food-producing animals at slaughter.

METHODS

Intestinal contents from cattle, pigs and broilers were randomly sampled (5-6 countries/host; ≥4 abattoirs/country; one sample/animal/farm) for isolation of Escherichia coli; antimicrobial susceptibilities were centrally determined by CLSI agar dilution. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation.

RESULTS

In total, 10 613 E. coli strains were recovered. In broilers, resistance percentages were the lowest (P ≤ 0.01) in the latest time period. A significant decrease in MDR over time was also observed for broilers and a tendency for a decrease for pigs. Resistance to meropenem and tigecycline was absent, and resistance to azithromycin was 0.2%-2.0%. Also, low resistance to third-generation cephalosporins (1.1%-7.4%) was detected in broilers. Resistance to colistin varied between 0.1%-4.8%. E. coli from broilers showed high resistance to ciprofloxacin (7.3%-23.3%), whereas for cattle and pigs this was 0.2%-2.5%. Low/moderate resistance to chloramphenicol (9.3%-21.3%) and gentamicin (0.9%-7.0%) was observed in pigs and broilers. The highest resistance was noted for ampicillin (32.7%-65.3%), tetracycline (41.3%-67.5%), trimethoprim (32.0%-35.7%) and trimethoprim/sulfamethoxazole (27.5%-49.7%) from pigs and broilers, with marked country differences. MDR peaked in pigs and broilers with 24 and 26 phenotypes, with 21.9%-26.2% and 18.7%-34.1% resistance, respectively.

CONCLUSIONS

In this pan-EU survey antibiotic susceptibility of commensal E. coli varied largely between antibiotics, animal species and countries. Resistance to critically important antibiotics for human medicine was absent or low, except for ciprofloxacin in broilers and ampicillin in pigs and broilers.

The prevalence of bovine mastitis-associated Staphylococcus aureus in China and its antimicrobial resistance rate: A meta-analysis

In this study, to optimize the Staphylococcus aureus control program, a meta-analysis was conducted to investigate the epidemiology and antimicrobial resistance (AMR) profile of S. aureus-associated bovine mastitis in China from 2000 to 2020. A total of 33 publications from PubMed, Google Scholar, and China National Knowledge Infrastructure (CNKI) database were included in our research, among which nine publications included the AMR test. The pooled prevalence of S. aureus was 36.23%, and subgroup analysis revealed that the prevalence dropped from 2000-2010 to 2011-2020, which shows that China is on the right track. The pooled AMR rate indicate isolates were most resistant to β-lactams (50.68%), followed by quinolones (36.23%), macrolides (34.08%), sulfonamides (32.25%), tetracyclines (27.83%), aminoglycosides (26.44%), lincosamides (23.39%), and amphenicol (10.33%). Both the pooled prevalence and AMR of S. aureus in China are higher than those in Western countries, such as Germany, Belgium, Ireland, and the United States-countries with a long animal husbandry history and good management. Thus, there is still room to improve the treatment of S. aureus-associated bovine mastitis in China.

Antimicrobial Resistance and Its Drivers-A Review

Antimicrobial resistance (AMR) is a critical issue in health care in terms of mortality, quality of services, and financial damage. In the battle against AMR, it is crucial to recognize the impacts of all four domains, namely, mankind, livestock, agriculture, and the ecosystem. Many sociocultural and financial practices that are widespread in the world have made resistance management extremely complicated. Several pathways, including hospital effluent, agricultural waste, and wastewater treatment facilities, have been identified as potential routes for the spread of resistant bacteria and their resistance genes in soil and surrounding ecosystems. The overuse of uncontrolled antibiotics and improper treatment and recycled wastewater are among the contributors to AMR. Health-care organizations have begun to address AMR, although they are currently in the early stages. In this review, we provide a brief overview of AMR development processes, the worldwide burden and drivers of AMR, current knowledge gaps, monitoring methodologies, and global mitigation measures in the development and spread of AMR in the environment.

Prevalence, molecular characterization, and antimicrobial resistance profile of Clostridium perfringens from India: A scoping review

Clostridium perfringens is one of the most important foodborne pathogens that causes histotoxic diseases and intestinal infections in both humans and animals. The present scoping review has been designed to analyze the literature published during 2000-2021 from India on the prevalence, molecular characterization, and antimicrobial resistance profile of C. perfringens isolates recovered from humans, animals, animal-based foods, and associated environmental samples. The peer-reviewed articles retrieved from four electronic databases (Google Scholar, PubMed, Science Direct, and Web of Science) were assessed using PRISMA-ScR guidelines. A total of 32 studies from India were selected on the basis of their relevance and inclusion criteria. The overall prevalence of C. perfringens among domestic animals having history of clinical symptoms and among healthy animals was found to be 65.8% (508/772) and 42.8% (493/1152), respectively. The pathogen was also detected in clinically affected wild animals (75%), healthy wild animals (35.4%), and captive birds (24.5%). The detection of C. perfringens among poultry having necrotic enteritis and among healthy birds was found to be 66.8% (321/480) and 25.6% (80/312), respectively. The detection of pathogen among animal-based foods (i.e., meat, milk, and fish and their products) and environmental samples depicted a prevalence of 20.8% (325/1562) and 30.2% (23/76), respectively. However, the prevalence of C. perfringens among humans having history of diarrhea and among healthy humans was found to be 25% (70/280) and 23.2% (36/155), respectively. The genotyping of C. perfringens isolates revealed that toxin type A was found to be the most prevalent genotype. Along with the alpha toxin gene (cpa), beta (cpb), epsilon (etx), iota (itx), enterotoxin (cpe), beta-2 toxin (cpb2), and NetB (netB) toxins were also detected in different combinations. Antimicrobial resistance profile of C. perfringens isolates recovered from different sources demonstrated that the highest resistance was detected against sulphonamides (76.8%) and tetracycline (41.3%) by phenotypic and genotypic detection methods, respectively. Comprehensive scientific studies covering different geographical areas at the human-animal-environment interface are crucial to generalize the real magnitude of C. perfringens-associated problem in India and for establishing a reliable database.

A Survey on the Rationale Usage of Antimicrobial Agents in Small Animal Clinics and Farms in Trinidad and Jamaica

The extensive and indiscriminate use of antibiotics is known to contribute to antimicrobial resistance. Unfortunately, there are no public records of antimicrobial use (frequency or dosage) administered to animals in two major CARICOM (Caribbean Community) countries: Trinidad and Tobago, and Jamaica. Surveillance would promote amendments and discussion on a Caribbean antimicrobial-use protocol. In this study, an online survey was conducted using cross-sectional qualitative interviews via email, targeting veterinary clinicians working in clinics and farms in Trinidad and Jamaica, to identify how antimicrobials are used in the two countries. Out of the thirty-two (32) clinicians interviewed in Trinidad, 22 (68.75%) were small animal practitioners, and 10 (45.45%) were mixed practitioners. While in Jamaica, a total of Twenty six (26) clinicians responded, of which 17 of them (65.38%) were small animal practitioners and nine (34.62%) were mixed practitioners. A total of 95.2% of clinics and farms in Jamaica and 87.1% in Trinidad did not use standard antimicrobial protocols, which could be due to the limited availability of resources. The broad-spectrum antibiotic, amoxicillin, and amoxicillin/clavulanic acid were the most commonly used drugs in small animal practices in both countries (71.9% and 53.8% in dogs), (78.1% and 65.9% in cats); amoxicillin is also used frequently in mixed animal practice in Jamaica (44.4% in goats, 33.3% in cattle and 22.2% in sheep and pigs), while procaine penicillin and streptomycin was the most frequently used in mixed practice in Trinidad (60% in cattle and goats, 50% in sheep), which could explain the potentially increased risk of antimicrobial resistance.

Chicken Skin Decontamination of Thermotolerant Campylobacter spp. and Hygiene Indicator Escherichia coli Assessed by Viability Real-Time PCR

Thermotolerant Campylobacter spp. are fecal contaminants of chicken meat with serious implications for human health. E. coli is considered as hygiene indicator since, in contrast to Campylobacter. spp., the bacterium is generally present in the avian gut. Stress exposure may transiently cease bacterial division. Therefore, colony forming units (CFU) may underestimate the infection risk of pathogens. We developed a viability real-time PCR (v-qPCR) for the quantification of viable E. coli targeting the uidA gene, encoding β-glucuronidase, which is usually detected for phenotypic species identification. The short- and long-term effects of decontaminating chicken skin on the survival of both C. jejuni and an ESBL-producing E. coli were evaluated by CFU and v-qPCR. The results showed that freezing and storage in cool conditions are potentially underestimated by CFU but not by v-qPCR. The effect of treatment with peroxyacetic acid on survival was consistently detected by CFU and v-qPCR. v-qPCR analysis detected bacterial survival upon the application of lactic acid, which awaits further analysis. Interestingly, both bacteria showed similar kinetics of inactivation upon the application of reduction strategies, suggesting that E. coli might be a complementary hygiene indicator. We conclude that v-qPCR can improve food safety under the consideration of some limitations.

Campylobacter spp. in Eggs and Laying Hens in the North-East of Tunisia: High Prevalence and Multidrug-Resistance Phenotypes

Despite the importance of eggs in the human diet, and unlike other products, for which food safety risks are widely investigated, information on the occurrence of Campylobacter and antimicrobial resistance in eggs and layer hen flocks is lacking in Tunisia. This study was conducted to determine the occurrence of Campylobacter and the antimicrobial resistance in layer hens and on eggshells. Thus, 366 cloacal swabs and 86 eggshell smear samples were collected from five layer hen farms in the North-East of Tunisia. The occurrence of Campylobacter infection, and the antimicrobial resistance rates and patterns, were analyzed. The occurrence rates of Campylobacter infection in laying hens and eggshells were 42.3% and 25.6%, respectively, with a predominance of C. jejuni (68.4%, 81.9%), followed by C. coli (31.6%, 18.2%). The antimicrobial susceptibility testing revealed high resistance rates against macrolides, tetracycline, quinolones, β-lactams, and chloramphenicol, with percentages ranging from 35.5% to 100%. All isolates were multidrug resistant (MDR) and five resistance patterns were observed. These results emphasized the risk to consumer health and the need to establish a surveillance strategy to control and prevent the emergence and the spread of resistant strains of Campylobacter in poultry and humans.

Assessing antimicrobial resistance occurrence in the Portuguese food system: Poultry, pigs and derived food, 2014-2018

Antimicrobial resistance (AMR) spread in the food system is a major threat to public and animal health. We describe AMR trends in zoonotic bacteria and identify risk factors associated with AMR occurrence in animals and derived food in Portugal. Data from the Portuguese AMR surveillance programme on food-producing animals, 2014-2018, were used. AMR frequencies were calculated for Escherichia coli, Campylobacter and Salmonella in broilers, turkeys, pig populations and their derived food products. AMR-associated factors were studied for Salmonella isolates: population, sampling stage (farm, slaughterhouse and processing plant), sample type (environmental, carcase and food), sampler (HACCP, industry, official and official and industry), sample context (control and eradication programmes and monitoring), year (2014-2018) and season. Logistic regression was applied to estimate crude odds ratio and adjusted odds ratio (aOR) with 95% confidence intervals (95% CI). The final models were obtained using a backward stepwise method. This study included 2,157 Escherichia coli, 561 Campylobacter and 1,071 Salmonella isolates. The highest prevalence estimates amongst tested antimicrobials for each bacterial species in 2014-2018 had the following ranges: (i) (fluoro)quinolones: E. coli: 84%-93%, Campylobacter: 94%-98%; (ii) tetracyclines: E. coli: 68%-91%, Campylobacter: 87%-91%, Salmonella: 72%; (iii) penicillins: E. coli: 82%-100%; (iv) sulphonamides: E. coli: 68%-82%. Compared with the reference categories for host (broiler), year (2014), season (winter) and sampler (HACCP own checks), resistance to at least one antimicrobial in Salmonella was significantly less likely in laying hens (aOR 0.28; 95% CI: 0.18-0.42), 2016 (aOR 0.56; 95% CI: 0.33-0.93), 2017 (aOR 0.29; 95% CI: 0.17-0.51) and 2018 (aOR 0.35; 95% CI: 0.20-0.61), autumn (aOR 0.63; 95% CI: 0.40-0.97) and more likely to occur in broiler products (aOR 5.14; 95% CI: 2.61-10.54), pork products (aOR 6.84; 95% CI: 3.74-12.98) and official and industry combined sampling (aOR 2.16; 95% CI: 1.06-4.47). This study reveals a high prevalence of Salmonella resistance, especially during the summer and in post-farm stages of the Portuguese food system to nearly all antimicrobials and in the summer in farms to (fluoro)quinolones. Measures to tackle resistance are required.

Systematic Review of the Pharmacological Evidence for the Selection of Antimicrobials in Bacterial Infections of the Central Nervous System in Dogs and Cats

Bacterial meningitis in dogs and cats is a rare disease associated with a high lethality rate. The spectrum of causative bacteria includes a diverse set of gram positive, gram negative and anaerobic species. Currently, no veterinary medicinal product is approved for this indication in these species in Europe. The objective of this review was to collect the available pharmacokinetic data for antibiotics approved in dogs and cats to enable a preliminary analysis of their potential effectiveness for the treatment of bacterial meningitis. This analysis yielded data for 13 different antibiotics in dogs and two in cats. Additionally, data about frequently recommended cephalosporines not approved in dogs and cats were included. The collected data was used to assess the potential of the respective antibiotics to attain certain simple pharmacokinetic-pharmacodynamic (PK-PD) indexes in the cerebrospinal fluid (CSF). A more sophisticated investigation using modern methods was not possible due to the limited data available. For this purpose, data about the sensitivity of four bacterial species commonly associated with meningitis in dogs and cats to these antibiotics were included. The analysis provided evidence for the potential effectiveness of ampicillin, doxycycline, enrofloxacin, ceftriaxone and cefoxitin against bacteria frequently detected in bacterial meningitis in dogs. Data were not available or insufficient for the assessment of several antibiotics, including frequently recommended substances like metronidazole and trimethoprim-sulphonamide. Little evidence is available for the use of antibiotics in cats afflicted with this disease, highlighting the need for further research to obtain data for evidence based therapeutic recommendations.

Cefotax-magnetic nanoparticles as an alternative approach to control Methicillin-Resistant Staphylococcus aureus (MRSA) from different sources

This study aimed to evaluate the efficacy of magnetic nanocomposite of cefotax against MRSA. A total of 190 samples were collected from milk, farm personnel and different environmental components from the dairy farm under the study to isolate S. aureus. Cefotax based magnetic nanoparticles was synthetized by the adsorption method and marked using Fourier-transform infrared spectrum (FT-IR), and X-ray diffraction (XRD), then it was characterized using Scanning and Transmission Electron Microscope (SEM and TEM). The obtained results revealed that number of positive samples of S. aureus isolation were 63 (33.1%), mainly from feed manger followed by milk machine swabs (60.0 and 53.3%, respectively) at X2 = 48.83 and P < 0.001. Obtained isolates were identified biochemically and by using molecular assays (PCR), also mec A gene responsible for resistance to cefotax was detected. Testing the sensitivity of 63 isolates of S. aureus showed variable degree of resistance to different tested antibiotics and significant sensitivity to cefotax based magnetic nanoparticles at P < 0.05. It was concluded that dairy environment might act a potential source for transmission of MRSA between human and animal populations. In addition, cefotax based magnetic nanoparticles verified an extreme antimicrobial efficacy against MRSA.

Antimicrobial resistance in the globalized food chain: a One Health perspective applied to the poultry industry

Antimicrobial resistance (AMR) remains a major global public health crisis. The food animal industry will face escalating challenges to increase productivity while minimizing AMR, since the global demand for animal protein has been continuously increasing and food animals play a key role in the global food supply, particularly broiler chickens. As chicken products are sources of low-cost, high-quality protein, poultry production is an important economic driver for livelihood and survival in developed and developing regions. The globalization of the food supply, markedly in the poultry industry, is aligned to the globalization of the whole modern society, with an unprecedented exchange of goods and services, and transit of human populations among regions and countries. Considering the increasing threat posed by AMR, human civilization is faced with a complex, multifaceted problem compromising its future. Actions to mitigate antimicrobial resistance are needed in all sectors of the society at the human, animal, and environmental levels. This review discusses the problems associated with antimicrobial resistance in the globalized food chain, using the poultry sector as a model. We cover critical aspects of the emergence and dissemination of antimicrobial resistance in the poultry industry and their implications to public health in a global perspective. Finally, we provide current insights using the multidisciplinary One Health approach to mitigate AMR at the human-animal-environment interface.

Antimicrobial Use and Susceptibility of Indicator Escherichia coli in Finnish Integrated Pork Production

In pigs, antimicrobial use (AMU) practices vary at different production phases between herds and between countries. Antimicrobial resistance (AMR) development is linked to AMU but recognized as a multi-factorial issue, and thus, any information increasing knowledge of AMU and AMR relationships is valuable. We described AMU and screened the carriage of different AMR phenotypes of indicator Escherichia coli in 25 selected Finnish piglet-producing and finishing herds that formed nine birth-to-slaughter production lines. Moreover, we studied associations between AMU and AMR in both herd types and throughout the production line. Treatment records were obtained from the national Sikava register for 1year, and AMU was quantified as mg/PCU (population correction unit) and TIs (treatment incidences). For phenotypic antimicrobial susceptibility testing, ten pen-level pooled feces samples (n=250) in each herd were collected from one room representing the oldest weaned piglets or the oldest finishing pigs. Majority of the medications (96.8%) was administered parenterally, and penicillin was the predominant antimicrobial in every herd. More different antimicrobial substances were used in piglet-producing than in finishing herds (median 5 and 1, respectively, p<0.001). As mg/PCU, sows had the highest AMU and suckling piglets had the highest TIs, whereas finishing pigs were the least treated age group. The proportion of susceptible indicator E. coli isolates of all studied isolates was 59.6%. Resistance was found most commonly against tetracycline, sulfamethoxazole, trimethoprim, and ampicillin, and multi-resistant (MR) isolates (46.5% of all resistant isolates) were resistant to a maximum of four different antimicrobials. Quinolone resistance was rare, and no resistance against 3rd-generation cephalosporins, meropenem, azithromycin, colistin, gentamicin, or tigecycline was detected. The main associations between AMU and AMR were found at antimicrobial group level when use was compared with the presence of AMR phenotypes. The proportion of resistant isolates was not associated with AMU, and herd size was not associated with either AMU or AMR. We suggest that the use of narrow-spectrum beta-lactams as a primary treatment option and lack of wide application of oral group medications potentially favors a good resistance pattern in integrated pork production.

Prevalence and Characterization of ESBL/AmpC Producing Escherichia coli from Fresh Meat in Portugal

The present study aimed to characterize the extended-spectrum β-lactamases and plasmid-mediated AmpC β-lactamases (ESBL/PMAβ) among Escherichia coli producers isolated from beef, pork, and poultry meat collected at retail, in Portugal. A total of 638 meat samples were collected and inoculated on selective medium for the search of E. coli resistant to 3rd generation cephalosporins. Isolates were characterized by antimicrobial susceptibility testing, molecular assays targeting ESBL/AmpC, plasmid-mediated quinolone resistance (PMQR), and plasmid-mediated colistin resistance (PMCR) encoding genes. The highest frequency of E. coli non-wild type to 3rd generation cephalosporins and fluoroquinolones was observed in broiler meat (30.3% and 93.3%, respectively). Overall, a diversity of acquired resistance mechanisms, were detected: bla_ESBL [bla_CTX-M-1 (n = 19), bla_CTX-M-15 (n = 4), bla_CTX-M-32 (n = 12), bla_CTX-M-55 (n = 8), bla_CTX-M-65 (n = 4), bla_CTX-M-27 (n = 2), bla_CTX-M-9 (n = 1), bla_CTX-M-14 (n = 11), bla_SHV-12 (n = 27), bla_TEM-52 (n = 1)], bla_PMAβ [bla_CMY-2 (n = 8)], PMQR [qnrB (n = 27), qnrS (n = 21) and aac(6')-Ib-type (n = 4)] and PMCR [mcr-1 (n = 8)]. Our study highlights that consumers may be exposed through the food chain to multidrug-resistant E. coli carrying diverse plasmid-mediated antimicrobial resistance genes, posing a great hazard to food safety and a public health risk.

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

BACKGROUND

The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.

RESULTS

We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.

CONCLUSIONS

The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.

Removal of antimicrobial prophylaxis and its effect on swine carriage of antimicrobial-resistant coliforms

The use of antimicrobials in the food animal industry has caused an increased prevalence of antimicrobial-resistant bacteria and antimicrobial resistance genes, which can be transferred to the microbiota of humans through the food chain or the environment. To reduce the development and spread of antimicrobial resistance, restrictions on antimicrobial use in food animals have been implemented in different countries. We investigated the impact of an antimicrobial restriction intervention during two generations of pigs. Fecal samples were collected in five growth phases. The frequency of antimicrobial-resistant coliforms and antimicrobial-resistant bacteria or antimicrobial resistance genes was analyzed. No differences in the richness or abundance of antimicrobial-resistant coliforms or antimicrobial resistance genes were found when animals fed with or without prophylactic antimicrobials were compared. Withholding antimicrobial supplementation did not negatively affect weight gain in pigs. Withdrawal of prophylactic antimicrobial consumption during two generations of pigs was not enough to reduce the prevalence of antimicrobial resistance genes, as measured by richness and abundance markers. This study indicates that the fitness costs associated with bacterial carriage of some antimicrobial resistance genes are low.

Hulless barley and β-glucanase affect ileal digesta soluble beta-glucan molecular weight and digestive tract characteristics of coccidiosis-vaccinated broilers

Exogenous β-glucanase (BGase) in barley-based feed has been shown to reduce digesta viscosity in chickens, and thereby improve performance. Less well studied is the potential for BGase to convert barley β-glucan into low molecular weight carbohydrates, which might influence digestive tract function and enteric disease. Coccidiosis-vaccinated broiler chickens were fed graded levels of hulless barley (HB) and BGase to determine their effects on β-glucan depolymerization and digestive tract characteristics. Broilers were fed high β-glucan HB (0%, 30% and 60% replacing wheat) and BGase (0%, 0.01% and 0.1%) in a 3 × 3 factorial arrangement. A total of 5,346 broilers were raised in litter floor pens and vaccinated for coccidiosis on d 5. Each treatment was assigned to 1 pen in each of 9 rooms. The significance level was set at P ≤ 0.05. At both 11 and 33 d of broiler ages, peak molecular weight of β-glucan in ileal digesta decreased with increasing BGase for 30% and 60% HB. The maximum molecular weight for the smallest 10% β-glucan molecules (MW-10%) decreased with BGase at both ages for 30% and 60% HB; for birds fed 0% HB, only 0.1% BGase decreased MW-10%. The 0.1% BGase increased caecal short chain fatty acids (SCFA) compared to the 0.01% BGase at d 11 only for the 60% HB. Ileal pH increased with increasing HB and BGase at d 11 and 33. Caecal pH was lower for 0.1% BGase than 0% BGase for 60% HB at d 11. Relative mRNA expression of interleukin 6 (IL-6) and IL-8 in the ileum increased with 0.1% BGase at d 11 and 33, respectively, whereas expression of ileal mucin 2 (MUC2) decreased with 0.1% BGase at d 33. In the caeca, interactions between HB and BGase were significant for monocarboxylate transporter 1 (MCT1) and mucin 5AC (MUC5 AC) on d 11, but no treatment effects were found at d 33. In conclusion, BGase depolymerized high molecular weight β-glucan in HB in a dose-dependent manner. Hulless barley and BGase did not increase SCFA concentrations (except for 60% HB with 0.1% BGase at d 11) and caused minor effects on digestive tract histomorphological measurements and relative mRNA gene expression.

Assessing Class 1 Integron Presence in Poultry Litter Amended with Wood Biochar and Wood Vinegar

Class 1 integrons are mobile genetic elements that facilitate the spread of antibiotic resistance genes among bacteria. The use of prophylactic antibiotics has resulted in the rise of antibiotic resistance genes accumulating in a wide range of settings, including poultry houses and the agricultural fields where poultry litter is applied as a fertilizer. Biochar and wood vinegar are forest products wastes that have generated increasing attention as additives to agricultural soils. The objectives of this study were to observe the prevalence of class 1 integrons in poultry litter blended with biochar and wood vinegar over time and to verify a modified class 1 integron screening assay. Poultry litter blends were sampled and screened for class 1 integrons using polymerase chain reaction, and 80 products, 79 of which showed positive, were sent for DNA sequencing. The GenBank® BLAST database was used to verify the presence of the class 1 integron-integrase gene (intI1). There was no change in prevalence over time in poultry litter blends. Out of 79 PCR products that were intI1 positive, 78 showed at least 95% sequence identity to intI1 encoding bacteria and 64 showed at least 97% sequence identity. This indicates that this method was effective for conducting baseline surveillance of class 1 integrons in poultry litter and poultry litter-blended biochar and/or wood vinegar. Most significantly, class 1 integron prevalence did not decrease over time, further supporting the recalcitrance of these elements and the need for improved monitoring systems.

Antimicrobial Resistance Profiles and Macrolide Resistance Mechanisms of Campylobacter coli Isolated from Pigs and Chickens

We identified 1218 Campylobacter coli isolates from fecal and carcass samples of pigs (n = 643) and chickens (n = 575) between 2010 and 2018. About 99% of the isolates were resistant to at least one antimicrobial agent. The isolates exhibited high resistance rates (>75%) to ciprofloxacin, nalidixic acid, and tetracycline. Azithromycin and erythromycin resistance rates were the highest in isolates from pigs (39.7% and 39.2%, respectively) compared to those of chickens (15.8% and 16.3%, respectively). Additionally, a low-to-moderate proportion of the isolates were resistant to florfenicol, gentamicin, clindamycin, and telithromycin. Multidrug resistance (MDR) was found in 83.1% of the isolates, and profiles of MDR usually included ciprofloxacin, nalidixic acid, and tetracycline. We found point mutation (A2075G) in domain V of the 23S rRNA gene in the majority of erythromycin-resistant isolates. Multilocus sequence typing of 137 erythromycin-resistant C. coli isolates revealed 37 previously reported sequence types (STs) and 8 novel STs. M192I, A103VI, and G74A substitutions were frequently noted in the ribosomal proteins L4 or L22. Further, we identified a considerable proportion (>90%) of erythromycin-resistant isolates carrying virulence factor genes: flaA, cadF, ceuE, and VirB. The prudent use of antimicrobials and regular microbiological investigation in food animals will be vital in limiting the public health hazards of C. coli in Korea.

Bovine and Pig Carcasses as a Source of Campylobacter in Poland: A Reservoir for Antimicrobial-Resistant Campylobacter coli

Campylobacter is one of the most common causes of foodborne bacterial infections worldwide. Why poultry has been shown to be one of the most significant sources of these bacteria, ruminants, especially cattle, are also responsible for a high number of human Campylobacter jejuni, and to a lesser extent Campylobacter coli, infections. In this study, bovine and pig carcasses in Poland were investigated for the presence of Campylobacter and for their antimicrobial resistance. A total of 204 swabs from bovine carcasses and 355 swab samples from pig carcasses were tested during 2014-2018. Campylobacter was identified in 129 (36.3%) of the pig and in 11 (5.4%) of the bovine carcasses, respectively. The pig isolates were classified as C. coli (121; 34.1%) or C. jejuni (8; 2.3%), whereas the bovine Campylobacter were identified either as C. jejuni (8; 3.9% isolates) or C. coli (3; 1.5% strains). Resistance of the isolates (n = 140) to erythromycin, ciprofloxacin, nalidixic acid, streptomycin, and tetracycline revealed that the vast majority of C. coli was resistant to streptomycin (106 isolates; 85.5%), tetracycline (97; 78.2%), nalidixic acid (90; 72.6%), and ciprofloxacin (88; 71.0%). Among C. jejuni isolates (n = 16) the resistance rates to all antibiotics were lower than in C. coli, irrespective of the origin. A total of 74 of 121 (61.2%) C. coli isolates from the pig carcasses and one of three such isolates from the bovine samples were multiresistant. Most of the C. coli (64 isolates; 85.3%) had the ciprofloxacin+nalidixic acid+streptomycin+tetracycline resistance profile. The results suggest that pig and bovine carcasses may be an underestimated reservoir of Campylobacter, especially for C. coli in pigs. The high antimicrobial resistance rates of such strains to streptomycin, quinolones, and tetracyclines highlight the need for monitoring of these bacteria in such food and food products.

Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. is influenced by production system, antimicrobial use, and biosecurity measures on Spanish pig farms

Background

Antimicrobial resistance (AMR) is a global public health threat consequence of antimicrobial use (AMU) in human and animal medicine. In food-producing animals factors such as management, husbandry or biosecurity may impact AMU. Organic and extensive Iberian swine productions are based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the AMR in indicator bacteria. Here, we evaluate the usefulness of commensal Escherichia coli and Enterococcus spp. isolates as AMR bioindicators when comparing 37 Spanish pig farms from both intensive and organic-extensive production systems, considering the effect of AMU and biosecurity measures, the last only on intensive farms.

Results

The production system was the main factor contributing to explain the AMR differences in E. coli and Enterococcus spp. In both bacteria, the pansusceptible phenotype was more common (p < 0.001) on organic-extensive farms when compared to intensive herds. The microbiological resistance in commensal E. coli was, for most of the antimicrobials evaluated, significantly higher (p < 0.05) on intensive farms. In enterococci, the lincosamides usage revealed the association between AMR and AMU, with an increase in the AMR for erythromycin (p < 0.01), quinupristin-dalfopristin (p < 0.01) and the multidrug-resistant (MDR) phenotype (p < 0.05). The biosecurity measures implemented on intensive farms influenced the AMR of these bioindicators, with a slightly lower resistance to sulfamethoxazole (p < 0.01) and the MDR phenotype (p < 0.05) in E. coli isolated from farms with better cleaning and disinfection protocols. On these intensive farms, we also observed that larger herds had a higher biosecurity when compared to smaller farms (p < 0.01), with no significant associations between AMU and the biosecurity scores.

Conclusions

Overall, this study evidences that the production system and, to a lesser extent, the biosecurity measures, contribute to the AMR development in commensal E. coli and Enterococcus spp., with antimicrobial usage as the main differential factor, and demonstrates the potential value of these bacteria as bioindicators on pig farms in AMR surveillance programs.

Pseudomonas putida actively forms biofilms to protect the population under antibiotic stress

Antibiotics are frequently used for clinical treatment and by the farming industry, and most of these are eventually released into the surrounding environment. The impact of these antibiotic pollutants on environmental microorganisms is a concern. The present study showed that after Pseudomonas putida entered the logarithmic growth phase, tetracycline strongly stimulated its biofilm formation in a dose-dependent manner. This was supported by the increased expression of the key adhesin gene lapA in response to tetracycline treatment. Tetracycline treatment also changed the expression levels of the exopolysaccharide gene clusters alg, bcs and pea and the adhesin gene lapF. However, these genes did not participate in the tetracycline-induced biofilm formation. When a biofilm had been established, the P. putida population became more tolerant to tetracycline. Confocal laser scanning microscopic images showed that the interior of the biofilm provided favorable conditions that protected bacterial cells from tetracycline. Besides, biofilm formation of P. putida was also promoted by several other antibiotics, including oxytetracycline, fluoroquinolones, rifampicin, and imipenem, but not aminoglycosides. Susceptibility tests suggested that biofilm conferred a higher tolerance on P. putida cells to specific antibiotics (e.g., tetracyclines and fluoroquinolones). These antibiotics exerted a stronger inducing effect on biofilm formation. Together, our results indicate that P. putida actively forms robust biofilms in response to antibiotic stress, and the biofilms improve the survival of bacterial population under such stress.

Effects of hulless barley and exogenous beta-glucanase levels on ileal digesta soluble beta-glucan molecular weight, digestive tract characteristics, and performance of broiler chickens

The reduced use of antibiotics in poultry feed has led to the investigation of alternatives to antibiotics, and one such substitution is fermentable carbohydrates. Exogenous β-glucanase (BGase) is commonly used in poultry fed barley-based diets to reduce digesta viscosity. The effects of hulless barley (HB) and BGase levels on ileal digesta soluble β-glucan molecular weight, digestive tract characteristics, and performance of broiler chickens were determined. A total of 360 day-old broilers were housed in battery cages (4 birds per cage) and fed graded levels of high β-glucan HB (CDC Fibar; 0, 30, and 60% replacing wheat) and BGase (Econase GT 200 P; 0, 0.01, and 0.1%) in a 3 × 3 factorial arrangement. Beta-glucan peak molecular weight in the ileal digesta was lower with 30 and 60 than 0% HB, whereas the peak decreased with increasing BGase. The weight average molecular weight was lower at 0.1 than 0% BGase in wheat diets, whereas in HB diets, it was lower at 0.01 and 0.1 than 0% BGase. The maximum molecular weight was lower with 0.01 and 0.1 than 0% BGase regardless of the HB level. The maximum molecular weight was lower with HB than wheat at 0 or 0.01% BGase. Overall, empty weights and lengths of digestive tract sections increased with increasing HB, but there was no BGase effect. Hulless barley decreased the duodenum and jejunum contents, whereas increasing the gizzard (diets with BGase), ileum, and colon contents. The jejunum and small intestine contents decreased with increasing BGase. Ileal and colon pH increased with increasing HB, but there was no BGase effect. Treatment effects were minor on short-chain fatty acids levels and performance. In conclusion, exogenous BGase depolymerized the ileal digesta soluble β-glucan in broiler chickens in a dose-dependent manner. Overall, feed efficiency was impaired by increasing HB levels. However, HB and BGase did not affect carbohydrate fermentation in the ileum and ceca, although BGase decreased ileal viscosity and improved feed efficiency at the 0.1% dietary level.

Effects of Glycyrrhiza polysaccharide in diet on growth performance, serum antioxidant capacity, and biochemistry of broilers

In the present study, we analyzed the effects of Glycyrrhiza polysaccharide (GCP) on growth performance, serum antioxidant capacity, and biochemistry of broilers. A total of 600, one-day-old AA broilers randomly divided into 5 treatment groups with 6 replicate pens of 20 birds per cage received dietary supplementation with GCP (0, 200, 500, 1,000, and 1,500 mg/kg) for 42 d. The supplementation of GCP linearly decreased (P < 0.05) feed conversion rate on day 22 to 42. Dietary supplementation with GCP reduced (P < 0.05) serum total cholesterol on day 21 and 42 and linearly improved (P < 0.05) albumin and high-density lipoprotein cholesterol. Dietary supplementation with 1,000 or 1,500 mg/kg GCP significantly increased (P < 0.05) serum total superoxide dismutase (T-SOD) activity on day 21 and 42 and reduced (P < 0.05) serum malondialdehyde content on 21 d. Dietary supplementation with 1,000 or 1,500 mg/kg GCP significantly improved (P < 0.05) interleukin-1β (IL-1β) and interferon-γ (IFN-γ) expressions in liver on day 21 and 42. At the end of the experiment, we randomly selected 20 broilers from 3 treatment groups (0, 1,000, and 1,500 mg/kg), respectively, to perform an lipopolysaccharide (LPS)-induced acute stress experiment. The 60 broilers were divided into 6 treatment groups with 10 birds per cage. The experiment was designed as a 3 × 2 factorial arrangement with GCP (0, 1,000, or 1,500 mg/kg) and LPS (injection of saline or 1 mg/kg body weight) levels as treatments. When the grouping was finished, the broilers were immediately intraperitoneally injected with LPS or normal saline. Six hours after challenged, serum antioxidant and liver immunity were analyzed. The results showed that dietary GCP prevented LPS-induced reductions in T-SOD activity and increases in malonaldehyde content (P < 0.05). Also, dietary GCP supplementation mitigated the LPS-induced increase in IL-1β and IFN-γ in the liver. Supplementation with 1,500 mg/kg GCP showed the most optimal effect in broilers. GCP has the potential to be used as feed additive in broilers.

Prevalence and antimicrobial susceptibility of Campylobacter isolated from retail chickens in Thailand

Campylobacter is an important foodborne pathogen causing bacterial gastroenteritis worldwide; however, there has been a lack of information over the past decade on its occurrence, antibiotic susceptibility and genetic diversity in Thailand. Poultry meat is considered as a reservoir for transmission of Campylobacter to humans. This study determines the prevalence and antimicrobial resistance patterns of Campylobacter spp. on chicken samples purchased from 50 local wet markets and supermarkets in central Thailand. Of the 296 samples, 99 (33.5%) were contaminated with C. jejuni, 54 (18.2%) were C. coli and 15 (5.1%) were contaminated with both species. Antibiotic resistance rate is higher among C. coli isolates; 100%, 76.8%, 37.7%, 36.2% and 13.0% were resistant to quinolones, cyclines, macrolides, clindamycin and gentamicin, respectively. Most of the C. jejuni isolates were resistant to quinolones (79.8%) and cyclines (38.6%) whereas resistance to macrolides, clindamycin and gentamicin was found to be 1.8%. Multi-drug resistance (i.e. to three or more unrelated antimicrobials) was detected in 37.7% of C. coli and 1.8% of C. jejuni isolates. This study has revealed high contamination rates and alarming levels of antimicrobial resistance in Campylobacter spp. isolated from retail chicken samples in Thailand, suggesting the necessity of implementing interventions to reduce its prevalence from farm to table in the country.

Changes in antibiotic resistance of Escherichia coli during the broiler feeding cycle

The purpose of this study was to investigate the drug-resistant phenotypes and genes of Escherichia coli in animal, environmental, and human samples before and after antibiotic use at a large-scale broiler farm to understand the respective effects on E. coli resistance during the broiler feeding cycle. The antibiotic use per broiler house was 143.04 to 183.50 mg/kg, and included tilmicosin, florfenicol, apramycin, and neomycin. All strains isolated on the first day the broilers arrived (T1; day 1) were antibiotic-resistant bacteria. E. coli strains isolated from animal samples were resistant to ampicillin, tetracycline, and sulfamethoxazole (100%), and those isolated from environmental samples were resistant to 5 different drugs (74.07%, 20 of 27). E. coli strains isolated on the last day before the broilers left (T2; day 47) had a higher resistance rate to florfenicol (100%, 36 of 36) than at T1 (P < 0.05). Multidrug resistance increased from T1 (84.21%, 32 of 38) to T2 (97.22%, 35 of 36). Most strains were resistant to 5 classes of antibiotics, and 2 strains were resistant to 6 classes of antibiotics. Among 13 identified drug resistance genes, 11 and 13 were detected at T1 and T2, respectively. NDM-1 was detected in 4 environmental samples and 1 animal sample. In conclusion, the use of antibiotics during breeding increases E. coli resistance to antibacterial drugs. Drug-resistant bacteria in animals and the environment proliferate during the feeding cycle, leading to the widespread distribution of drug resistance genes and an increase in the overall resistance of bacteria.

Multidrug-resistant bacteria as intestinal colonizers and evolution of intestinal colonization in healthy university students in Portugal

Multidrug-resistant bacteria have been increasingly described in healthcare institutions, however community resistance also seems to be emerging. Escherichia coli an intestinal commensal bacteria, is also a pathogen and represents an important intestinal reservoir of resistance. Our aim was the study of the intestinal colonization and of the persistence of antibiotic resistant intestinal bacteria in healthy university students of Porto, in the north of Portugal. Samples from 30 university students were collected and analysed. Two E. coli isolates were randomly obtained from each student and Gram-negative bacilli resistant to antibiotics were studied. In addition, we evaluated changes in the Gram-negative intestinal colonization of ten university students in a short period of time. Molecular characterization showed a high presence of bla _TEM in commensal E. coli . Gram-negative bacteria with intrinsic and extrinsic resistance were isolated, namely Pseudomonas spp., Enterobacter spp. and Pantoea spp. We isolated three ESBL-producing E. coli from two students. These isolates showed bla _CTX-M group 1 (n=1), bla _CTX-M group 9 (n=2), bla _TEM (n=2), bla _SHV (n=1) and tetA (n=2) genes. Additionally, they showed specific virulence factors and conjugational transfer of antibiotic resistance and virulence genes. One Pseudomonas spp. isolate resistant to carbapenems was detected colonizing one student. Our results confirm that healthy young adults may be colonized with commensals showing clinically relevant antibiotic resistance mechanisms, creating a risk of silent spread of these bacteria in the community.

Scorpion-Venom-Derived Antimicrobial Peptide Css54 Exerts Potent Antimicrobial Activity by Disrupting Bacterial Membrane of Zoonotic Bacteria

Antibiotic resistance is an important issue affecting humans and livestock. Antimicrobial peptides are promising alternatives to antibiotics. In this study, the antimicrobial peptide Css54, isolated from the venom of C. suffuses, was found to exhibit antimicrobial activity against bacteria such as Listeria monocytogenes, Streptococcus suis, Campylobacter jejuni, and Salmonella typhimurium that cause zoonotic diseases. Moreover, the cytotoxicity and hemolytic activity of Css54 was lower than that of melittin isolated from bee venom. Circular dichroism assays showed that Css54 has an α-helix structure in an environment mimicking that of bacterial cell membranes. We examined the effect of Css54 on bacterial membranes using N-phenyl-1-naphthylamine, 3,3'-dipropylthiadicarbbocyanine iodides, SYTOX green, and propidium iodide. Our findings suggest that the Css54 peptide kills bacteria by disrupting the bacterial membrane. Moreover, Css54 exhibited antibiofilm activity against L. monocytogenes. Thus, Css54 may be useful as an alternative to antibiotics in humans and animal husbandry.

Antimicrobial Resistance of Escherichia coli and Pseudomonas aeruginosa from Companion Birds

Antimicrobial resistance is a public health concern worldwide and it is largely attributed to the horizontal exchange of transferable genetic elements such as plasmids carrying integrons. Several studies have been conducted on livestock showing a correlation between the systemic use of antibiotics and the onset of resistant bacterial strains. In contrast, although companion birds are historically considered as an important reservoir for human health threats, little information on the antimicrobial resistance in these species is available in the literature. Therefore, this study was aimed at evaluating the antimicrobial resistance of Escherichia coli and Pseudomonasaeruginosa isolated from 755 companion birds. Cloacal samples were processed for E. coli and P. aeruginosa isolation and then all isolates were submitted to antimicrobial susceptibility testing. P. aeruginosa was isolated in 59/755 (7.8%) samples, whereas E. coli was isolated in 231/755 (30.7%) samples. Most strains showed multidrug resistance. This study highlights that companion birds may act as substantial reservoirs carrying antimicrobial resistance genes which could transfer directly or indirectly to humans and animals, and from a One Health perspective this risk should not be underestimated.

Effects of tourist flows on antibiotic resistance in wastewater of a Greek island

AIM

Antibiotic resistance in wastewaters reflects the clinical resistome. This study aimed at investigating whether changes in the population size and composition in the popular tourist destination of Zakynthos island are associated with differentiation in the antibiotic resistance of environmental micro-organisms isolated from wastewater.

METHODS AND RESULTS

The resistance profiles of four species (Escherichia coli, Staphylococcus sp., Pseudomonas sp. and Enterococcus sp.) were studied in 124 raw and treated municipal wastewaters from November 2015 to August 2016. Isolates were tested against their susceptibility to several antibiotics of different antimicrobial categories. Data concerning the alteration in the population size and composition, due to the tourist mobility, were collected and logistic regression models were used to examine the relationships between antimicrobial resistance and population changes. The decrease in resistance of E. coli to amoxicillin-clavulanate, of enterococci to norfloxacin and ampicillin, and of pseudomonads to almost all antibiotics tested was associated with population increase due to tourist flows. In contrast, the presence of tourists was linked to an increase in quinupristin-dalfopristin resistant enterococci. Resistance of staphylococci did not change during the tourist period.

CONCLUSION

Changes in population composition in touristic areas are reflected in antibiotic resistance of environmental bacteria in wastewater.

SIGNIFICANCE AND IMPACT OF THE STUDY

In touristic areas, where people carrying different resistomes are merged, medication should be adapted accordingly.

Prevalence and susceptibility to antibiotics from Campylobacter jejuni and Campylobacter coli isolated from chicken meat in southern Benin, West Africa

Objective

Poultry is commonly considered to be the primary vehicle for Campylobacter infection in humans. The aim of this study is to assess the risk of Campylobacteriosis in chicken meat consumers in southern Benin by assessing the prevalence and resistance profile of Campylobacter coli and Campylobacter jejuni isolated from chicken thigh in Southern Benin.

Results

The contamination rate of Campylobacter in the samples was 32.8%. From this percentage, 59.5% were local chicken thighs and 40.5% of imported chicken thighs (p = 0.045). After molecular identification, on the 256 samples analyzed, the prevalence of C. jejuni was 23.4% and 7.8% for C. coli, with a concordance of 0.693 (Kappa coefficient of concordance) with the results from phenotypic identification. Seventy-two-point seven percent of Campylobacter strains were resistant to Ciprofloxacin, 71.4% were resistant to Ampicillin and Tetracycline. 55.8% of the strains were multi-drug resistant.

Nano adamantane-conjugated BODIPY for lipase affinity and light driven antibacterial

The increasing number of resistant bacterial strains has raised efforts in developing alternative treatment strategies. Lipase is highly expressed in most bacteria and lipase targeting dyes will be non-sacrificed materials for a sustainable method against microorganism. The combination of chemotherapy and antimicrobial photodynamic inactivation (aPDI) method will be an effective method due to enhanced antibacterial activity. Here we reported the spectroscopic features of five boron dipyrrolylmethene (BODIPY) derivatives with different functional groups for lipase affinity and antibacterial activity. Lipase affinity tests and antibacterial assays were conducted by spectroscopic methods. Adamantane-conjugated BODIPY (BDP-2) was found to be the active compound against E. coli. Next, BDP-2 was brominated, and then assembled with PEG resulting biocompatible BDP2-Br₂@mPEG nanoparticles. The MTT assay indicated that BDP2-Br₂@mPEG was less toxicity on BGC-823 cancer cells without irradiation. The BDP2-Br₂@mPEG can inhibit the proliferation of E. coli and damage the membrane of bacterial cell under green LED light irradiation. The results proved BDP2-Br₂@mPEG can be a very promising green LED light driven antibacterial material.

Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro

Salmonella enterica serovar Typhimurium is an animal welfare and public health concern due to its ability to parasite livestock and potentially contaminate pork products. To reduce Salmonella shedding and the risk of pork contamination, antibiotic therapy is used and can contribute to antimicrobial resistance. Here we hypothesized that immune system education by the microbiota can play a role in intestinal resilience to infection. We used amoxicillin (15mg/Kg) to modulate the intestinal microbiome of 10 piglets, paired with same age pigs that received a placebo (n = 10) from 0 to 14 days of age. Animals were euthanized at 4-weeks old. Each pig donated colon sections for ex vivo culture (n = 20 explants/pig). Explants were inoculated with S. Typhimurium, PBS or LPS (n = 6 explants/pig/group, plus technical controls). The gut bacteriome was characterized by sequencing of the 16S rRNA at 7, 21 days of age, and upon in vitro culture. Explants response to infection was profiled through high-throughput mRNA sequencing. In vivo antibiotic treatment led to β-diversity differences between groups at all times (P<0.05), while α-diversity did not differ between amoxicillin and placebo groups on day 21 and at euthanasia (P<0.03 on day 7). Explant microbiomes were not different from in vivo. In vitro challenge with S. Typhimurium led to lower necrosis scores in explants from amoxicillin-treated pigs, when compared to explants placebo-treated pigs (P<0.05). This was coupled with the activation of immune-related pathways in explants from amoxicillin-treated pigs (IL-2 production, NO production, BCR activation), when compared to placebo-treated pigs. In addition, several DNA repair and intestinal wound healing pathways were also only activated in explants from amoxicillin-treated pigs. Taken together, these findings suggest that immune education by the amoxicillin-disturbed microbiota may have contributed to mitigate intestinal lesions following pathogen exposure.

mcr-Colistin Resistance Genes Mobilized by IncX4, IncHI2, and IncI2 Plasmids in Escherichia coli of Pigs and White Stork in Spain

Colistin has become the last-line antimicrobial for the treatment of multidrug resistant (MDR) Enterobacterales in human medicine. To date, several colistin resistance genes have been described. Of them mcr-1 is disseminated worldwide in Escherichia coli of human and animal origin. The aim of this study was to characterize mcr-mediated resistance plasmids from E. coli of animal origin in Spain. From our strain collection, 70 E. coli of pig origin collected between 2005 and 2014 (10 per year, except for years 2009–2010–2013) were randomly selected and screened for the presence of mcr-genes. Additionally, 20 E. coli isolated in 2011 from white storks (Ciconia ciconia) from the same urban household waste landfill associated colony were also included. Whole genome sequencing of mcr-positive isolates was carried out on a MiSeq (Illumina). Hybrid whole genome sequencing strategy combining nanopore and Illumina technologies were performed in a selection of isolates to close the genomes and plasmids and identify the presence of antimicrobial resistance genes. Minimum inhibitory concentration (MIC) was used to assess the susceptibility to colistin. Mating experiments were carried out to evaluate transferability of the mcr-genes. A total of 19 mcr-1 and one mcr-4 positive isolates were detected, 15 from pigs distributed during the study period, and five from storks collected in 2011. No other mcr-variants were found. The MICs for colistin ranged between 4 and >4 mg/L. High diversity of STs were detected among the mcr-1 positive E. coli isolates, with only ST-10 shared between pigs and white storks. Except for one isolate, all were genotypic and phenotypically MDR, and five of them also harbored cephalosporin resistance genes (bla_CTX–M–14, bla_SHV–12, and three bla_CMY–2). mcr-1 genes were mobilizable by conjugation, associated with IncX4, IncHI2, and IncI2 plasmids. In our study, mcr-1 genes have been circulating in pig farms since 2005 harbored by a variety of E. coli clones. Its persistence may be driven by co-selection since plasmids containing mcr-1 also exhibit resistance to multiple drugs used in veterinary medicine. Furthermore, this is the first report of the presence of mcr-1 gene in isolates from white storks in Spain. This finding highlights the potential importance of wildlife that forage at urban household waste landfills in the transmission and spread of colistin resistance genes.