Longitudinal study of CTX-M ESBL-producing E. coli strains on a UK dairy farm

Effects of feeding a simulated waste milk on growth, health, fecal microbiota, and antibiotic resistance in dairy heifer calves

Feeding waste milk, a common practice in dairy farming, exposes calves to subtherapeutic levels of antimicrobials, potentially contributing to antibiotic resistance-a growing concern globally. Many dairy farmers, including those in Ireland, continue this practice, feeding waste milk from antibiotic-treated cows to calves. Although previous studies have linked waste milk feeding to changes in calf growth and health during the preweaning period, its effects postweaning remain unclear. This study examined how the duration of antimicrobial exposure at levels equivalent to those found in waste milk influences health and growth outcomes of dairy heifer calves both before and after weaning. It also assessed the prevalence of extended-spectrum β-lactamase (ESBL)-resistant Escherichia coli in feces and changes in the fecal microbiota over time. To mimic waste milk, as derived from a cow treated with an intramammary suspension of antibiotics, a simulated waste milk (SWM) was prepared by adding amoxicillin (1.68 mg/L) and neomycin (2.28 mg/L) to a conventional milk replacer (MR). The study employed a randomized block design with 87 dairy heifer calves assigned to 1 of 3 treatments: (1) long-term antibiotic (LTA), with calves fed SWM until weaning at 12 wk; (2) short-term antibiotic (STA), with SWM fed from 3 to 5 wk; and (3) control (CONT), with calves fed antibiotic-free MR. Calves were weighed weekly, and health scores, including fecal scores (tail and hindquarters cleanliness as diarrhea indicator), were recorded twice per week. Fecal and blood samples were collected to analyze microbiome changes and the shedding of antimicrobial resistance. Blood samples were taken to measure systemic inflammation, using serum amyloid A as a biomarker. Results indicated that SWM feeding did not affect average daily gains before or after weaning. However, higher fecal scores were observed in the LTA group during weaning and after weaning in the STA group. Antibiotic-resistant isolates were present in all groups, with the highest prevalence in LTA. Fecal microbiota analysis revealed treatment-specific microbial community variations, with increase of Enterococcus faecium genes resistant to macrolide, aminoglycoside, and tetracycline antibiotics in LTA and STA compared with CONT. In summary, SWM feeding did not significantly affect growth or overall health, but it was associated with increased fecal shedding of resistant bacteria and some changes in the microbiota, indicating potential long-term implications for antimicrobial resistance in dairy herds.

Clonal and plasmidic dissemination of critical antimicrobial resistance genes through clinically relevant ExPEC and APEC-like lineages (ST) in the dairy cattle population of Québec, Canada

Antimicrobial resistance can be effectively limited by improving the judicious use of antimicrobials in food production. However, its effect on the spread of AMR genes in animal populations is not well described. In the province of Québec, Canada, a new legislation implemented in 2019 has led to an unprecedented reduction in the use of critical antimicrobials in dairy production. We aimed to investigate the potential link between ESBL/AmpC E. coli isolated before and after legislation and to determine the presence of plasmids carrying genes responsible for critical AMR. We collected fecal samples from calves, cows, and manure pit from 87 Québec dairy farms approximately 2 years before and 2 years after the legislation came into effect. The whole genomes of 183 presumptive ESBL/AmpC E. coli isolated after cefotaxime enrichment were sequenced. Their phylogenetic characteristics (MLST, serogroup, cgMLST) and the presence of virulence and resistance genes and replicons were examined. A maximum likelihood phylogenetic tree was constructed based on single nucleotide polymorphism (SNPs). We identified 10 clonal lineages (same cgMLST) and 7 clones (SNPs ≤ 52). Isolates belonging to these clones could be found on different farms before and after the legislation, strongly suggesting a clonal spread of AMR genes in the population during this 4-year period. All isolates were multidrug resistant (MDR), with clone 2 being notable for the presence of macrolide, fluoroquinolone, and third-generation cephalosporin resistance genes. We also identified clinically relevant ExPEC (ST10) and APEC-like lineages (ST117, ST58, ST88) associated with the presence of ExPEC and APEC virulence genes, respectively. Our data also suggests the presence of one epidemic plasmid belonging to the IncY incompatibility group and carrying qnrs1 and blaCTX-M-15. We demonstrated that AMR genes spread through farms and can persist over a 4-year period in the dairy cattle population through both plasmids and E. coli clones, despite the restriction of critical antimicrobial use. MDR ExPEC and APEC-like STs are present in the normal microbiota of cattle (more frequently in calves). These data increase our knowledge on gene dissemination dynamics and highlight the fact that biosecurity measures should be enhanced in this industry to limit such dissemination.

Dissemination of carbapenemase-producing Enterobacteriaceae and associated resistance determinants through global food systems

Antimicrobial agents are a critical component of modern healthcare systems, fulfilling a core function in patient care and improving individual patient outcomes and consequently overall public health. However, the efficacy of antimicrobial interventions is being consistently eroded by the emergence and dissemination of various antimicrobial resistance (AMR) mechanisms. One highly valued class of antimicrobial compounds is carbapenems, which retain efficacy in treating most multidrug-resistant infections and are considered "last line" agents. Therefore, recent trends in proliferation of carbapenem resistance (CR) via dissemination of carbapenemase-encoding genes among members of the Enterobacteriaceae family pose a significant threat to public health. While much of the focus relating to this has been on nosocomial environments, community-acquired carbapenemase-producing Enterobacteriaceae (CPE) infections and their associated transmission routes are less well studied. Among these community-associated vectors, the role of food chains and contaminated foods is important, since Enterobacteriaceae occupy niches within these settings. This review examines foodborne CPE transmission by exploring how interactions within and between food, the food chain, and agriculture not only promote and disseminate CPE, but also create reservoirs of mobile genetic elements that may lead to further carbapenemase gene proliferation both within and between microbial communities. Additionally, recent developments regarding the global occurrence and molecular epidemiology of CPEs in food chains will be reviewed.

Within-farm dynamics of ESBL-producing Escherichia coli in dairy cattle: Resistance profiles and molecular characterization by long-read whole-genome sequencing

A longitudinal study was designed in five dairy cattle farms to assess the within-farm dynamics of ESBL-/AmpC-/carbapenemase-producing E. coli and their resistance profiles, along with the genes conferring the resistance phenotypes. Twelve samplings were performed over a period of 16 months, collecting rectal feces from apparently healthy animals in three age groups (calves, heifers, and lactating cows) that were subjected to selective isolation in cefotaxime-containing media. Minimum inhibitory concentrations were determined by broth microdilution for 197 cefotaxime-resistant E. coli (1-3 isolates per age group and sampling date), and 41 of them were selected for long-read whole-genome sequencing. Cefotaxime-resistant E. coli were detected in the five farms, but isolation frequency and resistance profiles varied among farms and age groups. The genetic profiling of a selection of isolates recovered in two of the farms was described in full detail, showing the predominance of a few genomic subtypes of E. coli in one farm (F1) and great variability of strains in another one (F4). Two predominant distinct strains carrying the bla CTX-M-1 gene in IncX1 plasmids successively spread and persisted in F1 over a prolonged period. In F4, 13 different MLST types carrying a high diversity of ESBL-encoding genes in 6 different plasmid types were observed, probably as the result of multiple source contamination events. In both farms, the presence of certain plasmid types with the same repertoire of ARGs in different E. coli STs strongly suggested the occurrence of horizontal transfer of such plasmids among strains circulating within the farms. Considering the public health importance of ESBL-producing E. coli both as pathogens and as vectors for resistance mechanisms, the presence of β-lactamase- and other AMR-encoding genes in plasmids that can be readily transferred between bacteria is a concern that highlights the need for One Health surveillance.

An Overview of Waste Milk Feeding Effect on Growth Performance, Metabolism, Antioxidant Status and Immunity of Dairy Calves

Waste milk (WM) is a part of the milk produced on dairy farms, which is usually unsuitable for human consumption. The WM contains transition milk, mastitis milk, colostrum, milk with somatic cells, blood (Hemolactia), harmful pathogens, pathogenic and antibiotic residues. Due to the high cost of milk replacer (MR), dairy farmers prefer raw WM to feed their calves. It has been well established that WM has a greater nutritive value than MR. Hence WM can contribute to improved growth, rumen development, and immune-associated parameters when fed to dairy calves. However, feeding raw WM before weaning has continuously raised some critical concerns. The pathogenic load and antibiotic residues in raw WM may increase the risk of diseases and antibacterial resistance in calves. Thus, pasteurization has been recommended as an effective method to decrease the risk of diseases in calves by killing/inhibiting the pathogenic microorganisms in the raw WM. Altogether, the current review provides a brief overview of the interplay between the positive role of raw WM in the overall performance of dairy calves, limitations of raw WM as a feed source and how to overcome these issues arising from feeding raw WM.

Impact of a Regulation Restricting Critical Antimicrobial Usage on Prevalence of Antimicrobial Resistance in Escherichia coli Isolates From Fecal and Manure Pit Samples on Dairy Farms in Québec, Canada

To tackle antimicrobial resistance (AMR), one of the major health threats of this century, the World Health Organization (WHO) endorsed a global action plan in 2015. This plan calls countries to develop national actions to address AMR. The province of Québec, Canada, adopted a new regulation on the 25^th of February 2019, to limit the use in food animals of antimicrobials of very high importance in human medicine. We aimed to establish the impact of this regulation by comparing the AMR situation in dairy cattle in Québec ~2 years before and 2 years after its introduction. We sampled calves, cows, and the manure pit in 87 farms. Generic and putative ESBL/AmpC E. coli were tested for susceptibility to 20 antimicrobials. Logistic regression was used to investigate whether the probability of antimicrobial resistance differed between isolates obtained from the pre and post regulation periods by sample type (calves, cows, manure pit) and in general. To identify AMR genes dissemination mechanisms, we sequenced the whole genome of 15 generic isolates. In the generic collection, at the herd level, the proportion of multidrug resistant (MDR) isolates, decreased significantly from 83 to 71% (p = 0.05). Folate inhibitor and aminoglycoside resistances demonstrated a significant decrease. However, when analyzed by sample type (calves, cows, manure pit), we did not observe a significant AMR decrease in any of these categories. In the ESBL/AmpC collection, we did not detect any significant difference between the two periods. Also, the general resistance gene profile was similar pre and post regulation. We identified both clonal and plasmidic dissemination of resistance genes. In conclusion, as early as 2 years post regulation implementation, we observed a significant decrease in MDR in the dairy industry in Quebec in the generic E. coli collection with folate inhibitor and aminoglycoside resistances showing the most significant decrease. No other significant decreases were yet observed.

Analysis of Antimicrobial Use and the Presence of Antimicrobial-Resistant Bacteria on Austrian Dairy Farms-A Pilot Study

The assumed link between high levels of antimicrobial use on farms and selection for antimicrobial-resistant (AMR) bacteria on that farm remains difficult to prove. In the pilot study presented here, we analysed total antimicrobial use on 50 dairy farms in Austria and also collected environmental samples to ascertain whether specific AMR bacteria were present. Antimicrobial use (AMU) analysis was based on electronic veterinary treatment records over a one-year period. Faecal samples for the assessment of extended-spectrum beta-lactamase (ESBL)-producing E. coli were collected from cowsheds, calf pens, and youngstock housing areas, as well as dust samples from barns, to isolate methicillin-resistant Staphylococcus aureus (MRSA). Bacteriological cultures were carried out on selective agar. Farms were split into groups of 25 of the highest antimicrobial users and 25 of the lowest users. Overall, samples from 13/50 (26.0%) farms were found to be positive for the presence of ESBL-producing E. coli. Of these, eight farms were in the low user group and five were in the high user group. Only one farm was confirmed to harbour MRSA. Statistical analyses demonstrated that there was no significant difference in this study population between high or low antimicrobial use with respect to the presence of ESBL-producing E. coli on farms (p = 0.33). In conclusion, the presence of specific AMR bacteria on farms in this study population was not found to have a statistically proven relationship with their level of antimicrobial use.

Factors influencing the detection of antibacterial-resistant Escherichia coli in faecal samples from individual cattle

AIMS

To investigate whether on-farm antibacterial usage (ABU), environmental antibacterial-resistant (ABR) Escherichia coli prevalence, sampling and sample handling methodologies are associated with ABR E. coli positivity in individual faecal samples from dairy heifers.

METHODS AND RESULTS

Three hundred and sixty-four heifers from 37 farms were sampled via rectal or faecal pat sampling. Samples were stored at -80°C for variable periods before microbiological analysis. Data analysis was done through a multilevel, multivariable logistic regression approach. Individual rectal samples had increased odds of positivity for amoxicillin-, cefalexin- and tetracycline-resistant E. coli. Sample storage for 6-12 months was associated with decreased odds of finding amoxicillin- and tetracycline-resistant E. coli. On-farm ABU had little influence, and environmental ABR E. coli prevalence had no significant influence on the odds of sample-level positivity for ABR E. coli.

CONCLUSIONS

Sampling methodology and sample handling have a greater association than on-farm factors with the detection of ABR E. coli in individual faecal samples from dairy heifers.

SIGNIFICANCE AND IMPACT OF THE STUDY

Sampling and storage methodologies should be considered carefully at the point of designing ABR surveillance studies in livestock and their environments and, where possible, these methodologies should be standardized between and within future studies.

Prevalence and Risk Factors for ESBL/AmpC-E. coli in Pre-Weaned Dairy Calves on Dairy Farms in Germany

The objectives of this study were to ascertain the fecal ESBL/AmpC-E. coli prevalence and to detect risk factors for their occurrence in young pre-weaned calves and their dams on large dairy farms in Germany. From 2018-2019 we investigated 2816 individual fecal samples from pre-weaned dairy calves and their dams, representing seventy-two farms (mean = 667 milking cows) from eight German federal states. To assess possible risk factors associated with ESBL/AmpC-E. coli prevalence in calves and dams, a questionnaire was performed, collecting management data. We observed an ESBL/AmpC-E. coli prevalence of 63.5% (95% CI: 57.4-69.5) among the sampled calves and 18.0% (95% CI: 12.5-23.5) among the dams. On all farms, at least one positive sample was obtained. To date, this is the highest ESBL/AmpC-E. coli prevalence observed in dairy herds in Europe. Feeding with waste milk was identified as a significant risk factor for a high prevalence of ESBL/AmpC-E. coli in calves. Many calves at large dairies in Germany are fed with waste milk due to the large amounts generated as a result of antibiotic dry-off routines and mastitis treatment with antibiotics. Other notable risk factors for high ESBL/AmpC-E. coli in calves were the general fitness/health of dams and calves, and the quality of farm hygiene. Taken together, these findings suggest that new or improved approaches to animal health management, for example, antibiotic dry cow management (selective dry cow therapy) and mastitis treatment (high self-recovery), as well as farm hygiene, should be researched and implemented.

A 1-Year Investigation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Bovine Mastitis at a Large-Scale Dairy Farm in Japan

In a large-scale dairy farm, it is important to take countermeasure of prevention against mastitis of dairy cows, and it is especially important to establish hygiene and risk management to prevent the emergence and spread of antibiotic-resistant bacteria. In this study, we have performed bacteriological testing of clinical and subclinical mastitis and investigation of antimicrobial resistance bacteria in a large-scale farm for 1 year. The bacteria isolated most frequently from 1,549 samples of 952 cow, including cows with recurring mastitis were Staphylococcus non-aureus (SNA) (27.6%), followed by Escherichia coli (18.9%), Klebsiella pneumoniae (12.3%). Although Staphylococcus aureus was isolated at 7.7% from milk sample, no methicillin-resistant S. aureus was found. The incidence of extended-spectrum β-lactamase (ESBL)-producing E. coli was 1.4% and ESBL-producing K. pneumoniae was 1.4% of all samples, even though third- and fourth-generation cephalosporins were not used for antimicrobial treatment of mastitis in this farm. Although these genotypes of ESBL-producing E. coli and K. pneumoniae were mainly composed of CTX-M-15 and TEM-1 and CTX-M-2 and TEM-116, respectively, there was no spread and persist of predominant clonal type. Appropriate farm management, such as segregation and culling of infected animals and monitors of trends in antimicrobial resistance among mastitis pathogens, may have contributed these results.

Reduced Antibacterial Drug Resistance and bla CTX-M β-Lactamase Gene Carriage in Cattle-Associated Escherichia coli at Low Temperatures, at Sites Dominated by Older Animals, and on Pastureland: Implications for Surveillance

Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g., CTX-M β-lactamase-positive Escherichia coli). We collected samples monthly between January 2017 and December 2018 on 53 dairy farms in South West England, along with data for 610 variables concerning antibacterial usage, management practices, and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin, streptomycin, and tetracycline in 2,754/4,145 (66%), 263/4,145 (6%), 1,475/4,145 (36%), and 2,874/4,145 (69%), respectively, of samples from fecally contaminated on-farm and near-farm sites. E. coli positive for bla _CTX-M were detected in 224/4,145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibacterial dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with higher odds of bla _CTX-M positivity. Low average monthly ambient temperature was associated with lower odds of bla _CTX-M E. coli positivity in samples and with lower odds of finding E. coli resistant to each of the four test antibacterials. This was in addition to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had higher odds of having E. coli resistant to each antibacterial, as well as E. coli positive for bla _CTX-M Samples collected on pastureland had lower odds of having E. coli resistant to amoxicillin or tetracycline, as well as lower odds of being positive for bla _CTX-M IMPORTANCE Antibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including tracking impacts of interventions aimed at reducing the prevalence of resistance. In this longitudinal survey of dairy farm antibacterial resistance, we showed that local temperature-as it changes over the course of a year-was associated with the prevalence of antibacterial-resistant E. coli We also showed that prevalence of resistant E. coli was lower on pastureland and higher in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm regarding the presence of samples containing resistant E. coli.

Surveillance of Extended-Spectrum β-Lactamase-, Cephalosporinase- and Carbapenemase-Producing Gram-Negative Bacteria in Raw Milk Filters and Healthy Dairy Cattle in Three Farms in Île-de-France, France

The aim of this work was to test a surveillance protocol able to detect extended-spectrum β-lactamase (ESBL)-, cephalosporinase (AmpC)- and carbapenemase (CP)-producing gram-negative bacteria in three conveniently chosen dairy farms with known prior occurrences of ESBL- and CP-producing strains. The protocol was applied monthly for a year. At each visit, 10 healthy lactating dairy cows were rectally swabbed, and raw milk filters (RMFs) were sampled in two of the three farms. Bacterial isolation was based on a first screening step with MacConkey agar supplemented with 1 mg/L cefotaxime and commercial carbapenem-supplemented media. We failed to detect CP-producing strains but showed that ESBL-Escherichia strains, found in one farm only (13 strains), were closely associated with multi-drug resistance (12 out of 13). The limited number of conveniently selected farms and the fact that RMFs could not be retrieved from one of them limit the validity of our findings. Still, our results illustrate that ESBL-status changes monthly based on fecal swabs and negative herds should be qualified as “unsuspected” as proposed by previous authors. Although surveillance of farm statuses based on RMF analysis could theoretically allow for a better sensitivity than individual swabs, we failed to illustrate it as both farms where RMFs could be retrieved were constantly negative. Determination of CP herd-level status based on RMFs and our surveillance protocol was hindered by the presence of intrinsically resistant bacteria or strains cumulating multiple non-CP resistance mechanisms which means our protocol is not specific enough for routine monitoring of CP in dairy farms.

The Effects of Feeding Waste Milk Containing Antimicrobial Residues on Dairy Calf Health

A number of studies have reported that there is a high prevalence of antimicrobial-resistant faecal bacteria excreted by dairy calves. Although faecal shedding is influenced by a variety of factors, such as the environment and calf age, feeding milk with antimicrobial residues contributes significantly to an increased prevalence of antimicrobial-resistant (AMR) bacteria, such as extended spectrum beta-lactamase (ESBL)-producing E. coli. As a follow-up to the European Food Safety Authority (EFSA) Scientific Opinion on the risk of AMR development in dairy calves published in January 2017, this review aims to illustrate more recent research in this area, focusing on the period 2016 to 2020. A total of 19 papers are reviewed here. The vast majority assess the commensal faecal bacteria, E. coli, isolated from dairy calves, in particular its antimicrobial-resistant forms such as ESBL-producing E. coli and AmpC-producing E. coli. The effect of waste milk feeding on the prevalence of pathogens such as Salmonella spp. has also been investigated. Current research findings include positive effects on daily liveweight gain and other advantages for calf health from feeding waste milk compared to milk replacer. However, the negative effects, such as the demonstrable selection for antimicrobial-resistant bacteria, the shift in the intestinal microbiome and the possible negative consequences that these could have on global public health, should always be taken into consideration.

Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms

Objectives

To explore the dynamics of faecal ESBL/AmpC shedding in dairy cattle and farmers, a study was conducted to examine changes in shedding by individual animals, as well as environmental exposure, and to study the association between antimicrobial use (AMU) and ESBL/AmpC shedding.

Methods

The study comprised a cross-sectional survey of 20 farms and a 1 year follow-up of 10 farms. Faecal samples were cultured by both direct inoculation on MacConkey agar + 1 mg/L cefotaxime (MC+) and enrichment in LB-broth + 1 mg/L cefotaxime with subsequent inoculation on MC+. Dust samples were collected using electrostatic dustfall collectors (EDCs). Human faecal samples were collected by the farmers. Presence of ESBL/AmpC genes was screened for by PCR and sequencing. Using mixed effects logistic regression, ORs were determined and population-attributable fractions (PAFs) calculated subsequently.

Results

In Phase 1, 8/20 farms were positive for ESBL/AmpC and, with 2 negative farms, were selected for Phase 2. Transient shedding of dominant allele variants was observed in the animals. EDCs and human faecal samples did not reflect what was observed in the animals. AMU was related to shedding of ESBLs in the next sampling moment [OR 14.6 (95% CI 3.0–80.0)] and the PAF of AMU was 0.36 (95% CI 0.08–0.77). Calves fed with colostrum from cows on dry-off therapy was not a risk factor [OR 1.7 (95% CI 0.7–4.9, P = 0.28)].

Conclusions

The presence of ESBL/AmpC could only be partly explained by AMU. No link was shown between shedding in cattle and humans or the environment. Interventions should focus on prevention of introduction.

Fecal Carriage and Whole-Genome Sequencing-Assisted Characterization of CMY-2 Beta-Lactamase-Producing Escherichia coli in Calves at Czech Dairy Cow Farm

The study aimed to monitor the fecal shedding of cefotaxime-resistant Escherichia coli (CREC) in a cohort of healthy calves on a dairy farm with documented antimicrobial usage and to characterize selected AmpC beta-lactamase-producing E. coli isolates. Fecal samples from 13 suckling calves (1-63 d of age; 113 samples in total) were repeatedly collected and cultivated on MacConkey agar with cefotaxime (2 mg/L). Resistant colonies were counted, and one colony obtained from the highest dilution of each fecal sample was identified by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. Susceptibility to antimicrobials and production of AmpC and extended-spectrum beta-lactamase (ESBL) were tested. No ESBL-producing E. coli was found, but representative AmpC-positive E. coli isolates were subjected to further typing and whole-genome sequencing (WGS) for the analysis of clonal relationships, resistance genes, virulence factors, and plasmid replicons. High amounts of CREC were detected in the feces of all 13 calves during the study. The number of CREC colonies varied from 1.0 log₁₀ to 8.0 log₁₀ colony-forming unit per gram. Drops in CREC density or its discontinued shedding were recorded at the end of the study period. A total of 82 (94%, n = 87) CREC isolates were confirmed as AmpC producers and all but one showed resistance to multiple antimicrobials. Twenty-nine selected AmpC-positive E. coli isolates belonged to 12 and 13 unique rep-PCR fingerprints and pulsed-field gel electrophoresis types, respectively, highlighting the variation in E. coli genotypes in individual calves. WGS of 10 selected isolates showed diverse antimicrobial resistance and virulence gene content and the presence of a bla_CMY-2 gene carried by an IncK2 plasmid. Clinically important multiresistant E. coli isolates belonging to emerging extraintestinal pathogenic E. coli ST69 and ST648 lineages were found. Our findings reinforce the urgency of efforts to prevent the spread of ESBL-/AmpC-producing bacteria in dairy cow farms.

A sensitive method for the recovery of Escherichia coli serogroup O55 including Shiga toxin-producing variants for potential use in outbreaks

AIM

Shiga toxin-producing Escherichia coli (STEC) cause bloody diarrhoea, kidney failure and occasionally death. However, identifying the source of infection caused by STEC other than serogroup O157 is hampered by the availability of sensitive methods for detecting these pathogens. In this study, we developed novel tools for detecting E. coli O55 that is potentially associated with human outbreaks.

METHODS AND RESULTS

Overall specificity of immuno-magnetic separation (IMS) beads coated with anti-O55 serum was good with exception of cross-reactivity with E. coli O22 and O23, which was eliminated using an O55-specific PCR. Limit of detection for E. coli O55 using O55-IMS beads in spiked cattle faeces was on average 50 CFU per ml (range 1-90), and improved to <10 CFU per ml using the O55-specific PCR, following IMS on samples enriched for 2 h with E. coli O55. Application of these tools to test cattle faeces collected on-farm allowed the isolation of O55:H19, which through whole genome sequencing was compared to STEC O55:H7 human outbreak strains.

CONCLUSION

These tools provide a sensitive method which could be used to screen samples for STEC O55, whether environmental or human clinical.

SIGNIFICANCE AND IMPACT OF THE STUDY

Several human outbreaks reported in England were caused by STEC O55:H7. Tools developed here could assist in identification of the environmental source for these isolates, which has not yet been established.

Punica granatum sarcotesta lectin (PgTeL) has antibacterial activity and synergistic effects with antibiotics against β-lactamase-producing Escherichia coli

The sarcotesta of Punica granatum fruit contains an antimicrobial lectin called PgTeL. In this work, we evaluated the antibacterial activity of PgTeL against five drug-resistant Escherichia coli isolates able to produce β-lactamases. Minimum inhibitory (MIC) and bactericidal (MBC) concentrations were determined by broth dilution. Morphometric and viability analyses were performed by flow cytometry, and ultrastructural changes were evaluated by scanning electron microscopy. Potential synergistic effects of PgTeL with antibiotics and anti-biofilm effect were also evaluated. PgTeL showed antibacterial activity against all isolates with MIC and MBC values ranging from 12.5 to 50.0 μg/mL and from 25.0 to 100.0 μg/mL, respectively. For most isolates, PgTeL postponed the growth start by at least ten hours. At the MIC, the lectin caused alterations in size, shape and structure of bacterial cells. The combination PgTeL-ceftazidime showed a synergistic effect for all isolates. Synergy was also detected with ampicillin (one isolate), carbenicillin (one isolate), cefotaxime (one isolate), cephalexin (four isolates) and cefuroxime (three isolates). PgTeL exhibited anti-biofilm activity against all isolates, causing ≥50% inhibition of biofilms at or above 6.25 μg/mL. The antibacterial effect of PgTeL and its synergy with antibiotics indicate that this fruit-derived molecule may have potential for future treatment of multidrug-resistant infections.

Prevalence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli in Dutch dairy herds

This study was conducted to assess: (1) a change in between-herd prevalence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-EC) between 2011 and 2013, the period during which the antimicrobial policy in animal husbandry in the Netherlands changed significantly, and (2) the prevalence of ESBL/AmpC-EC in individual calves, young stock, and dairy cows in the Netherlands. In 196 randomly selected conventional dairy herds, faecal samples were collected from calves (maximum n = 15), and randomly selected young stock (n = 5) and dairy cows (n = 15). Additionally, fresh faecal samples were collected from five different places on the floors where the dairy cows were housed. Samples were screened for E. coli with non-wild type susceptibility for cefotaxime and isolates were phenotypically confirmed as ESBL/AmpC-producing by disc diffusion, using cefotaxime and ceftazidime with and without clavulanic acid, and cefoxitin. Samples containing ESBL/AmpC-EC were examined semi-quantitatively. In 59.6% of the dairy herds one or more samples tested positive for ESBL/AmpC-EC. The between-herd prevalence based on floor samples in 2013 (18.0%) was significantly lower than the prevalence in 2011 based on comparable samples (32.7%). The individual animal prevalence of ESBL/AmpC-EC, with a minimum shedding level of 10³ cfu/g of faeces, was 19.3% in calves, 0.9% in young stock, and 0.8% in dairy cows. Although ESBL/AmpC-EC was found in the majority of dairy herds, the herd prevalence declined significantly between 2011 and 2013. Calves were found to have both, a much higher individual animal prevalence and a higher level of shedding than young stock and cows.

Extended-spectrum beta-lactamase-producing Escherichia coli in chickens from small-scale (backyard) poultry farms in Maiduguri, Nigeria

Aim: This study investigated the occurrence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in chickens from small-scale (backyard) commercial poultry farms in Maiduguri. Materials and Methods: A total of 96 cloacal swab samples were collected. This comprised of 24 samples each from broiler chicks, pullets, layers, and broilers (adults). The samples were examined for the presence of E. coli using conventional microbiological culture and biochemical tests. The pure E. coli isolates were screened for ESBL production by culturing onto BrillianceTM ESBL agar. Isolates that showed positive reactions with production of bluish or pinkish colonies were tested for susceptibilities against some selected β-lactam antibiotics which include cefotaxime (30 μg), ceftriaxone (30 μg), cefpodoxime (10 μg), aztreonam (30 μg), and ceftazidime (30 μg). Isolates that exhibited resistance to any two or three of the antibiotics were selected and confirmed by combination disk diffusion method with ceftazidime (30 μg) and cefotaxime (30 μg) alone and in combination with clavulanic acid (30 μg/10 μg). Results: The total occurrence of E. coli was 67.6% (65/96) with the highest occurrence of 83.3% (20/24) from broiler chicks and least detection of 54.2% (13/24) from layers. Of this, 32.0% were ESBL-producing E. coli with the highest detection rate from layers (38.5%) and least occurrence from pullets (26.7%). Conclusion: This study revealed the presence of ESBL-producing E. coli in chickens from small-scale commercial poultry farms in Maiduguri, thus indicating that chickens may serve as important reservoirs for the transmission of antimicrobial resistant pathogens to humans through the food chain.

Detection of extended-spectrum β-lactam, AmpC and carbapenem resistance in Enterobacteriaceae in beef cattle in Great Britain in 2015

AIMS

This study investigated the occurrence and genetic diversity of Enterobacteriaceae with extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase-mediated resistance in British beef cattle, and related risk factors.

METHODS AND RESULTS

Faecal samples (n = 776) were obtained from farms in England and Wales (n = 20) and Scotland (n = 20) in 2015. Isolates from selective agars were identified by MALDI ToF mass spectrometry. Selected isolates were characterized by multiplex PCR (bla_{CTX -M,} bla_{OXA ,} bla_SHV and bla_TEM genes), whole-genome sequencing (WGS), minimum inhibitory concentrations and pulsed-field gel electrophoresis. None of the faecal samples yielded carbapenem-resistant Escherichia coli. Ten (25%) of the farms tested positive for ESBL-producing CTX-M Enterobacteriaceae, 15 (37·5%) of the farms were positive for AmpC phenotype E. coli and none were positive for carbapenem-resistant E. coli. WGS showed a total of 30 different resistance genes associated with E. coli, Citrobacter and Serratia from ESBL agars, and colocation of resistance genes with bla_{CTX -M1} . Buying bulls and bringing in fattening cattle from another farm were identified as significant risk factors for positive samples harbouring CTX-M Enterobacteriaceae or AmpC phenotype E. coli respectively.

CONCLUSIONS

Beef cattle on a proportion of farms in GB carry ESBL-producing Enterobacteriaceae. Factors, such as operating as a closed herd, may have an important role in reducing introduction and transmission of resistant Enterobacteriaceae. The results indicate management factors may play an important role in impacting ESBL prevalence. In particular, further study would be valuable to understand the impact of maintaining a closed herd on reducing the introduction of resistant Enterobacteriaceae.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study showing the presence of ESBL-producing Enterobacteriaceae in British beef cattle.

Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure

The production of extended-spectrum β-lactamases (ESBLs) conferring resistance to new derivatives of β-lactams is a major public health threat if present in pathogenic Gram-negative bacteria. The objective of this study was to characterize ceftiofur (TIO)- or cefotaxime (FOX)-resistant Escherichia coli isolated from dairy cow manure. Twenty-four manure samples were collected from four farms and incubated under anaerobic conditions for 20 weeks at 4 °C or at 25 °C. A total of 37 TIO- or FOX-resistant E. coli were isolated from two of the four farms to determine their susceptibility to 14 antibiotics. Among the 37 resistant E. coli, 10 different serotypes were identified, with O8:H1 being the predominant serotype (n = 17). Five isolates belonged to each of serotypes O9:NM and O153:H42, respectively. All 37 cephalosporin resistant isolates were multi-resistant with the most prevalent resistance spectrum being amoxicillin-clavulanic acid-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-sulfisoxazole-tetracycline-trimethoprim-sulfamethoxazole. The genomes of 18 selected isolates were then sequenced and compared to 14 selected human pathogenic E. coli reference genomes obtained from public repositories using different bioinformatics approaches. As expected, all 18 sequenced isolates carried at least one β-lactamase bla gene: TEM-1, TEM-81, CTX-M115, CTX-M15, OXA-1, or CMY-2. Several other antibiotic resistance genes (ARGs) and virulence determinants were detected in the sequenced isolates and all of them harbored antimicrobial resistance plasmids belonging to classic Inc groups. Our results confirm the presence of diverse ESBL producing E. coli isolates in dairy cow manure stored for a short period of time. Such manure might constitute a reservoir of resistance and virulence genes for other bacteria that share the same environment.

Risk for the development of Antimicrobial Resistance (AMR) due to feeding of calves with milk containing residues of antibiotics

EFSA was requested to: 1) assess the risk for the development of antimicrobial resistance (AMR) due to feeding on farm of calves with colostrum potentially containing residues of antibiotics; 2) assess the risk for the development of AMR due to feeding on farm of calves with milk of cows treated during lactation with an antibiotic and milked during the withdrawal period, and 3) propose possible options to mitigate the risk for the development of AMR derived from such practices. Treatment of dairy cows during the dry period and during lactation is common in the EU Member States. Penicillins, alone or in combination with aminoglycosides, and cephalosporins are most commonly used. Residue levels of antimicrobials decrease with the length of the dry period. When the interval from the start of the drying-off treatment until calving is as long as or longer than the minimum specified in the Summary of Product Characteristics of the antimicrobial, faecal shedding of antimicrobial-resistant bacteria will not increase when calves are fed colostrum from treated cows. Milk from cows receiving antimicrobial treatment during lactation contains substantial residues during the treatment and withdrawal period. Consumption of such milk will lead to increased faecal shedding of antimicrobial-resistant bacteria by calves. A range of possible options exist for restricting the feeding of such milk to calves, which could be targeting the highest priority critically important antimicrobials. β-Lactamases can reduce the concentration of β-lactams which are the most frequently used antimicrobials in milking cows. Options to mitigate the presence of resistant bacteria in raw milk or colostrum are mainly based on thermal inactivation.