Cross-sectional study on prevalence and molecular characteristics of plasmid mediated ESBL/AmpC-producing Escherichia coli isolated from veal calves at slaughter

Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases

While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10-3 transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.

Prevalence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli in young calves on Dutch dairy farms

In young calves on dairy farms the animal prevalence of extended-spectrum and AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-EC) is significantly higher compared with the animal prevalence in young stock and dairy cows. Hitherto it was unknown at what age antimicrobial resistant bacteria appear for the first time in the gut of calves on dairy farms, and how long these infections persist. The aim of this study was to examine the prevalence of ESBL/AmpC-EC, the number of excreted ESBL/AmpC-EC (in cfu/g of feces), as well as the ESBL/AmpC genotypes in young dairy calves (0-21 d of age) and the variation of these parameters between calves of different ages. Next to this, the course of shedding ESBL/AmpC-EC during the first year in dairy calves was studied. In a cross-sectional study, fecal samples from 748 calves, from 0 to 88 d of age, on 188 Dutch dairy farms were collected. The prevalence of calves testing positive for ESBL/AmpC-EC in a phenotypic assay was determined for different age categories (per 2 d of age). Positive samples were subjected to a semiquantitative test to determine the numbers of ESBL/AmpC-EC per gram of feces and for a selection of ESBL/AmpC-EC isolates the ESBL/AmpC genotype was determined. Ten of the 188 farms were selected for a longitudinal study based on the presence of at least 1 female calf with ESBL/Amp-EC in the cross-sectional study. These farms were additionally visited 3 times with a 4-mo interval. All calves that were sampled in the cross-sectional study were, if still present, resampled during the follow-up visits. Results show that from the day of birth ESBL/AmpC-EC can be present in the gut of calves. The phenotypic prevalence of ESBL/AmpC-EC was 33.3% in 0- to 21-d-old calves and 28.4% in 22- to 88-d-old calves. The prevalence of ESBL/AmpC-EC positive calves varied per age category among calves up to 21 d of age: significant increases and decreases at an early age were shown. Results of the longitudinal study show that after 4, 8, and 12 mo the prevalence of ESBL/AmpC-EC positive calves dropped to 3.8% (2/53), 5.8% (3/52), and 2.0% (1/49), respectively. This indicates that early gut colonization in young calves with ESBL/AmpC-EC is transient and does not lead to long-term shedding of these bacteria.

Antimicrobial Use and Resistance in Surplus Dairy Calf Production Systems

Surplus calves, which consist predominately of male calves born on dairy farms, are an underrecognized source of antimicrobial-resistant (AMR) pathogens. Current production systems for surplus calves have important risk factors for the dissemination of pathogens, including the high degree of commingling during auction and transportation and sometimes inadequate care early in life. These circumstances contribute to an increased risk of respiratory and other infectious diseases, resulting in higher antimicrobial use (AMU) and the development of AMR. Several studies have shown that surplus calves harbor AMR genes and pathogens that are resistant to critically important antimicrobials. This is a potential concern as the resistant pathogens and genes can be shared between animal, human and environmental microbiomes. Although knowledge of AMU and AMR has grown substantially in dairy and beef cattle systems, comparable studies in surplus calves have been mostly neglected in North America. Therefore, the overall goal of this narrative review is to summarize the existing literature regarding AMU and AMR in surplus dairy calf production, highlight the management practices contributing to the increased AMU and the resulting AMR, and discuss potential strategies and barriers for improved antimicrobial stewardship in surplus calf production systems.

Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments

Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.

Antimicrobial Resistance in New Zealand-A One Health Perspective

Antimicrobial resistance (AMR) is an increasing global threat that affects human, animal and, often less acknowledged, environmental health. This complex issue requires a multisectoral One Health approach to address the interconnectedness of humans, animals and the natural environment. The prevalence of AMR in these reservoirs varies widely among countries and thus often requires a country-specific approach. In New Zealand (NZ), AMR and antimicrobial usage in humans are relatively well-monitored and -understood, with high human use of antimicrobials and the frequency of resistant pathogens increasing in hospitals and the community. In contrast, on average, NZ is a low user of antimicrobials in animal husbandry systems with low rates of AMR in food-producing animals. AMR in New Zealand’s environment is little understood, and the role of the natural environment in AMR transmission is unclear. Here, we aimed to provide a summary of the current knowledge on AMR in NZ, addressing all three components of the One Health triad with a particular focus on environmental AMR. We aimed to identify knowledge gaps to help develop research strategies, especially towards mitigating AMR in the environment, the often-neglected part of the One Health triad.

Preparing Male Dairy Calves for the Veal and Dairy Beef Industry

Surplus male dairy calves experience significant health challenges after arrival at the veal and dairy beef facilities. To curb these challenges, the engagement of multiple stakeholders is needed starting with improved care on some dairy farms and better management of transportation. Differing management strategies are also needed if calves arrive at veal and dairy beef facilities under poor condition.

Plasmid Replicon Diversity of Clinical Uropathogenic Escherichia coli Isolates from Riyadh, Saudi Arabia

The aim of this study was to identify and compare the plasmid replicons of clinical uropathogenic Escherichia coli (UPEC) isolates, involving extended spectrum β-lactamase (ESBL)-positive and ESBL-negative, E. coli ST131 and non-ST131 and various ST131 subclones. Plasmid replicon typing on 24 clinical UPEC isolates was carried out using polymerase chain reaction-based replicon typing. A statistical analysis was performed to assess the associations between plasmid replicon types and ESBL carriage, and to evaluate the link between ST131 isolates and high replicon carriage. Eight replicons, I1α, N2, Iγ, X1, FIIS, K, FIA, and FII were detected. The FII was the most common replicon identified here. ESBL-positive E. coli isolates were highly associated with I1α, N2, Iγ, X1, and FIIS replicons, while FIA was present only in ESBL-negative group. ST131 isolates were highly associated with I1α and N2 replicons compared to non-ST131. No link was found between replicon carriage and the number or type of ESBLs in E. coli isolates. The diversity observed in replicon patterns of our clinical E. coli isolates indicates that they might be originated from different sources. The presence of replicons reported previously in animal sources suggests a possible transfer of antimicrobial resistance between animal and human bacterial isolates.

Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves

Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying bla_ESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [bla_CTX-M-1 (64.7%), bla_CTX-M-14 (33.5%), or bla_CTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and bla_CTX-M-carrying plasmids, few bla_CTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of bla_CTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.

Phylogenetic Characterization and Multilocus Sequence Typing of Extended-Spectrum Beta Lactamase-Producing Escherichia coli from Food-Producing Animals, Beef, and Humans in Southwest Nigeria

Multidrug-resistant extended-spectrum beta lactamase (ESBL)-producing Escherichia coli strains are emerging globally in both humans and animals. Antimicrobial susceptibility testing and ESBL screening were performed on pure cultures of 216 E. coli isolates from human and animal fecal samples as well as beef. Polymerase chain reaction was performed for the detection of resistance genes. Representative isolates of ESBL-producing E. coli were randomly selected for multilocus sequence typing and pulsed field gel electrophoresis (PFGE). Sixty of the isolates were identified as ESBL producers, and seven resistance genes were amplified in them: TEM (61.7%), blaCTX-M-15 (51.7%), AAC-6-LB (43.3%), blaCTX-M-1 (38.3%), blaCTX-M-9 (33.3%), blaCTX-M-2 (21.7%), and SHV (11.7%); they were classified into four phylogroups: A (25%), B1 (45%), B2 (20%), and D (10%). Thirty of these isolates were clustered into 10 sequence types with ST131 being mostly prevalent. Six PFGE types were discovered, each of which was shared by isolates from different subjects and had the same phylogroups and resistance gene profiles. There was a dissemination of PFGE types across various groups among humans, animals, and beef. This underlines the fact that the spread of ESBL E. coli could be from humans to animals, from animals to humans, as well as across animal species.

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world

Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.

Rapid identification of respiratory bacterial pathogens from bronchoalveolar lavage fluid in cattle by MALDI-TOF MS

Respiratory tract infections are a major health problem and indication for antimicrobial use in cattle and in humans. Currently, most antimicrobial treatments are initiated without microbiological results, holding the risk of inappropriate first intention treatment. The main reason for this empirical treatment is the long turnaround time between sampling and availability of identification and susceptibility results. Therefore the objective of the present study was to develop a rapid identification procedure for pathogenic respiratory bacteria in bronchoalveolar lavage fluid (BALf) samples from cattle by MALDI-TOF MS, omitting the cultivation step on agar plates to reduce the turnaround time between sampling and identification of pathogens. The effects of two different liquid growth media and various concentrations of bacitracin were determined to allow optimal growth of Pasteurellaceae and minimise contamination. The best procedure was validated on 100 clinical BALf samples from cattle with conventional bacterial culture as reference test. A correct identification was obtained in 73% of the samples, with 59.1% sensitivity (Se) (47.2–71.0%) and 100% specificity (Sp) (100–100%) after only 6 hours of incubation. For pure and dominant culture samples, the procedure was able to correctly identify 79.2% of the pathogens, with a sensitivity (Se) of 60.5% (45.0–76.1%) and specificity (Sp) of 100% (100–100%). In mixed culture samples, containing ≥2 clinically relevant pathogens, one pathogen could be correctly identified in 57% of the samples with 57.1% Se (38.8–75.5%) and 100% Sp (100–100%). In conclusion, MALDI-TOF MS is a promising tool for rapid pathogen identification in BALf. This new technique drastically reduces turnaround time and may be a valuable decision support tool to rationalize antimicrobial use.

Short communication: Whole-genome sequence analysis of 4 fecal blaCMY-2-producing Escherichia coli isolates from Holstein dairy calves

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 4 fecal bla_CMY-2-producing Escherichia coli isolated from Holstein dairy calves on the same farm using whole-genome sequencing. Genomic analysis revealed that 3 of the 4 isolates shared similar genetic features, including sequence type (ST), serotype, plasmid characteristics, insertion ST, and virulence genes. In addition to genes encoding for complex multidrug resistance efflux systems, all 4 isolates were carriers of genes conferring resistance to β-lactams (bla_CMY-2, bla_TEM-1B), tetracyclines (tetA, tetB, tetD), aminoglycosides [aadA1, aph(3")-lb, aph(6)-ld], sulfonamides (sul2), and trimethoprim (dfrA1). We also detected 4 incompatibility plasmid groups: Inc.F, Inc.N, Inc.I, and Inc.Q. A novel ST showing a new purA and mdh allelic combination was found. The 4 isolates were likely enterotoxigenic pathotypes of E. coli, based on serotype and presence of the plasmid Inc.FII(pCoo). This study provides information for comparative genomic analysis of AMR genes and mobile genetic elements. This analysis could give some explanation to the multidrug resistance characteristics of bacteria colonizing the intestinal tract of dairy calves in the first few weeks of life.

Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae

Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.

Antimicrobial Usages and Antimicrobial Resistance in Commensal Escherichia coli From Veal Calves in France: Evolution During the Fattening Process

Extended-Spectrum-Cephalosporin (ESC)-resistant Enterobacteriaceae have widely spread in all settings worldwide. In animals, Extended-Spectrum Beta-Lactamase (ESBL) producers have been frequently identified in veal calves. The objectives of this study were to investigate the trends in the ESBL load and antimicrobial resistance (AMR) proportions, and antimicrobial usages (AMU) in veal calves during the fattening process. Ten fattening farms were selected and 50 animals per farm were sampled. AMR was assessed in bacteria from the dominant flora (collected on non-selective MacConckey agar) and in ESBL/AmpC-carrying bacteria from the subdominant flora (selected on ChromID ESBL selective plates) upon arrival and 5-6 months later before slaughter. The number and types of treatments during fattening were also collected. Rates of ESBL-producing E. coli from the subdominant flora significantly decreased in all farms (arrival: 67.7%; departure: 20.4%) whereas rates of multidrug-resistant E. coli from the dominant flora have significantly increased (arrival: 60.2%; departure: 67.2%; p = 0.025). CTX-M-1 was the most frequently identified ESBL enzyme (arrival: 59.3%; departure: 52.0%). The plasmid-mediated mcr-1 gene was also identified occasionally. In parallel, levels of resistances to non-critically important antimicrobials were already high upon arrival but have still further increased over time until slaughter. Our study also highlighted that if only ESBL-producing isolates were monitored, it might have led to a partial (and partly false) picture of AMR rates globally decreasing during the fattening period. The mean number of antimicrobial treatments per calf (NTPC) was 8.75 but no association between AMU and AMR was evidenced. Most ESBL producers were clonally unrelated suggesting multiple sources and not cross-contaminations among calves during transportation. Feeding milk containing antimicrobial residues to veal calves is hypothesized to explain the high ESBL loads in animals at the entrance on farms.

Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis

Background

In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.

Objectives

To quantify molecular similarities between different reservoirs as a first step towards risk attribution.

Methods

Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising >27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).

Results

Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human-animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7-0.8), while similarities to livestock or food reservoirs were lower (0.3-0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.

Conclusions

Our 'One Health' approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.

Diversity of Plasmids and Genes Encoding Resistance to Extended Spectrum Cephalosporins in Commensal Escherichia coli From Dutch Livestock in 2007-2017

Extended-spectrum β-lactamase (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) genes confer resistance to extended spectrum cephalosporin’s. The spread of these genes is mostly facilitated by plasmid-mediated horizontal transfer. National surveillance activities to detect ESBL/pAmpC-producers in commensal bacteria from livestock are in place in the Netherlands since several years. This study aimed at reporting gene and plasmid diversity of commensal ESBL/pAmpC-producing Escherichia coli isolated from healthy animals during surveillance activities between 2007 and 2017. A collection of 2304 extended-spectrum cephalosporin-resistant (ESC-R) E. coli isolated from feces of broilers, dairy cattle, slaughter pigs, turkeys, ducks, and veal calves was investigated and ESBL/pAmpC genes were determined. Gene location of a selection of 473 E. coli isolates was determined and typing of plasmids linked to the ESBL/pAmpC genes was performed. Twenty-two different ESBL/pAmpC genes were identified with bla_CTX-M-1 being the most prevalent gene in livestock (43.7%), followed by bla_{CMY -2} and bla_{SHV -12}, independent of the animal source. Prevalence of typically human associated bla_CTX-M-15 was highest in cattle. Less than 10% E. coli isolates owed their ESC-R phenotype to promoter mutations of the chromosomal ampC gene. Majority (92%) of ESBL/pAmpC genes analyzed were plasmid located, with IncI1α being the most represented plasmid family in isolates from all animals, followed by IncF (veal calves, dairy cattle and slaughter pigs), IncK (broilers and laying hens), IncX1 in broilers, and emerging IncX3 in broilers and dairy cattle. Prevalence and molecular diversity of ESC-R E. coli isolated from livestock over an 11-year period revealed a composite scenario of gene-plasmid combinations.

Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Dairy Farm Environments: A New Zealand Perspective

Antimicrobial resistance (AMR) is a global issue for both human and animal health. Infections caused by antimicrobial-resistant bacteria present treatment option challenges and are often associated with heightened severity of infection. Antimicrobial use (AMU) in human and animal health is a main driver for the development of antimicrobial-resistant bacteria. Increasing levels of AMU and the development and spread of AMR in food-producing animals, especially in poultry and swine production, has been identified as a food safety risk, but dairy production systems have been less studied. A number of farm management practices may impact on animal disease and as a result can influence the use of antimicrobials and subsequently AMR prevalence. However, this relationship is multifactorial and complex. Several AMR transmission pathways between dairy cattle, the environment, and humans have been proposed, including contact with manure-contaminated pastures, direct contact, or through the food chain from contaminated animal-derived products. The World Health Organization has defined a priority list for selected bacterial pathogens of concern to human health according to 10 criteria relating to health and AMR. This list includes human pathogens such as the extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), which can be associated with dairy cattle, their environment, as well as animal-derived food products. ESBL-E represent a potential risk to human and animal health and an emerging food safety concern. This review addresses two areas; first, the current understanding of the role of dairy farming in the prevalence and spread of AMR is considered, highlighting research gaps using ESBL-E as an exemplar; and second, a New Zealand perspective is taken to examine how farm management practices may contribute to on-farm AMU and AMR in dairy cattle.

Antimicrobial-Resistant E. coli from Surface Waters in Southwest Ontario Dairy Farms

Untreated surface waters can be contaminated with a variety of bacteria, including , some of which can be pathogenic for both humans and animals. Therefore, such waters need to be treated before their use in dairy operations to mitigate risks to dairy cow health and milk safety. To understand the molecular ecology of , this study aimed to assess antimicrobial resistance (AMR) in recovered from untreated surface water sources of dairy farms. Untreated surface water samples ( = 240) from 15 dairy farms were collected and processed to isolate . A total of 234 isolates were obtained and further characterized for their serotypes and antimicrobial susceptibility. Of the 234 isolates, 71.4% were pan-susceptible, 23.5% were resistant to one or two antimicrobial classes, and 5.1% were resistant to three or more antimicrobial classes. Whole genome sequence analysis of 11 selected multidrug-resistant isolates revealed AMR genes including and that confer resistance to the critically important extended-spectrum cephalosporins, as well as a variety of plasmids (mainly of the replicon type) and class 1 integrons. Phylogenetic and comparative genome analysis revealed a genetic relationship between some of the sequenced and Shiga toxin-producing O157:H7 (STEC), which warrants further investigation. This study shows that untreated surface water sources contain antimicrobial-resistant which may serve as a reservoir of AMR that could be disseminated through horizontal gene transfer. This is another reason why effective water treatment before usage should be routinely done on dairy farm operations.

Molecular Tools To Study Preharvest Food Safety Challenges

Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.

Plasmids of Distinct IncK Lineages Show Compatible Phenotypes

IncK plasmids are some of the main carriers of bla_CTX-M-14 and bla_CMY-2 genes and show high similarity to other plasmids belonging to the I complex, including IncB/O plasmids. Here, we studied the phylogenetic relationship of 37 newly sequenced IncK and IncB/O plasmids. We show that IncK plasmids can be divided into two compatible lineages named IncK1 and IncK2.

Nosocomial Intravascular Catheter Infections with Extended-spectrum Beta-lactamase-producing Escherichia coli in Calves after Strain Introduction from a Commercial Herd

An outbreak of intravascular catheter-related infections by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in calves in an animal teaching hospital is reported. Pulsed-field gel electrophoresis was used for strain typing to determine the origin and dissemination of these strains. All 19 strains harboured the blaCTX-M-14, and six strains also overexpressed their chromosomal AmpC gene. Evidence on the introduction of the strain from a beef herd, experiencing neonatal diarrhoea and increased mortality, to the clinic through admission of diarrhoeic calves was provided. Strains isolated from phlebitis cases from other herds up to 5 months later showed a high similarity with the initial strain, suggesting that the strain had become nosocomial. The catheter infections with ESBL/AmpC-producing E. coli resulted in a prolonged hospitalization, increased anti-microbial use and mortality. This report points towards the potential dangers of the emergence of ESBL/AmpC-producing bacteria in susceptible food animals and warns farmers and veterinarians for the facility by which they are introduced into another environment.

Chromosome-Based blaOXA-48-Like Variants in Shewanella Species Isolates from Food-Producing Animals, Fish, and the Aquatic Environment

Carbapenems are considered last-resort antibiotics in health care. Increasing reports of carbapenemase-producing bacteria in food-producing animals and in the environment indicate the importance of this phenomenon in public health. Surveillance for carbapenemase genes and carbapenemase-producing bacteria in Dutch food-producing animals, environmental freshwater, and imported ornamental fish revealed several chromosome-based bla_OXA-48-like variants in Shewanella spp., including two new alleles, bla_OXA-514 and bla_OXA-515 Carbapenemase genes were not associated with mobile genetic elements or Enterobacteriaceae.

Dominant plasmids carrying extended-spectrum β-lactamases blaCTX-M genes in genetically diverse Escherichia coli from slaughterhouse and urban wastewaters

Wastewater treatment plants (WWTP) receiving effluents from food-producing animals and humans may contribute to the spread of extended-spectrum β-lactamases (ESBL)-carrying plasmids. This study was designed to investigate extended-spectrum cephalosporin resistant Escherichia coli strains, CTX-M distributions and the genetic lineage of bla_CTX-M -carrying plasmids from urban and slaughterhouse wastewaters. The level of extended-spectrum cephalosporin-resistant E. coli in slaughterhouse wastewater entering the WWTP was negligible compared with that of urban wastewater. The bla_CTX-M-1 gene was predominant in slaughterhouse wastewater whereas diverse bla_CTX-M genes were encountered in urban wastewater and WWTP outlet. Characterization of the main CTX-M-producing E. coli isolates by antibiotic resistance phenotyping, genotyping and typing of plasmids carrying bla_CTX-M genes revealed that bla_CTX-M-1 and bla_CTX-M-15 genes were harboured by the predominant bla_CTX-M-1 IncI1/ST3 and bla_CTX-M-15 F31:A4:B1 plasmids, which were recovered from unrelated E. coli genotypes in both slaughterhouse and urban wastewaters. This study highlighted the spread of predominant bla_CTX-M-1 and bla_CTX-M-15 plasmid lineages in diverse E. coli genotypes from humans and food-producing animals, their mixing in WWTP and final release into the aquatic environment. This could have a serious negative impact on public health and requires further evaluation.

Prevalence, risk factors and molecular epidemiology of highly resistant gram negative rods in hospitalized patients in the Dutch region Kennemerland

Background

This paper describes (1) the Highly Resistant Gram Negative Rod (HR-GNR) prevalence rate, (2) their genotypes, acquired resistance genes and (3) associated risk factors of HR-GNR colonization among the hospitalized population in the Dutch region Kennemerland.

Methods

Between 1 October 2013 and 31 March 2014, cross-sectional prevalence measurements were performed in three regional hospitals as part of each hospitals infection control program. Rectal swabs were analyzed at the Regional Public Health Laboratory Kennemerland by direct culturing. Genotypes and acquired resistance genes of positive isolates were determined using Whole Genome Sequencing with the MiSeq instrument (Illumina). Association between several independent variables and HR-GNR positivity was examined using logistic regression models.

Results

Out of 427 patients, 24 HR-GNR positive isolates were recovered from 22 patients, resulting in a regional HR-GNR colonization prevalence (95 % CI) of 5.2 % (3.6–7.9). Of these 22 positive patients, 15 were Extended Spectrum Beta-Lactamase (ESBL) positive (3.5 % (2.1–5.7)), 7 patients were positive for a Fluoroquinolones and Aminoglycosides (Q&A) resistant Enterobacteriaceae (1.6 % (0.8–3.3)) and from one patient (0.2 % (0–1.3)) a Stenotrophomonas maltophilia resistant towards co-trimoxazole was isolated. No carbapenemase producing Enterobacteriaceae (CPE), multi-resistant Acinetobacter species or multi-resistant Pseudomonas aeruginosa were isolated. The ESBL genes found were bla_CTX-M-1 (n = 4, 25.0 %), bla_CTX-M-15 (n = 3, 18.8 %), bla_CTX-M-27 (n = 2, 12.5 %), bla_CTX-M-14b (n = 2, 12.5 %), bla_CTX-M-9 (n = 2, 12.5 %), bla_CTX-M-14 (n = 1, 6.3 %), bla_CTX-M-3 (n = 1, 6.3 %), bla_SHV-11 (n = 1, 6.3 %) and bla_SHV-12 (n = 1, 6.3 %). Being known HR-GNR positive in the past was the only significant associated risk factor for HR-GNR positivity, odds ratio (95 % CI): 7.32 (1.82–29.35), p-value = 0.005.

Conclusions

Similar ESBL prevalence rates and genotypes (3.5 %) were found in comparison to other Dutch studies. When previously HR-GNR positive patients are readmitted, they should be screened for HR-GNR colonization since colonization with GR-GNRs could be prolonged. We recommend for future studies to include all defined HR-GNRs in addition to ESBLs in prevalence studies, in order to obtain a more comprehensive overview of colonization with HR-GNRs.

Emerging issues in antimicrobial resistance of bacteria from food-producing animals

During the last decade, antimicrobial resistance in bacteria from food-producing animals has become a major research topic. In this review, different emerging resistance properties related to bacteria of food-producing animals are highlighted. These include: extended-spectrum β-lactamase-producing Enterobacteriaceae; carbapenemase-producing bacteria; bovine respiratory tract pathogens, such as Pasteurella multocida and Mannheimia haemolytica, which harbor the multiresistance mediating integrative and conjugative element ICEPmu1; Gram-positive and Gram-negative bacteria that carry the multiresistance gene cfr; and the occurrence of numerous novel antimicrobial resistance genes in livestock-associated methicillin-resistant Staphylococcus aureus. The emergence of the aforementioned resistance properties is mainly based on the exchange of mobile genetic elements that carry the respective resistance genes.

Providencia stuartii Isolates from Greece: Co-Carriage of Cephalosporin (blaSHV-5, blaVEB-1), Carbapenem (blaVIM-1), and Aminoglycoside (rmtB) Resistance Determinants by a Multidrug-Resistant Outbreak Clone

Providencia stuartii has emerged as an important nosocomial pathogen. We describe an outbreak due to a multidrug-resistant strain over a 4-month period in a critical care unit in Athens. Molecular typing revealed each of the isolates to be clonally related with coresistance to cephalosporins, carbapenems, aminoglycosides, and quinolones. Each isolate contained a 220-kb multi-replicon (IncA/C and IncR) conjugative plasmid encoding TEM-1, SHV-5, VEB-1, and VIM-1 β-lactamases and the 16S rDNA methylase RmtB. Antimicrobial therapy was unsuccessful in 3 of 6 cases, and resistance was readily transmissible to susceptible strains of Escherichia coli by transformation and conjugation. This highlights the clinical importance of P. stuartii and its ability to disseminate critical resistance determinants to other bacterial pathogens.

Molecular characteristics of extended-spectrum cephalosporin-resistant Enterobacteriaceae from humans in the community

OBJECTIVE

To investigate the molecular characteristics of extended-spectrum cephalosporin (ESC)-resistant Enterobacteriaceae collected during a cross-sectional study examining the prevalence and risk factors for faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in humans living in areas with high or low broiler density.

METHODS

ESC-resistant Enterobacteriaceae were identified by combination disc-diffusion test. ESBL/AmpC/carbapenemase genes were analysed using PCR and sequencing. For E. coli, phylogenetic groups and MLST were determined. Plasmids were characterized by transformation and PCR-based replicon typing. Subtyping of plasmids was done by plasmid multilocus sequence typing.

RESULTS

175 ESC-resistant Enterobacteriaceae were cultured from 165/1,033 individuals. The isolates were Escherichia coli(n=65), Citrobacter freundii (n=52), Enterobacter cloacae (n=38), Morganella morganii (n=5), Enterobacter aerogenes (n=4), Klebsiella pneumoniae (n=3), Hafnia alvei (n=2), Shigella spp. (n=2), Citrobacter amalonaticus (n=1), Escherichia hermannii (n=1), Kluyvera cryocrescens (n=1), and Pantoea agglomerans (n=1). The following ESBL genes were recovered in 55 isolates originating from 49 of 1,033 (4.7 %) persons: blaCTX-M-1 (n=17), blaCTX-M-15 (n=16), blaCTX-M-14 (n=9), blaCTX-M-2 (n=3), blaCTX-M-3 (n=2), blaCTX-M-24 (n=2), blaCTX-M-27 (n=1), blaCTX-M-32 (n=1), blaSHV-12 (n=2), blaSHV-65 (n=1) and blaTEM-52 (n=1). Plasmidic AmpC (pAmpC) genes were discovered in 6 out of 1,033 (0.6 %) persons. One person carried two different E. coli isolates, one with blaCTX-M-1 and the other with blaCMY-2 and therefore the prevalence of persons carrying Enterobacteriaceae harboring ESBL and/or pAmpC genes was 5.2 %. In eight E. coli isolates the AmpC phenotype was caused by mutations in the AmpC promoter region. No carbapenemase genes were identified. A large variety of E. coli genotypes was found, ST131 and ST10 being most common.

CONCLUSIONS

ESBL/pAmpC genes resembled those from patients in Dutch hospitals, indicating that healthy humans form a reservoir for transmission of these determinants to vulnerable people. The role of poultry in the transmission to humans in the community remains to be elucidated.

Extended-spectrum and AmpC β-lactamase-producing Escherichia coli in broilers and people living and/or working on broiler farms: prevalence, risk factors and molecular characteristics

OBJECTIVES

The objectives of this study were to: estimate the prevalence of extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase-producing Escherichia coli carriage among broiler farmers, their family members and employees; identify and quantify risk factors for carriage, with an emphasis on contact with live broilers; and compare isolates from humans and broilers within farms with respect to molecular characteristics to gain insight into transmission routes.

METHODS

A cross-sectional prevalence study was conducted on 50 randomly selected Dutch broiler farms. Cloacal swabs were taken from 20 randomly chosen broilers. Faecal swabs were returned by 141 individuals living and/or working on 47 farms. ESBL/AmpC-producing E. coli were isolated and, for selected isolates, phylogenetic groups, plasmids and sequence types were determined. Questionnaires were used for risk factor analysis.

RESULTS

All sampled farms were positive, with 96.4% positive pooled broiler samples. The human prevalence was 19.1%, with 14.3% and 27.1% among individuals having a low and a high degree of contact with live broilers, respectively. Five pairs of human-broiler isolates had identical genes, plasmid families and E. coli sequence types, showing clonal transmission. Furthermore, similar ESBL/AmpC genes on the same plasmid families in different E. coli sequence types in humans and broilers hinted at horizontal gene transfer.

CONCLUSIONS

The prevalence among people on broiler farms was higher than in previous studies involving patients and the general population. Furthermore, an increased risk of carriage was shown among individuals having a high degree of contact with live broilers. The (relative) contribution of transmission routes that might play a role in the dissemination of ESBL/AmpC-encoding resistance genes to humans on broiler farms should be pursued in future studies.

Comparative prevalence and characterization of ESBL-producing Enterobacteriaceae in dominant versus subdominant enteric flora in veal calves at slaughterhouse, France

Food-producing animals have become a growing reservoir of Extended-Spectrum Beta-Lactamase (ESBL)-producing bacteria. In cattle, veal calves are exposed to high amounts of antibiotics but ESBL prevalence data are still limited compared to other food sectors such as poultry production. Based on the investigation of 491 veal calves from different slaughtering batches at 12 abattoirs, this study shows a prevalence of 29.4% of ESBL producers in the faecal flora of veal calves in France in 2012. A variety of blaCTX-M genes was found, reflecting possible diverse pathways of dissemination in cattle. Another major conclusion is the comparison of the ESBL prevalence in the dominant versus sub-dominant Escherichia coli population of the same calves (1% and 29.4%, respectively). Also, the ESBL E. coli clones in the sub-dominant flora mostly differed from the non-ESBL dominant E. coli clones of the same calves. Of note, the distribution of blaCTX-M genes and E. coli phylogroups were similar to the ones previously found in ESBL E. coli clones from diseased calves. The hypothesis that ESBL genes may distribute more abundantly in certain backgrounds of E. coli was also discussed. In all, as recently reported in the Netherlands, these results strongly suggest a recent increase in the prevalence of ESBL carriage in French veal calves, which should be considered one of the major ESBL reservoirs in food animals.

Characteristics of cefotaxime-resistant Escherichia coli from wild birds in the Netherlands

Cloacal swabs from carcasses of Dutch wild birds obtained in 2010 and 2011 were selectively cultured on media with cefotaxime to screen for the presence of extended-spectrum β-lactamase (ESBL)/AmpC-producing Escherichia coli. Subsequently, all cefotaxime-resistant E. coli isolates were tested by broth microdilution and microarray. The presence of ESBL/AmpC and coexisting plasmid-mediated quinolone resistance (PMQR) genes was confirmed by PCR and sequencing. To determine the size of plasmids and the location of ESBL and PMQR genes, S1 pulsed-field gel electrophoresis (PFGE) was performed on transformants, followed by Southern blot hybridization. The study included 414 cloacal swabs originating from 55 different bird species. Cefotaxime-resistant E. coli isolates were identified in 65 birds (15.7%) from 21 different species. In all, 65 cefotaxime-resistant E. coli ESBL/AmpC genes were detected, mainly comprising variants of blaCTX-M and blaCMY-2. Furthermore, PMQR genes [aac(6')-lb-cr, qnrB1, and qnrS1] coincided in seven cefotaxime-resistant E. coli isolates. Overall, replicon typing of the ESBL/AmpC-carrying plasmids demonstrated the predominant presence of IncI1 (n = 31) and variants of IncF (n = 18). Our results indicate a wide dissemination of ESBL and AmpC genes in wild birds from The Netherlands, especially among aquatic-associated species (waterfowl, gulls, and waders). The identified genes and plasmids reflect the genes found predominantly in livestock animals as well as in humans.

High prevalence of fecal carriage of extended spectrum β-lactamase/AmpC-producing Enterobacteriaceae in cats and dogs

Extended-spectrum-β-lactamase (ESBL)/AmpC producing Enterobacteriaceae have been reported worldwide amongst isolates obtained from humans, food-producing animals, companion animals, and environmental sources. However, data on prevalence of fecal carriage of ESBL/AmpC producing Enterobacteriaceae in healthy companion animals is limited. This pilot study describes the prevalence of ESBL/AmpC encoding genes in healthy cats and dogs, and cats and dogs with diarrhea. Twenty fecal samples of each group were cultured on MacConkey agar supplemented with 1 mg/L cefotaxime and in LB-enrichment broth supplemented with 1 mg/L cefotaxime, which was subsequently inoculated on MacConkey agar supplemented with 1 mg/L cefotaxime. ESBL/AmpC genes were identified using the Check-Points CT103 micro array kit and subsequently by sequencing analysis. Chromosomal ampC promoter mutations were detected by PCR and sequencing analysis. From the healthy and diarrheic dogs, respectively 45 and 55% were positive for Escherichia coli with reduced susceptibility for cefotaxime. From the healthy and diarrheic cats, the estimated prevalence was respectively 0 and 25%. One diarrheic cat was positive for both reduced susceptible E.coli and Proteus mirabilis. The ESBL/AmpC genes found in this study were mainly bla_CTX-M-1, but also bla_CTX-M-14, bla_CTX-M-15, bla_{TEM-52-StPaul}, bla_SHV-12, and bla_CMY-2 were detected. This pilot study showed that the prevalence of ESBL/AmpC producing Enterobacteriaceae in healthy and diarrheic dogs, and diarrheic cats was relatively high. Furthermore, the genes found were similar to those found in isolates of both human and food-producing animal origin. However, since the size of this study was relatively small, extrapolation of the data to the general population of cats and dogs should be done with great care.