Role of calf-adapted Escherichia coli in maintenance of antimicrobial drug resistance in dairy calves

The effect of Enterococcus faecium M74 feed additive on the extended-spectrum beta-lactamases/AmpC-positive Escherichia coli faecal counts in pre-weaned dairy calves

The increasing occurrence of extended-spectrum beta-lactamases and/or AmpC-positive Escherichia coli among different species of food producing animals poses a threat to public health. The animal gut plays a key role in the development of antibiotic resistant bacteria, allowing the selection, multiplication and subsequent contamination of the farm environment. However, applicable procedures for reducing such bacteria on farms are currently unavailable. The present study was aimed to determine whether a probiotic administration to new-born dairy calves would reduce faecal shedding of extended-spectrum beta-lactamases and/or AmpC-positive Escherichia coli during the pre-weaning period. Ten randomly assigned new-born Holstein calves on a dairy farm with recent evidence of high occurrence of AmpC-positive Escherichia coli among calves were treated by a probiotic mix within 12 h after birth. Nine control calves were not treated. Faecal samples were collected from each calf daily on days 2 through 5, and then on days 7, 10, and 14. The faecal samples were cultured, and the mean numbers of cefotaxime-resistant Escherichia coli and confirmed enteroaggregative Escherichia coli were compared between the two groups. Results suggested that the Enterococcus faecium probiotic treatment (Enterococcus faecium M74, NCIMB 11181) of new-born calves did not reduce the enteroaggregative Escherichia coli counts in their faeces. There was no significant difference in the shedding of enteroaggregative Escherichia coli between the probiotic-treated and control calves throughout the two-week study period.

Prevalence and Transmission of Antimicrobial Resistance in a Vertically Integrated Veal Calf Production System

Transmission of antimicrobial resistance (AMR) from animal production systems to humans through the food supply is a public health concern. Currently, little is known about the prevalence of AMR among veal calves in the United States. Therefore, the objective of this prospective cohort study was to estimate the prevalence of AMR and multidrug resistance (MDR) among Escherichia coli within a vertically integrated production system. In addition, this study aimed to identify genes associated with phenotypic resistance to third- and fourth-generation cephalosporins (3GC and 4GC). Calves from four veal cohorts were randomly sampled resulting in a total of 166 farm fecal samples, 159 harvest fecal swabs, 164 preevisceration swabs, and 122 final carcass swabs. The prevalence of MDR among random-pick E. coli isolates recovered from the respective samples was 97% (161/166), 35% (55/159), 61% (51/84), and 24% (5/21). A selective isolation protocol found cefotaxime (a 3GC)-resistant isolates in 91% (127/140) of farm fecal samples, 34% (55/164) of preevisceration swabs, and 19% (23/122) of final carcass swabs tested. Isolates resistant to cefepime, a 4GC, were found among 24% (33/140), 6.7% (11/164), and 0.8% (1/122) of the same, respective samples. Isolates resistant to ciprofloxacin, a fluoroquinolone, were recovered from 75% (73/98) of farm fecal samples, 23% (38/164) of preevisceration swabs, and 6.6% (8/122) of final carcass swabs. The bla_CMY-2 and bla_CTX-M resistance genes were found in 89% (93/105) and 100% (42/42) of tested subsets of 3GC- and 4GC-resistant isolates, respectively. Pulsed-field gel electrophoresis (PFGE) analysis conducted on 3GC- and fluoroquinolone-resistant isolates showed three indistinguishable PFGE patterns from cefotaxime-resistant isolates recovered at farm and from two preevisceration carcass swabs. Although the prevalence of resistance declined between initial farm fecal samples and final carcass swabs, resistant bacteria recovered from carcasses illustrate the potential transmission of AMR to the human food supply.

Concerning Increase in Antimicrobial Resistance in Shiga Toxin-Producing Escherichia coli Isolated from Young Animals during 1980-2016

This study was conducted in order to assess the antimicrobial resistance patterns of E. coli isolated from young animals affected between 1980 and 2016. The selected isolates for this study (n=175) carried stx₁/stx₂ genes and the most prevalent type of pathogenic E. coli found belonged to serogroup O101, antigen (K99)–F41 positive. All STEC-positive isolates were tested for susceptibility to 11 antimicrobials. Multidrug resistance (MDR) increased from 11% during the 1980s to 40% between 2000 and 2016. Resistance to tetracycline and streptomycin was the most frequent co-resistance phenotype (37%). Co-resistance to tetracycline and sulfonamide was found in 21% of E. coli isolates, while the MDR pattern to tetracycline, sulfonamide, and streptomycin was observed in 12% of the strains tested. Only 8% of isolates were co-resistant to tetracycline, ampicillin, streptomycin, and sulfonamide. The most common resistance genes found were those encoding for tetracycline, sulphonamides, and streptomycin, with 54% (n=95) of the tested isolates containing at least one of the genes encoding tetracycline resistance. A total of 87% of E. coli that tested positive for tetracycline (tetA, tetB, and tetC) and sulphonamide (sul1) resistance genes were isolated between 2000 and 2016. A large number of isolates (n=21) carried int1 and a nucleotide sequence analysis revealed that all class 1 integron gene cassettes carried sul1, tet, and dfrA1 resistance genes. An increase was observed in the level of resistance to antimicrobials in Romania, highlighting the urgent need for a surveillance and prevention system for antimicrobial resistance in livestock in Eastern Europe.

Short communication: Extended-spectrum cephalosporin-resistant Escherichia coli in colostrum from New Brunswick, Canada, dairy cows harbor blaCMY-2 and blaTEM resistance genes

Dairy calves are colonized shortly after birth by multidrug resistant (MDR) bacteria, including Escherichia coli. The role of dairy colostrum fed to calves as a potential source of MDR bacteria resistance genes has not been investigated. This study determined the recovery rate of extended-spectrum cephalosporin-resistant (ESC-R) E. coli in colostrum from cows. The ESC-R E. coli isolates were further investigated to determine their phenotypic antimicrobial resistance pattern and the genes conferring ESC-R. Fresh colostrum was collected from 452 cows from 8 dairy herds in New Brunswick, Canada. The ESC-R E. coli was isolated from the colostrum by using the VACC agar, a selective media for extended-spectrum β-lactamase producing Enterobacteriaceae. Minimum inhibitory concentration was determined for all the suspected ESC-R E. coli isolates using a commercial gram-negative broth microdilution method. Two multiplex PCR were conducted on all the suspected ESC-R E. coli isolates to determine the presence of the bla_CTX-M (groups 1, 2, 9, and 8/25) bla_CMY-2, bla_SHV, and bla_TEM resistance genes. The ESC-R E. coli were detected in 20 (4.43%) of the colostrum samples. At least 1 ESC-R E. coli isolate was detected in 6 (75%) of the dairy herds. All ESC-R E. coli had MDR profiles based on minimum inhibitory concentration testing. No bla_CTX-M groups genes were detected; however, the bla_CMY-2 gene was detected in 9 or 20 (45%) and bla_TEM was detected in 7 of 20 (35%) of the ESC-R E. coli. No ESC-R E. coli had both bla_CMY-2 and bla_TEM resistance genes. This is the first report of bla_CMY-2 and bla_TEM genes found in E. coli isolates cultured from dairy colostrum to our knowledge.

Effects of feeding pasteurized waste milk to dairy calves on phenotypes and genotypes of antimicrobial resistance in fecal Escherichia coli isolates before and after weaning

The aim of this study was to evaluate the effects of feeding pasteurized waste milk (pWM) to calves on antimicrobial resistance of fecal Escherichia coli at both phenotypic and genotypic levels. Fifty-two Holstein female calves (3 ± 1.3 d of age) were fed 1 of the 2 different types of milk: milk replacer (MR) without antimicrobials or pWM with β-lactam residues until weaning at 49 d of age. Fecal swabs of all calves were obtained on d 0, 35, and 56 of the study and 3 E. coli isolates per sample were studied. Phenotypic resistance was tested by the disk diffusion method against a panel of 12 antimicrobials. A total of 13 resistance genes consisting of β-lactam, sulfonamide, tetracycline, and aminoglycoside families were examined by PCR. Feeding pWM to calves increased the presence of phenotypic resistance to ampicillin, cephalotin, ceftiofur, and florfenicol in fecal E. coli compared with MR-fed calves. However, the presence of resistance to sulfonamides, tetracyclines, and aminoglycosides was common in dairy calves independent of their milk-feeding source, suggesting other factors apart from the feeding source are involved in the emergence of antimicrobial resistance.

Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health

Early gut microbiota plays a vital role in the long-term health of the host. However, understanding of these microbiota is very limited in livestock species, especially in dairy calves. Neonatal calves are highly susceptible to enteric infections, one of the major causes of calf death, so approaches to improving gut health and overall calf health are needed. An increasing number of studies are exploring the microbial composition of the gut, the mucosal immune system, and early dietary interventions to improve the health of dairy calves, revealing possibilities for effectively reducing the susceptibility of calves to enteric infections while promoting growth. Still, comprehensive understanding of the effect of dietary interventions on gut microbiota-one of the key aspects of gut health-is lacking. Such knowledge may provide in-depth understanding of the mechanisms behind functional changes in response to dietary interventions. Understanding of host-microbial interactions with dietary interventions and the role of the gut microbiota during pathogenesis at the site of infection in early life is vital for designing effective tools and techniques to improve calf gut health.

Feeding of waste milk to Holstein calves affects antimicrobial resistance of Escherichia coli and Pasteurella multocida isolated from fecal and nasal swabs

The use of milk containing antimicrobial residues in calf feeding programs has been shown to select for resistant fecal Escherichia coli in dairy calves. However, information is scarce about the effects of feeding calves waste milk (WM) on the prevalence of multidrug-resistant bacteria. The objective of this study was to determine the antimicrobial resistance patterns of fecal E. coli and nasal Pasteurella multocida isolates from calves fed either milk replacer (MR) or WM in 8 commercial dairy farms (4 farms per feeding program). Fecal and nasal swabs were collected from 20 ± 5 dairy calves at 42 ± 3.2 d of age, and from 10 of these at approximately 1 yr of age in each study farm to isolate the targeted bacteria. Furthermore, resistance of E. coli isolates from calf-environment and from 5 calves at birth and their dams was also evaluated in each study farm. Resistances were tested against the following antimicrobial agents: amoxicillin-clavulanic acid, ceftiofur, colistin, doxycycline (DO), enrofloxacin (ENR), erythromycin, florfenicol, imipenem, and streptomycin. A greater number of fecal E. coli resistant to ENR, florfenicol, and streptomycin and more multidrug-resistant E. coli phenotypes were isolated in feces of calves fed WM than in those fed MR. However, the prevalence of fecal-resistant E. coli was also influenced by calf age, as it increased from birth to 6 wk of age for ENR and DO and decreased from 6 wk to 1 yr of age for DO regardless of the feeding program. From nasal samples, an increase in the prevalence of colistin-resistant P. multocida was observed in calves fed WM compared with those fed MR. The resistance patterns of E. coli isolates from calves and their dams tended to differ, whereas similar resistance profiles among E. coli isolates from farm environment and calves were observed. The findings of this study suggest that feeding calves WM fosters the presence of resistant bacteria in the lower gut and respiratory tracts of dairy calves.

Impact of Low and High Doses of Marbofloxacin on the Selection of Resistant Enterobacteriaceae in the Commensal Gut Flora of Young Cattle: Discussion of Data from 2 Study Populations

In the context of requested decrease of antimicrobial use in veterinary medicine, our objective was to assess the impact of two doses of marbofloxacin administered on young bulls (YBs) and veal calves (VCs) treated for bovine respiratory disease, on the total population of Enterobacteriaceae in gut flora and on the emergence of resistant Enterobacteriaceae. In two independent experiments, 48 YBs from 6 commercial farms and 33 VCs previously colostrum deprived and exposed to cefquinome were randomly assigned to one of the three groups LOW, HIGH, and Control. In LOW and HIGH groups, animals received a single injection of, respectively, 2 and 10 mg/kg marbofloxacin. Feces were sampled before treatment, and at several times after treatment. Total and resistant Enterobacteriaceae enumerating were performed by plating dilutions of fecal samples on MacConkey agar plates that were supplemented or not with quinolone. In YBs, marbofloxacin treatment was associated with a transient decrease in total Enterobacteriaceae count between day (D)1 and D3 after treatment. Total Enterobacteriaceae count returned to baseline between D5 and D7 in all groups. None of the 48 YBs harbored marbofloxacin-resistant Enterobacteriaceae before treatment. After treatment, 1 out of 20 YBs from the Control group and 1 out of 14 YBs from the HIGH group exhibited marbofloxacin-resistant Enterobacteriaceae. In VCs, the rate of fluoroquinolone-resistant Enterobacteriaceae significantly increased after low and high doses of marbofloxacin treatment. However, the effect was similar for the two doses, which was probably related to the high level of resistant Enterobacteriaceae exhibited before treatment. Our results suggest that a single treatment with 2 or 10 mg/kg marbofloxacin exerts a moderate selective pressure on commensal Enterobacteriaceae in YBs and in VCs. A fivefold decrease of marbofloxacin regimen did not affect the selection of resistances among commensal bacteria.

Development of a Polymerase Chain Reaction Assay for the Detection of Antibiotic Resistance Genes in Community DNA

Many methods are used to detect antibiotic resistance genes in samples. The objective of the study reported here was to compare polymerase chain reaction (PCR) analysis of community DNA with fecal culturing for detecting antibiotic resistance genes in cattle samples. In the laboratory-based portion of this study, known concentrations of an Escherichia coli strain with 3 antibiotic resistance genes ( cmy-2, flo, and cat) were added to feces from dairy cattle. These genes were used to assess the effect of various primer pairs, chromosomally versus plasmid-encoded genes, and gene copy number on the sensitivity of PCR amplification. Gene-specific PCR amplification was performed on the community DNA extracted from the feces. Feces were cultured for the inoculated strain. In the field-based portion of the study, 80 cattle fecal samples of unknown gene status were compared by use of similar methods. Culture and PCR amplification from community DNA extractions produced variable results, and this variability was most noticeable at dilutions that approached the detection limit of the assay. Typically, PCR amplification had a higher sensitivity than did culture for detecting the gene of interest. However, the sensitivity of culture was improved by plating on selective media containing antibiotics. The community DNA approach enables assessment of bacterial communities in complex samples such as feces, a task that can be prohibitive by budget or time constraints associated with culture methods. Through a strategic combination of culture and community DNA approaches, the relationship between specific selection pressures and the persistence and dissemination of specific resistance genes can be elucidated.

Occurrence and Spread of Quinolone-Resistant Escherichia coli on Dairy Farms

Quinolone-resistant Escherichia coli (QREC) is common in feces from young calves, but the prevalence and genetic diversity of QREC in groups of cattle of other ages and the farm environment are unknown. The aims of the study were to obtain knowledge about the occurrence of QREC on dairy farms, the genetic diversity of QREC within and between farms, and how these relate to the number of purchased animals and geographic distances between farms. We analyzed the within-sample prevalence of QREC in individual fecal samples from preweaned dairy calves and postpartum cows and in environmental samples from 23 Swedish dairy farms. The genetic diversity of the QREC isolates on 10 of these farms was assessed. In general, QREC was more prevalent in the dairy farm environment and in postpartum cows if QREC was commonly found in calves than if QREC was rare in calves. In particular, we found more QREC organisms in feed and water troughs and in environments that may come into contact with young calves. Thus, the results suggest that QREC circulates between cattle and the farm environment and that calves are important for the maintenance of QREC. Some genotypes of QREC were widespread both within and between farms, indicating that QREC has spread within the farms and likely also between farms, possibly through purchased animals. Farms that had purchased many animals over the years had greater within-farm diversity than farms with more closed animal populations. Finally, animals on more closely located farms were more likely to share the same genotype than animals on farms located far apart.

IMPORTANCE

This study investigates the occurrence of a specific type of antimicrobial-resistant bacterium on dairy farms. It contributes to increased knowledge about the occurrence and spread of these bacteria, and the results pave the way for actions or further studies that could help mitigate the spread of these bacteria on dairy farms and in the community as a whole.

Not All Antibiotic Use Practices in Food-Animal Agriculture Afford the Same Risk

The World Health Organization has identified quinolones, third- and fourth-generation cephalosporins, and macrolides as the most important antibiotics in human medicine. In the context of agricultural use of antibiotics, the principle zoonotic agents of concern are , spp., , and spp. Antibiotic exposure provides a selective advantage to resistant strains of these bacteria relative to their susceptible conspecifics. This is a dose-dependent process, and consequently antibiotic use practices that involve higher doses will exert greater and longer-lasting selective pressure in favor of resistant bacterial populations and will therefore increase the probability of transmission to people and other animals. Oral administration has a greater impact on enteric flora with the exception of fluoroquinolone treatments, which appear to affect the enteric flora equally if administered orally or parenterally. The use of quinolones in agriculture deserves heightened scrutiny because of the ease with which these broad-spectrum antibiotics favor spontaneously resistant bacteria in exposed populations. When present at sufficient concentrations, excreted antibiotics have the potential to selectively favor resistant bacteria in the environment and increase the probability of transmission to people and animals. The bioavailability of antibiotics varies greatly: some antibiotics remain active in soils (florfenicol, β-lactams), whereas others may be rapidly sorbed and thus not bioavailable (tetracycline, macrolides, quinolones). When considering the risks of different antibiotic use practices in agriculture, it would be prudent to focus attention on practices that involve high doses, oral delivery, and residues of antibiotics that remain active in soils.

Antibiotic Resistance in Animal and Environmental Samples Associated with Small-Scale Poultry Farming in Northwestern Ecuador

In developing countries, small-scale poultry farming employing antibiotics as growth promoters is being advanced as an inexpensive source of protein and income. Here, we present the results of a large ecoepidemiological study examining patterns of antibiotic resistance (AR) in E. coli isolates from small-scale poultry production environments versus domestic environments in rural Ecuador, where such backyard poultry operations have become established over the past decade. Our previous research in the region suggests that introduction of AR bacteria through travel and commerce may be an important source of AR in villages of this region. This report extends the prior analysis by examining small-scale production chicken farming as a potential source of resistant strains. Our results suggest that AR strains associated with poultry production likely originate from sources outside the study area and that these outside sources might be a better place to target control efforts than local management practices.

The effects of animal agriculture on the spread of antibiotic resistance (AR) are cross-cutting and thus require a multidisciplinary perspective. Here we use ecological, epidemiological, and ethnographic methods to examine populations of Escherichia coli circulating in the production poultry farming environment versus the domestic environment in rural Ecuador, where small-scale poultry production employing nontherapeutic antibiotics is increasingly common. We sampled 262 “production birds” (commercially raised broiler chickens and laying hens) and 455 “household birds” (raised for domestic use) and household and coop environmental samples from 17 villages between 2010 and 2013. We analyzed data on zones of inhibition from Kirby-Bauer tests, rather than established clinical breakpoints for AR, to distinguish between populations of organisms. We saw significantly higher levels of AR in bacteria from production versus household birds; resistance to either amoxicillin-clavulanate, cephalothin, cefotaxime, and gentamicin was found in 52.8% of production bird isolates and 16% of household ones. A strain jointly resistant to the 4 drugs was exclusive to a subset of isolates from production birds (7.6%) and coop surfaces (6.5%) and was associated with a particular purchase site. The prevalence of AR in production birds declined with bird age (P < 0.01 for all antibiotics tested except tetracycline, sulfisoxazole, and trimethoprim-sulfamethoxazole). Farming status did not impact AR in domestic environments at the household or village level. Our results suggest that AR associated with small-scale poultry farming is present in the immediate production environment and likely originates from sources outside the study area. These outside sources might be a better place to target control efforts than local management practices.

IMPORTANCE In developing countries, small-scale poultry farming employing antibiotics as growth promoters is being advanced as an inexpensive source of protein and income. Here, we present the results of a large ecoepidemiological study examining patterns of antibiotic resistance (AR) in E. coli isolates from small-scale poultry production environments versus domestic environments in rural Ecuador, where such backyard poultry operations have become established over the past decade. Our previous research in the region suggests that introduction of AR bacteria through travel and commerce may be an important source of AR in villages of this region. This report extends the prior analysis by examining small-scale production chicken farming as a potential source of resistant strains. Our results suggest that AR strains associated with poultry production likely originate from sources outside the study area and that these outside sources might be a better place to target control efforts than local management practices.

Cross-sectional survey of antibiotic resistance in Escherichia coli isolated from diseased farm livestock in England and Wales

Between 2005 and 2007, E. coli obtained from clinical diagnostic submissions from cattle, goats, pigs and sheep to government laboratories in England and Wales were tested for sensitivity to 16 antimicrobials. Resistance was most commonly observed against ampicillin, streptomycin, sulphonamides and tetracyclines. Resistance levels varied significantly between species, with isolates from cattle frequently showing the highest levels. Verocytotoxigenic E. coli (VTEC) expressed less resistance than non-VTEC. Only 19·3% of non-VTEC and 43·5% of VTEC were susceptible to all antimicrobials, while 47·1% and 30·4%, respectively, were resistant to ⩾5 antimicrobials. The resistance phenotype SSuT was commonly observed, and isolates resistant to third-generation cephalosporins were also identified. We recommend judicious antimicrobial usage in the livestock industry in order to preserve efficacy.

Prevalence and patterns of antimicrobial resistance among Escherichia coli isolated from Zambian dairy cattle across different production systems

This study focused on the use of antibiotics on small, medium and commercial-sized dairy farms in the central region of Zambia and its relationship to antibiotic resistance in Escherichia coli. A stratified random sample of 104 farms was studied, representing approximately 20% of all dairy farms in the region. On each farm, faecal samples were collected from a random sample of animals and a standardised questionnaire on the usage of antibiotics was completed. An E. coli isolate was obtained from 98.67% (371/376) of the sampled animals and tested for resistance to six classes of antibiotics. The estimated prevalence of resistance across the different farming systems was: tetracycline (10.61; 95%CI: 7.40–13.82), ampicillin (6.02; 95%CI: 3.31–8.73), sulfamethoxazole/ trimethoprim (4.49; 95%CI: 2.42–6.56), cefpodoxime (1.91; 95%CI: 0.46–3.36), gentamicin (0.89; 95%CI: 0.06–1.84) and ciprofloxacin (0%). Univariate analyses indicated certain diseases, exotic breeds, location, farm size and certain management practices as risk factors for detection of resistance, whereas multivariate analyses showed an association with lumpy skin disease and a protective effect for older animals (>25 months). This study has provided novel insights into the drivers of antibiotic use and their association with antibiotic resistance in an under-studied region of Southern Africa.

Genome-Wide Screening Identifies Six Genes That Are Associated with Susceptibility to Escherichia coli Microcin PDI

The microcin PDI inhibits a diverse group of pathogenic Escherichia coli strains. Coculture of a single-gene knockout library (BW25113; n=3,985 mutants) against a microcin PDI-producing strain (E. coli 25) identified six mutants that were not susceptible (ΔatpA, ΔatpF, ΔdsbA, ΔdsbB, ΔompF, and ΔompR). Complementation of these genes restored susceptibility in all cases, and the loss of susceptibility was confirmed through independent gene knockouts in E. coli O157:H7 Sakai. Heterologous expression of E. coli ompF conferred susceptibility to Salmonella enterica and Yersinia enterocolitica strains that are normally unaffected by microcin PDI. The expression of chimeric OmpF and site-directed mutagenesis revealed that the K47G48N49 region within the first extracellular loop of E. coli OmpF is a putative binding site for microcin PDI. OmpR is a transcriptional regulator for ompF, and consequently loss of susceptibility by the ΔompR strain most likely is related to this function. Deletion of AtpA and AtpF, as well as AtpE and AtpH (missed in the original library screen), resulted in the loss of susceptibility to microcin PDI and the loss of ATP synthase function. Coculture of a susceptible strain in the presence of an ATP synthase inhibitor resulted in a loss of susceptibility, confirming that a functional ATP synthase complex is required for microcin PDI activity. In trans expression of ompF in the ΔdsbA and ΔdsbB strains did not restore a susceptible phenotype, indicating that these proteins are probably involved with the formation of disulfide bonds for OmpF or microcin PDI.

Prevalence and Antimicrobial Resistance of Salmonella and Escherichia coli from Australian Cattle Populations at Slaughter

Antimicrobial agents are used in cattle production systems for the prevention and control of bacteria associated with diseases. Australia is the world's third largest exporter of beef; however, this country does not have an ongoing surveillance system for antimicrobial resistance (AMR) in cattle or in foods derived from these animals. In this study, 910 beef cattle, 290 dairy cattle, and 300 veal calf fecal samples collected at slaughter were examined for the presence of Escherichia coli and Salmonella, and the phenotypic AMR of 800 E. coli and 217 Salmonella isolates was determined. E. coli was readily isolated from all types of samples (92.3% of total samples), whereas Salmonella was recovered from only 14.4% of samples and was more likely to be isolated from dairy cattle samples than from beef cattle or veal calf samples. The results of AMR testing corroborate previous Australian animal and retail food surveys, which have indicated a low level of AMR. Multidrug resistance in Salmonella isolates from beef cattle was detected infrequently; however, the resistance was to antimicrobials of low importance in human medicine. Although some differences in AMR between isolates from the different types of animals were observed, there is minimal evidence that specific production practices are responsible for disproportionate contributions to AMR development. In general, resistance to antimicrobials of critical and high importance in human medicine was low regardless of the isolate source. The low level of AMR in bacteria from Australian cattle is likely a result of strict regulation of antimicrobials in food animals in Australia and animal management systems that do not favor bacterial disease.

Effect of heifer-raising practices on E. coli antimicrobial resistance and Salmonella prevalence in heifer raisers

Although cattle movement and commingling play an important role in the inter-herd transmission of pathogens, little is known about the effect of commingling of heifers at raising operations. The objective of this study was to compare the resistance of E. coli and prevalence of Salmonella from pooled faecal pats of heifers raised off-farm at multi-source raisers (MULTI) that raised heifers from at least two farms compared with on-farm raisers (HOME), with heifers from only that farm. MULTI faecal pat samples were collected from pens with animals that had arrived at the farm within the previous 2 months (AP) and from animals that would be departing the heifer raiser in 2-3 months (DP). Corresponding age sampling was conducted at HOME raisers. Odds of ampicillin resistance were 3·0 times greater in E. coli collected from MULTI compared to HOME raisers. E. coli from AP pens had significantly (P < 0·05) higher odds of resistance to ampicillin, neomycin, streptomycin, and tetracycline compared to DP pens. Salmonella recovery was not significantly different between heifer-raising systems (P = 0·3). Heifer-raising system did not have a major overall impact on selection of resistant E. coli, which was strongly affected by the age of the animals sampled.

A review of 40 years of enteric antimicrobial resistance research in Eastern Africa: what can be done better?

The emergence and persistence of antimicrobial resistance is driven by varied factors including the indiscriminate use of antibiotics and variable drug efficacy and presents a major threat to the control of infectious diseases. Despite the high burden of disease in sub-Saharan Africa and the potential health and economic consequences, the level of research on antimicrobial resistance in the region remains unknown. Little data exists to quantify the contribution of different factors to the current levels of antimicrobial resistance. To identify the factors that contribute most to the emergence, amplification, persistence and dissemination of antimicrobial resistance in humans and animals, we used the PRISMA 2009 guidelines to conduct a systematic review of studies on antibiotic-resistant enteric bacteria in Eastern Africa. We searched PubMed and Google Scholar databases and identified 2,155 probable articles, of which 89 studies on humans and 28 on animals remained after full-text review. These were articles from Kenya, Tanzania, Uganda, Ethiopia, Rwanda and Burundi, published between 1974 and 2013, that reported resistance in Salmonella, Shigella, Escherichia coli and Vibrio sp. The majority (98%) of human studies were based on hospital- (rather than community-wide) sampling and although they report high levels of antimicrobial resistance in the region, study design and methodological differences preclude conclusions about the magnitude and trends of antimicrobial resistance. To remedy this, we discuss and propose minimum reporting guidelines for the level of detail that should be explicitly provided for antimicrobial resistance study designs, testing of samples and reporting of results that would permit comparative inferences and enable meta-analyses. Further, we advocate for increased focus on community- rather than hospital-based sampling to provide a better indication of population-wide trends in antimicrobial resistance. This approach, together with the establishment of a robust regional surveillance network, should over time build a pool of evidence-based data useful for policy decisions and interventions aimed at controlling antimicrobial resistance.

Prevalence of virulence determinants and antimicrobial resistance among commensal Escherichia coli derived from dairy and beef cattle

Cattle is a reservoir of potentially pathogenic E. coli, bacteria that can represent a significant threat to public health, hence it is crucial to monitor the prevalence of the genetic determinants of virulence and antimicrobial resistance among the E. coli population. The aim of this study was the analysis of the phylogenetic structure, distribution of virulence factors (VFs) and prevalence of antimicrobial resistance among E. coli isolated from two groups of healthy cattle: 50 cows housed in the conventional barn (147 isolates) and 42 cows living on the ecological pasture (118 isolates). The phylogenetic analysis, identification of VFs and antimicrobial resistance genes were based on either multiplex or simplex PCR. The antimicrobial susceptibilities of E. coli were examined using the broth microdilution method. Two statistical approaches were used to analyse the results obtained for two groups of cattle. The relations between the dependent (VFs profiles, antibiotics) and the independent variables were described using the two models. The mixed logit model was used to characterise the prevalence of the analysed factors in the sets of isolates. The univariate logistic regression model was used to characterise the prevalence of these factors in particular animals. Given each model, the odds ratio (OR) and the 95% confidence interval for the population were estimated. The phylogroup B1 was predominant among isolates from beef cattle, while the phylogroups A, B1 and D occurred with equal frequency among isolates from dairy cattle. The frequency of VFs-positive isolates was significantly higher among isolates from beef cattle. E. coli from dairy cattle revealed significantly higher resistance to antibiotics. Some of the tested resistance genes were present among isolates from dairy cattle. Our study showed that the habitat and diet may affect the genetic diversity of commensal E. coli in the cattle. The results suggest that the ecological pasture habitat is related to the increased spreading rate of the VFs, while the barn habitat is characterised by the higher levels of antimicrobial resistance among E. coli.

In vivo selection of resistant E. coli after ingestion of milk with added drug residues

Antimicrobial resistance represents a major global threat to modern medicine. In vitro studies have shown that very low concentrations of drugs, as frequently identified in the environment, and in foods and water for human and animal consumption, can select for resistant bacteria. However, limited information is currently available on the in vivo impact of ingested drug residues. The objective of our study was to evaluate the effect of feeding preweaned calves milk containing antimicrobial drug residues (below the minimum inhibitory concentration), similar to concentrations detected in milk commonly fed to dairy calves, on selection of resistant fecal E. coli in calves from birth to weaning. At birth, thirty calves were randomly assigned to a controlled feeding trial where: 15 calves were fed raw milk with no drug residues (NR), and 15 calves were fed raw milk with drug residues (DR) by adding ceftiofur, penicillin, ampicillin, and oxytetracycline at final concentrations in the milk of 0.1, 0.005, 0.01, and 0.3 µg/ml, respectively. Fecal samples were rectally collected from each calf once a week starting at birth prior to the first feeding in the trial (pre-treatment) until 6 weeks of age. A significantly greater proportion of E. coli resistant to ampicillin, cefoxitin, ceftiofur, streptomycin and tetracycline was observed in DR calves when compared to NR calves. Additionally, isolates from DR calves had a significant decrease in susceptibility to ceftriaxone and ceftiofur when compared to isolates from NR calves. A greater proportion of E. coli isolates from calves in the DR group were resistant to 3 or more antimicrobial drugs when compared to calves in the ND group. These findings highlight the role that low concentrations of antimicrobial drugs have on the evolution and selection of resistance to multiple antimicrobial drugs in vivo.

Risk factors for antimicrobial resistance in fecal Escherichia coli from preweaned dairy calves

The primary objective of this study was to investigate calf and farm factors associated with antimicrobial-resistant Escherichia coli in the feces of preweaned dairy calves in Sweden. In particular, we investigated the effects of feeding calves colostrum and milk from cows treated with antimicrobials. The secondary objective was to describe the prevalence of resistant E. coli in feces of preweaned dairy calves in Sweden. Fecal samples from 3 calves, aged 7 to 28d, from 243 farms were analyzed for the within-sample prevalence of E. coli resistant to nalidixic acid, streptomycin, and cefotaxime using selective agars supplemented with antimicrobials. In addition, resistance to 12 antimicrobials was tested in one randomly selected E. coli isolate per calf. Information was collected from the farmers via questionnaires regarding the use of colostrum and milk from cows treated with antimicrobials as calf feed and other uses of antimicrobials in the herd. Multivariable zero-inflated negative binomial and logistic regression models were used to assess the effect of various risk factors for shedding of resistant E. coli. Escherichia coli resistant to streptomycin, nalidixic acid, or cefotaxime were isolated from 90, 49, and 11% of the calves, respectively. Resistance to at least one antimicrobial was found in a random isolate of E. coli from 48% of the calves. Feeding colostrum from cows treated with antimicrobials at drying off did not affect the prevalence of resistant E. coli. In contrast, feeding milk from cows treated with antimicrobials during lactation resulted in significantly more nalidixic acid- and streptomycin-resistant E. coli than when such milk was discarded; no significant effect was seen for other resistance traits. Furthermore, an interaction was found between feeding milk from cows treated with antimicrobials and use of fluoroquinolones in cows. In general, the prevalence of resistance was lower for older calves and calves on small farms. Other factors that were associated with the shedding of resistant E. coli were administration of oral dihydrostreptomycin to calves, administration of systemic tetracycline and ceftiofur to cows and calves, housing of the calves, predominant breed of the herd, and geographic location of the farm. The presence of resistant E. coli in calves was clearly due to multiple factors, but minimizing the feeding of milk from cows treated with antimicrobials during lactation should lower the prevalence of resistant E. coli in the gastrointestinal tract of the calves.

Microcin MccPDI reduces the prevalence of susceptible Escherichia coli in neonatal calves

AIMS

Microcin MccPDI-producing Escherichia coli have a fitness advantage in dairy calves. For this project, we determined whether MccPDI is responsible for the in vivo fitness advantage, which is a necessary condition before MccPDI strains can be considered viable candidates for inhibiting pathogenic serovars of E. coli.

METHODS AND RESULTS

Neonatal calves were coinoculated with either MccPDI-producing E. coli or MccPDI-knockout mutants in conjunction with a susceptible strain. After 6 days, the MccPDI-producing E. coli-25 strain clearly dominated the E. coli-186 susceptible strain in the inoculated calves (P = 0·003). MccPDI-producing E. coli composed a higher log percentage of the total population of lactose-fermenting bacteria in the faeces (5·51 log CFU per 8·03 log CFU) compared with the knockout strain (2·6 log CFU per 8·23 log CFU) (P = 0·01), and it was more consistently recovered from the lower gastrointestinal tract at the time of necropsy (P = 0·01).

CONCLUSION

Our findings support the hypothesis that MccPDI is functional in vivo and it is most likely responsible for a fitness advantage in vivo.

SIGNIFICANCE AND IMPACT OF THE STUDY

MccPDI-producing E. coli strongly inhibit pathogenic E. coli strains in vitro. We show herein that MccPDI functions in vivo, and thus, these strains may be candidate probiotics against pathogenic strains of E. coli.

Characterization of multi-antibiotic-resistant Escherichia coli Isolated from beef cattle in Japan

The emergence of multiple-antibiotic-resistance bacteria is increasing, which is a particular concern on livestock farms. We previously isolated 1,347 antimicrobial-resistant (AMR) Escherichia coli strains from the feces of beef cattle on 14 Japanese farms. In the present study, the genetic backgrounds and phylogenetic relationships of 45 AMR isolates were characterized by the chromosome phylotype, AMR phenotype, AMR genotype, and plasmid type. These isolates were classified into five chromosome phylotypes, which were closely linked to the farms from which they were isolated, suggesting that each farm had its own E. coli phylotype. AMR phenotype and plasmid type analyses yielded 8 and 14 types, all of which were associated with the chromosomal phylotype and, thus, to the original farms. AMR genotype analysis revealed more variety, with 16 types, indicating both inter- and intra-farm diversity. Different phylotype isolates from the same farm shared highly similar plasmid types, which indicated that plasmids with AMR genes could be transferred between phylotypes, thereby generating multi-antibiotic-resistant microorganisms. This ecological study demonstrated that the chromosome phylotype was strongly correlated with the farm from which they were isolated, while the AMR phenotype, genotype, and plasmid type were generally correlated with the chromosome phylotype and farm source.

Patterns of antimicrobial resistance in pathogenic Escherichia coli isolates from cases of calf enteritis during the spring-calving season

Neonatal enteritis is a common condition of young calves and can be caused by pathogenic strains of Escherichia coli. We hypothesised that on-farm antimicrobial use would result in an increased frequency of resistance in these strains during the calving season. We also sought to determine if the frequency of resistance reflected on-farm antimicrobial use. Faecal samples were collected from cases of calf enteritis on 14 spring-calving dairy farms during two 3 week periods: Period 1 - February 11th through March 2nd 2008 and Period 2 - April 14th through May 5th 2008. E. coli were cultured from these samples, pathogenic strains were identified and antimicrobial susceptibility testing was carried out on these pathogenic isolates. Antimicrobial prescribing data were collected from each farm for the previous 12 months as an indicator of antimicrobial use. The correlation between antimicrobial use and resistance was assessed using Spearman's correlation coefficient. Logistic regression analysis was used to investigate the relationship between resistance, sampling period and pathotype. Penicillins and aminopenicillins, streptomycin, and tetracyclines were the most frequently prescribed antimicrobials and the greatest frequencies of resistance were detected to these 3 antimicrobial classes. A strong correlation (ρ=0.879) was observed between overall antimicrobial use and frequencies of antimicrobial resistance on farms. Sampling period was significant in the regression model for ampicillin resistance while pathotype was significant in the models for streptomycin, tetracycline and trimethoprim/sulphamethoxazole resistance. The frequencies of resistance observed have implications for veterinary therapeutics and prudent antimicrobial use. Resistance did not increase during the calving season and factors other than antimicrobial use, such as calf age and bacterial pathotype, may influence the occurrence of resistance in pathogenic E. coli.

Genetic mechanisms of antimicrobial resistance identified in Salmonella enterica, Escherichia coli, and Enteroccocus spp. isolated from U.S. food animals

The prevalence of antimicrobial resistance (AR) in bacteria isolated from U.S. food animals has increased over the last several decades as have concerns of AR foodborne zoonotic human infections. Resistance mechanisms identified in U.S. animal isolates of Salmonella enterica included resistance to aminoglycosides (e.g., alleles of aacC, aadA, aadB, ant, aphA, and StrAB), β-lactams (e.g., bla_{CMY−2, TEM−1, PSE−1}), chloramphenicol (e.g., floR, cmlA, cat1, cat2), folate pathway inhibitors (e.g., alleles of sul and dfr), and tetracycline [e.g., alleles of tet(A), (B), (C), (D), (G), and tetR]. In the U.S., multi-drug resistance (MDR) mechanisms in Salmonella animal isolates were associated with integrons, or mobile genetic elements (MGEs) such as IncA/C plasmids which can be transferred among bacteria. It is thought that AR Salmonella originates in food animals and is transmitted through food to humans. However, some AR Salmonella isolated from humans in the U.S. have different AR elements than those isolated from food animals, suggesting a different etiology for some AR human infections. The AR mechanisms identified in isolates from outside the U.S. are also predominantly different. For example the extended spectrum β-lactamases (ESBLs) are found in human and animal isolates globally; however, in the U.S., ESBLs thus far have only been found in human and not food animal isolates. Commensal bacteria in animals including Escherichia coli and Enterococcus spp. may be reservoirs for AR mechanisms. Many of the AR genes and MGEs found in E. coli isolated from U.S. animals are similar to those found in Salmonella. Enterococcus spp. isolated from animals frequently carry MGEs with AR genes, including resistances to aminoglycosides (e.g., alleles of aac, ant, and aph), macrolides [e.g., erm(A), erm(B), and msrC], and tetracyclines [e.g., tet(K), (L), (M), (O), (S)]. Continuing investigations are required to help understand and mitigate the impact of AR bacteria on human and animal health.

Enterobacterial detection and Escherichia coli antimicrobial resistance in parrots seized from the illegal wildlife trade

Enteric bacteria are considered important potential pathogens in avian clinical medicine, causing either primary or opportunistic infections. The aim of this study was to evaluate the frequency of enterobacteria in the intestinal microbiota of psittacine birds and to determine the antimicrobial susceptibility of the Escherichia coli isolates cultured. Fecal samples were collected from 300 parrots captured from the illegal wildlife trade in Goiás, Brazil and were processed using conventional bacteriological procedures. A total of 508 isolates were obtained from 300 fecal samples: 172 E. coli (33.9% of isolates; 57.3% of individuals); 153 Enterobacter spp. (30.1% of isolates; 51.0% of individuals); 89 Klebsiella spp. (17.7% of isolates; 29.7% of individuals); 59 Citrobacter spp. (11.6% of isolates; 19.7% of individuals), 21 Proteus vulgaris (4.2% of isolates; 7.0% of individuals), 5 Providencia alcalifaciens (0.98% of isolates; 1.67% of individuals), 5 Serratia sp. (0.98% of isolates; 1.67% of individuals), 3 Hafnia aivei (0.59% of isolates; 1.00% of individuals), and 1 Salmonella sp. (0.20% of isolates; 0.33% of individuals). Escherichia coli isolates were subsequently tested for susceptibility to the following antibiotics: amoxicillin (70.93% of the isolates were resistant), ampicillin (75.58%), ciprofloxacin (23.25%), chloramphenicol (33.14%), doxycycline (64.53%), enrofloxacin (41.28%), tetracycline (69.19%), and sulfonamide (71.51%). Multi-resistance to three and four groups of antibiotics occurred in 40 samples (23.25%) and 4 samples (2.32%), respectively. These results demonstrate that illegally traded birds are carriers of potentially pathogenic bacteria, including E. coli strains with antimicrobial resistance.

Influence of therapeutic ceftiofur treatments of feedlot cattle on fecal and hide prevalences of commensal Escherichia coli resistant to expanded-spectrum cephalosporins, and molecular characterization of resistant isolates

In the United States, the blaCMY-2 gene contained within incompatibility type A/C (IncA/C) plasmids is frequently identified in extended-spectrum-cephalosporin-resistant (ESC(r)) Escherichia coli strains from both human and cattle sources. Concerns have been raised that therapeutic use of ceftiofur in cattle may increase the prevalence of ESC(r) E. coli. We report that herd ESC(r) E. coli fecal and hide prevalences throughout the residency of cattle at a feedlot, including during the period of greatest ceftiofur use at the feedlot, were either not significantly different (P ≥ 0.05) or significantly less (P < 0.05) than the respective prevalences at arrival. Longitudinal sampling of cattle treated with ceftiofur demonstrated that once the transient increase of ESC(r) E. coli shedding that follows ceftiofur injection abated, ceftiofur-injected cattle were no more likely than untreated members of the same herd to shed ESC(r) E. coli. Pulsed-field gel electrophoresis (PFGE) genotyping, antibiotic resistance phenotyping, screening for presence of the blaCMY-2 gene, and plasmid replicon typing were performed on 312 ESC(r) E. coli isolates obtained during six sampling periods spanning the 10-month residence of cattle at the feedlot. The identification of only 26 unique PFGE genotypes, 12 of which were isolated during multiple sampling periods, suggests that clonal expansion of feedlot-adapted blaCMY-2 E. coli strains contributed more to the persistence of blaCMY-2 than horizontal transfer of IncA/C plasmids between E. coli strains at this feedlot. We conclude that therapeutic use of ceftiofur at this cattle feedlot did not significantly increase the herd prevalence of ESC(r) E. coli.

Prevalence and molecular epidemiological characterization of antimicrobial-resistant Escherichia coli isolates from Japanese black beef cattle

We investigated the prevalence of antimicrobial-resistant Escherichia coli in Japanese black beef cattle from the three major production regions of Japan. We collected and examined 291 fecal samples from Japanese black beef cattle in Hokkaido, Chubu, and Kyushu. Of the 3,147 E. coli isolates, 1,397 (44.4%) were resistant to one or more antibiotics; these included 553 (39.8%) of 1,388 isolates from Hokkaido, 352 (54.4%) of 647 isolates from Chubu, and 492 (44.2%) of 1,112 isolates from Kyushu. The difference in resistance rates between the three regions was significant. The antibiotics with the highest rates of resistance were oxytetracycline and dihydrostreptomycin (35.8% each), followed by ampicillin (21.4%). Further, E. coli isolates from calves had higher resistance rates than those from growing cattle and mature cattle, and the calf isolates showed high rates of resistance to gentamicin (20.2%), enrofloxacin (9.4%), and ceftiofur (4.2%). In addition, the high degrees of similarity in the genotypes of the isolates and in the resistance patterns on each farm suggest that resistance bacteria and resistance genes were horizontally transferred. Most isolates, in each of the three regions, harbored resistance genes such as blaTEM, strA, strB, aphA1, aphAI-IAB, and catI. In contrast to the isolates from Kyushu, most of which harbored aacC2, tetB, and dfrA12, the isolates from Hokkaido and Chubu harbored a variety of resistance genes. Furthermore, the prevalence of genes for resistance to dihydrostreptomycin, gentamicin, chloramphenicol, and trimethoprim differed significantly between the regions. This is the first large-scale study describing and comparing antimicrobial-resistant bacteria from different regions in Japan. The results will contribute to improving food safety and promoting careful usage of antimicrobial agents.

Feeding untreated and pasteurized waste milk and bulk milk to calves: effects on calf performance, health status and antibiotic resistance of faecal bacteria

Non-saleable milk (waste milk, WM) is contaminated with an undefined spectrum of potentially harmful pathogens and antimicrobial residues. The objective of this study was to determine the impact of feeding bulk milk (BM) or WM - both pasteurized or not - on calf performance, health and the antibiotic resistance of specific faecal bacteria. A total of 114 calves from a large-scale dairy were housed outdoors in individual hutches and were randomly assigned to one of four feeding groups. The calves were fed either WM, pasteurized WM (pWM), BM or pasteurized BM (pBM) from day 3 to 56 of life. Milk samples taken from the pasteurizer and calves' nipple buckets were investigated at regular intervals for total plate count and counts of thermoduric bacteria, coliforms and mastitis pathogens. Faecal samples were taken on days 2, 14, 28 and 56 of life from randomly selected calves of the WM, pWM and BM groups (each N = 8-9) and processed to obtain from each sample preferably two isolates of Escherichia (E.) coli and Enterococcus spp. respectively. Isolates were tested for their antimicrobial susceptibility to 25 antimicrobial agents by broth microdilution. Daily weight gain, milk and calf starter intake and health parameters did not differ significantly between the calves of the four feeding groups. The proportion of resistant E. coli isolates was significantly higher in calves fed WM and in calves fed pWM (most pronounced for cephalosporins) than in calves receiving BM. No differences in resistance were found for Enterococus spp. Thus, the concerns for selecting resistant faecal bacteria by feeding WM seem to be justified. Nonetheless, pasteurized WM of cows not treated with antimicrobials represents an acceptable feed for young calves.

Mathematical model of plasmid-mediated resistance to ceftiofur in commensal enteric Escherichia coli of cattle

Antimicrobial use in food animals may contribute to antimicrobial resistance in bacteria of animals and humans. Commensal bacteria of animal intestine may serve as a reservoir of resistance-genes. To understand the dynamics of plasmid-mediated resistance to cephalosporin ceftiofur in enteric commensals of cattle, we developed a deterministic mathematical model of the dynamics of ceftiofur-sensitive and resistant commensal enteric Escherichia coli (E. coli) in the absence of and during parenteral therapy with ceftiofur. The most common treatment scenarios including those using a sustained-release drug formulation were simulated; the model outputs were in agreement with the available experimental data. The model indicated that a low but stable fraction of resistant enteric E. coli could persist in the absence of immediate ceftiofur pressure, being sustained by horizontal and vertical transfers of plasmids carrying resistance-genes, and ingestion of resistant E. coli. During parenteral therapy with ceftiofur, resistant enteric E. coli expanded in absolute number and relative frequency. This expansion was most influenced by parameters of antimicrobial action of ceftiofur against E. coli. After treatment (>5 weeks from start of therapy) the fraction of ceftiofur-resistant cells among enteric E. coli, similar to that in the absence of treatment, was most influenced by the parameters of ecology of enteric E. coli, such as the frequency of transfer of plasmids carrying resistance-genes, the rate of replacement of enteric E. coli by ingested E. coli, and the frequency of ceftiofur resistance in the latter.

Antimicrobial resistance and virulence factors in Escherichia coli from Swedish dairy calves

Background

In Sweden, knowledge about the role of enteropathogenic Escherichia coli in neonatal calf diarrhea and the occurrence of antimicrobial resistance in E. coli from young calves is largely unknown. This has therapeutic concern and such knowledge is also required for prudent use of antimicrobials.

Methods

In a case control study Esherichia coli isolated from faecal samples from dairy calves were phenotyped by biochemical fingerprinting and analyzed for virulence genes by PCR. Antimicrobial susceptibility was tested by determination of minimum inhibitory concentration (MIC). Farm management data were collected and Fisher's exact test and univariable and multivariable logistic regression analysis were performed.

Results

Of 95 E. coli tested for antimicrobial susceptibility 61% were resistant to one or more substances and 28% were multi-resistant. The virulence gene F5 (K99) was not found in any isolate. In total, 21 out of 40 of the investigated virulence genes were not detected or rarely detected. The virulence genes espP, irp, and fyuA were more common in resistant E. coli than in fully susceptible isolates (P < 0.05). The virulence gene terZ was associated with calf diarrhea (P ≤ 0.01).

The participating 85 herds had a median herd size of 80 lactating cows. Herds with calf diarrhea problems were larger (> 55 cows; P < 0.001), had higher calf mortality (P ≤ 0.01) and calf group feeders were more in use (P < 0.05), compared to herds without calf diarrhea problems.

There was no association between calf diarrhea and diversity of enteric E. coli.

Conclusions

Antimicrobial resistance was common in E. coli from pre-weaned dairy calves, occurring particularly in calves from herds experiencing calf diarrhea problems. The results indicate that more factors than use of antimicrobials influence the epidemiology of resistant E. coli.

Enteropathogenic E. coli seems to be an uncommon cause of neonatal calf diarrhea in Swedish dairy herds. In practice, calf diarrhea should be regarded holistically in a context of infectious agents, calf immunity, management practices etc. We therefore advice against routine antimicrobial treatment and recommend that bacteriological cultures, followed by testing for antimicrobial susceptibility and for virulence factors, are used to guide decisions on such treatment.

Antimicrobial resistance in Escherichia coli isolated from retail milk-fed veal meat from Southern Ontario, Canada

This study estimated the prevalence of Escherichia coli isolates in fresh retail milk-fed veal scallopini pieces obtained from grocery stores in Ontario, Canada. In addition, the prevalence and antimicrobial resistance patterns were examined for points of public health significance. One hundred fifty-three milk-fed veal samples were collected over the course of two sampling phases, January to May 2004 and November 2004 to January 2005. E. coli isolates were recovered from 87% (95% confidence interval, 80.54 to 91.83%) of samples, and antimicrobial susceptibility testing was conducted on 392 isolates. The prevalence of resistance to one or more antimicrobials was 70% (274 of 392), while the resistance to five or more antimicrobials was 33% (128 of 392). Resistance to ceftiofur (2.8%), ceftriaxone (3.6%), nalidixic acid (12%), and ciprofloxacin (3.8%) alone or in combination was observed. Eighty-five resistance patterns were observed; resistance to tetracycline only (7.4%) was observed most frequently. Individual antimicrobial resistance prevalence levels were compared with grain-fed veal and retail beef data from samples collected in Ontario. In general, resistance to individual antimicrobials was observed more frequently in E. coli isolates from milk-fed veal than in isolates from grain-fed veal and beef. Resistance to one or more antimicrobials and to five or more antimicrobials in E. coli isolates was more frequent in isolates from milk-fed veal than in isolates from grain-fed veal and beef. This study provides baseline data on the occurrence of resistance in E. coli isolates from milk-fed veal that can be compared with data for other commodities. Additionally, E. coli resistance patterns may serve as an indicator of antimicrobial exposure.

Antimicrobial resistance in Campylobacter, Salmonella, and Escherichia coli isolated from retail grain-fed veal meat from Southern Ontario, Canada

This study estimated the prevalence of Salmonella, Campylobacter, and Escherichia coli isolates in fresh retail grain-fed veal obtained in Ontario, Canada. The prevalence and antimicrobial resistance patterns were examined for points of public health significance. Veal samples (n = 528) were collected from February 2003 through May 2004. Twenty-one Salmonella isolates were recovered from 18 (4%) of 438 samples and underwent antimicrobial susceptibility testing. Resistance to one or more antimicrobials was found in 6 (29%) of 21 Salmonella isolates; 5 (24%) of 21 isolates were resistant to five or more antimicrobials. No resistance to antimicrobials of very high human health importance was observed. Ampicillin-chloramphenicolstreptomycin-sulfamethoxazole-tetracycline resistance was found in 5 (3%) of 21 Salmonella isolates. Campylobacter isolates were recovered from 5 (1%) of 438 samples; 6 isolates underwent antimicrobial susceptibility testing. Resistance to one or more antimicrobials was documented in 3 (50%) of 6 Campylobacter isolates. No Campylobacter isolates were resistant to five or more antimicrobials or category I antimicrobials. E. coli isolates were recovered from 387 (88%) of 438 samples; 1,258 isolates underwent antimicrobial susceptibility testing. Resistance to one or more antimicrobials was found in 678 (54%) of 1,258 E. coli isolates; 128 (10%) of 1,258 were resistant to five or more antimicrobials. Five (0.4%) and 7 (0.6%) of 1,258 E. coli isolates were resistant to ceftiofur and ceftriaxone, respectively, while 34 (3%) of 1,258 were resistant to nalidixic acid. Ciprofloxacin resistance was not detected. There were 101 different resistance patterns observed among E. coli isolates; resistance to tetracycline alone (12.7%, 161 of 1,258) was most frequently observed. This study provides baseline prevalence and antimicrobial resistance data and highlights potential public health concerns.

Longer-duration uses of tetracyclines and penicillins in U.S. food-producing animals: Indications and microbiologic effects

We review and analyze regulatory categories for longer duration of use (defined as ≥ 7 day) tetracyclines (TCs) and penicillins (PNs) approved for U.S. livestock and poultry, together with scientific studies, surveillance programs and risk assessments pertaining to antimicrobial resistance. Indications listed on a government database were grouped into three broad categories according to the terminology used to describe their use: disease control (C), treatment (T) and growth improvement (G). Consistent with mostly therapeutic uses, the majority (86%) of listed indications had C and/or T terms. Several studies showed interruption of early disease stages in animals and modulation of intestinal microflora. Longer-duration exposures are consistent with bacteriostatic modes of action, where adequate exposure time as well as concentration is needed for sufficient antimicrobial activity. Other effects identified included reduced animal pathogen prevalence, toxin formation, inflammation, environmental impacts, improved animal health, reproductive measures, nutrient utilization, and others. Several animal studies have shown a limited, dose-proportionate, selective increase in resistance prevalence among commensal animal bacteria following longer-duration exposures. Pathogen surveillance programs showed overall stable or declining resistance trends among sentinel bacteria. Quantitative, microbiologically detailed resistance risk assessments indicate small probabilities of human treatment failure due to resistance under current conditions. Evaluations of longer-duration uses of TCs, PNs, and other antimicrobial classes used in food-producing animals should consider mechanisms of activity, known individual- and population-level health and waste reduction effects in addition to resistance risks.

Selection pressure required for long-term persistence of blaCMY-2-positive IncA/C plasmids

Multidrug resistance blaCMY-2 plasmids that confer resistance to expanded-spectrum cephalosporins have been found in multiple bacterial species collected from different hosts worldwide. The widespread distribution of blaCMY-2 plasmids may be driven by antibiotic use that selects for the dissemination and persistence of these plasmids. Alternatively, these plasmids may persist and spread in bacterial populations in the absence of selection pressure if a balance exists among conjugative transfer, segregation loss during cell division, and fitness cost to the host. We conducted a series of experiments (both in vivo and in vitro) to study these mechanisms for three blaCMY-2 plasmids, peH4H, pAR060302, and pAM04528. Results of filter mating experiments showed that the conjugation efficiency of blaCMY-2 plasmids is variable, from <10(-7) for pAM04528 and peH4H to ∼10(-3) for pAR060302. Neither peH4H nor pAM04528 was transferred from Escherichia coli strain DH10B, but peH4H was apparently mobilized by the coresident trimethoprim resistance-encoding plasmid pTmpR. Competition studies showed that carriage of blaCMY-2 plasmids imposed a measurable fitness cost on the host bacteria both in vitro (0.095 to 0.25) and in vivo (dairy calf model). Long-term passage experiments in the absence of antibiotics demonstrated that plasmids with limited antibiotic resistance phenotypes arose, but eventually drug-sensitive, plasmid-free clones dominated the populations. Given that plasmid decay or loss is inevitable, we infer that some level of selection is required for the long-term persistence of blaCMY-2 plasmids in bacterial populations.

Genotypic-phenotypic discrepancies between antibiotic resistance characteristics of Escherichia coli isolates from calves in management settings with high and low antibiotic use

We hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence of dysfunctional resistance genes (resistance pseudogenes) could provide a measure of the level of antibiotic exposure present in a given environment. As a proof-of-concept test, we assayed field strains of Escherichia coli for their resistance genotypes using a resistance gene microarray and further characterized isolates that had resistance phenotype-genotype discrepancies. We found a small but significant association between the prevalence of isolates with resistance pseudogenes and the lower antibiotic use environment of a beef cow-calf operation versus a higher antibiotic use dairy calf ranch (Fisher's exact test, P = 0.044). Other significant findings include a very strong association between the dairy calf ranch isolates and phenotypes unexplained by well-known resistance genes (Fisher's exact test, P < 0.0001). Two novel resistance genes were discovered in E. coli isolates from the dairy calf ranch, one associated with resistance to aminoglycosides and one associated with resistance to trimethoprim. In addition, isolates resistant to expanded-spectrum cephalosporins but negative for bla(CMY-2) had mutations in the promoter regions of the chromosomal E. coli ampC gene consistent with reported overexpression of native AmpC beta-lactamase. Similar mutations in hospital E. coli isolates have been reported worldwide. Prevalence or rates of E. coli ampC promoter mutations may be used as a marker for high expanded-spectrum cephalosporin use environments.

Genotyping and antimicrobial resistance patterns of Escherichia coli O157 originating from cattle farms

During a Escherichia coli O157 prevalence study on cattle farms, 324 E. coli O157 isolates were collected from 68 out of 180 cattle farms. All isolates harbored the eaeA gene and the enterohemolysin (ehxA) gene. The majority of the strains only contained vtx2 (245 isolates), the combination of vtx1 and vtx2 was detected in 50 isolates, and in 29 isolates none of the vtx genes was present. Pulsed-field gel electrophoresis (PFGE) revealed that at a similarity level of 98% the isolates grouped into 83 different genotypes, 76 of which were only detected on one farm. Twenty-two out of the 68 positive farms harbored isolates belonging to more than one PFGE type, with a maximum of four different PFGE types. Minimal inhibitory concentrations of 10 antimicrobial agents were determined on a subset of 116 isolates, that is, one isolate per positive age category per farm. Acquired resistance to at least one antimicrobial agent was detected in 18 isolates and within a farm, only one resistance pattern was observed. All these 18 isolates were resistant toward streptomycin, and 16 of them also showed resistance toward sulfisoxazole. Six isolates were resistant to three or more antimicrobial agents.

Proximity-dependent inhibition in Escherichia coli isolates from cattle

We describe a novel proximity-dependent inhibition phenotype of Escherichia coli that is expressed when strains are cocultured in defined minimal media. When cocultures of "inhibitor" and "target" strains approached a transition between logarithmic and stationary growth, target strain populations rapidly declined >4 log CFU per ml over a 2-h period. Inhibited strains were not affected by exposure to conditioned media from inhibitor and target strain cocultures or when the inhibitor and target strains were incubated in shared media but physically separated by a 0.4-μm-pore-size membrane. There was no evidence of lytic phage or extracellular bacteriocin involvement, unless the latter was only present at effective concentrations within immediate proximity of the inhibited cells. The inhibitory activity observed in this study was effective against a diversity of E. coli strains, including enterohemorrhagic E. coli serotype O157:H7, enterotoxigenic E. coli expressing F5 (K99) and F4 (K88) fimbriae, multidrug-resistant E. coli, and commensal E. coli. The decline in counts of target strains in coculture averaged 4.8 log CFU/ml (95% confidence interval, 4.0 to 5.5) compared to their monoculture counts. Coculture of two inhibitor strains showed mutual immunity to inhibition. These results suggest that proximity-dependent inhibition can be used by bacteria to gain a numerical advantage when populations are entering stationary phase, thus setting the stage for a competitive advantage when growth conditions improve.

Geographic, farm, and animal factors associated with multiple antimicrobial resistance in fecal Escherichia coli isolates from cattle in the western United States

OBJECTIVE

To describe geographic, farm-type, and animal-type factors associated with multiple antimicrobial resistance (MAR) in fecal Escherichia coli isolates from cattle.

DESIGN

Cross-sectional field study.

SAMPLE POPULATION

1,736 fecal samples from cattle on 38 farms in California, Oregon, and Washington.

PROCEDURES

Fecal samples were collected from preweaned calves (2 to 4 weeks old) and cows that recently calved on dairy and beef cow-calf farms, preweaned calves on calf ranches, and 1-year-old steers on feedlots. One fecal E coli isolate per sample was isolated, and antimicrobial susceptibility was tested. Escherichia coli isolates were initially clustered by antimicrobial resistance patterns and categorized by number of antimicrobial resistances. A generalized estimating equations cumulative logistic regression model was used to identify factors associated with an increase in MAR in fecal E coli isolates from cattle.

RESULTS

MAR was higher in E coli isolates from cattle in California, compared with those from cattle in Washington or Oregon. Multiple antimicrobial resistance was highest in E coli isolates from calves on calf ranches and progressively lower in isolates from feedlot steers, dairy cattle, and beef cattle. Multiple antimicrobial resistance was higher in E coli isolates from calves than from adult cattle, in E coli isolates from cattle of conventional farms than of organic farms, and in isolates from beef cattle in intensive dairy farm regions than from beef cattle distant from dairy farm regions.

CONCLUSIONS AND CLINICAL RELEVANCE

MAR in fecal E coli isolates from cattle was influenced by factors not directly associated with the use of antimicrobials, including geographic region, animal age, and purpose (beef vs dairy).

Prevalence of antimicrobial resistance in fecal Escherichia coli isolates from stray pet dogs and hospitalized pet dogs in Korea

A total of 628 Escherichia coli isolates recovered from 877 intestinal samples of stray pet dogs (n = 565) and hospitalized pet dogs (n = 312) in Korea were analyzed for resistance to 15 antimicrobial agents. Most common resistance observed in E. coli isolated from both groups of dogs was to tetracycline (52.4-53.6%), streptomycin (35.8-41.7%), ampicillin (32.9-47.1%), nalidixic acid (21.6-37.4%), and trimethoprim/sulfamethoxazole (19.7-36.4%). Resistance to chloramphenicol, gentamicin, and ciprofloxacin was observed in 19.4% (17.1-24.3%), 18% (16.1-21.8%), and 16.1% (13.5-21.4%) of the isolates, respectively. No E. coli isolated from hospitalized dogs showed resistance to imipenem and cefepime, whereas three (0.7%) isolates from stray dogs were resistant to cefepime. Some of the isolates from both groups showed resistance to cefotaxime (2.4-3.9%) and amikacin (0.5-1.5%). In general, the frequency of resistance tended to be higher in isolates from hospitalized dogs than isolates from stray dogs against most antimicrobials tested. Around 39% (162/422) and 27% (55/206) of E. coli isolates from stray dogs and hospitalized dogs were susceptible to all antimicrobials tested, respectively. Multiresistance (> or = 3 subclasses of antimicrobials) was observed in 32% and 48% of E. coli isolates from stray dogs and hospitalized dogs, respectively. More attention should be paid to the use of antimicrobials and the occurrence of antimicrobial resistance in companion animals.

Phenotypic and genotypic characteristics of antimicrobial resistant Escherichia coli isolated from symbovine flies, cattle and sympatric insectivorous house martins from a farm in the Czech Republic (2006-2007)

The prevalence of antimicrobial resistant Escherichia coli was tested in symbovine flies and sympatric house martins (Delichon urbica) at a dairy farm. Antimicrobial resistant E. coli was detected in 89% (n=147) of isolates from flies within a calf barn. Isolates with the same antimicrobial resistance phenotypes, genes, and pulsotypes were found between both fly and calf E. coli isolates, suggesting that the calves were the initial source of the antimicrobial resistant strains in fly isolates. Symbovine flies were considered as important reservoirs of antimicrobial resistant E. coli strains at a dairy farm, due to their intensive contact with cattle feces and manure. House martin fecal samples from the same farm contained 4.5% (n=393) of antimicrobial resistant E. coli. House martin isolates displayed different macrorestriction profiles than fly isolates and the significance of house martins as a reservoir and vector of antimicrobial resistant E. coli appears low.

Model or meal? Farm animal populations as models for infectious diseases of humans

In recent decades, theory addressing the processes that underlie the dynamics of infectious diseases has progressed considerably. Unfortunately, the availability of empirical data to evaluate these theories has not grown at the same pace. Although laboratory animals have been widely used as models at the organism level, they have been less appropriate for addressing issues at the population level. However, farm animal populations can provide empirical models to study infectious diseases at the population level.

Distribution and possible transmission of ampicillin- and nalidixic acid-resistant Escherichia coli within the broiler industry

This study was performed to determine the origin and transmission of beta-lactam- and (fluoro)quinolone-resistant Escherichia coli in healthy, untreated broiler flocks. We focused on the dynamics of bacteria resistant to critically important antimicrobials for public and veterinary health in view of the possible link between antimicrobial resistant bacteria in farm animals and humans. By processing faecal samples collected with the sock method in broiler parent and broiler flocks, E. coli resistant to ampicillin and nalidixic acid were frequently isolated, while resistance to ciprofloxacin was detected at a very low frequency, and resistance to cephalosporins was not detected. Similarly, resistance to ampicillin and nalidixic acid were the only phenotypes detected in a collection of clinical E. coli isolates associated with first-week-mortality in broiler parent chicks. Although antimicrobial resistant E. coli were genetically diverse by means of amplified fragment length polymorphism (AFLP) typing, indistinguishable isolates were present in different flocks, including isolates from broiler parent chicks, broiler parents and broilers. In the absence of apparent selective pressure, the genotypic heterogeneity that we describe is likely the consequence of multiple introductions of antimicrobial resistant bacteria into the production system. The confinement under which broilers are raised limits the possibilities of bacterial transmission among different flocks. Our findings are consistent with vertical transmission of ampicillin- and nalidixic acid-resistant E. coli through the broiler production system. The persistence of antimicrobial resistant E. coli in healthy, untreated chicken flocks emphasises the need of careful evaluation of therapeutic options at any level of the broiler production.

Changes in multidrug resistance of enteric bacteria following an intervention to reduce antimicrobial resistance in dairy calves

An intervention study was conducted to determine whether discontinuing the feeding of milk replacer medicated with oxytetracycline and neomycin to preweaned calves reduced antimicrobial resistance in Salmonella, Campylobacter, and Escherichia coli bacteria. Results demonstrated that the intervention did reduce multidrug resistance in these bacteria but that other factors also influenced multidrug resistance.

Longitudinal characterization of resistant Escherichia coli in fecal deposits from cattle fed subtherapeutic levels of antimicrobials

Model fecal deposits from cattle fed or not fed antimicrobial growth promoters were examined over 175 days in the field for growth and persistence of total Escherichia coli and numbers and proportions of ampicillin-resistant (Amp(r)) and tetracycline-resistant (Tet(r)) E. coli. In addition, genotypic diversity and the frequency of genetic determinants encoded by Amp(r) and Tet(r) E. coli were investigated. Cattle were fed diets containing chlortetracycline (44 ppm; A44 treatment group), chlortetracycline plus sulfamethazine (both at 44 ppm; AS700 treatment group), or no antibiotics (control). Fecal deposits were sampled 12 times over 175 days. Numbers of Tet(r) E. coli in A44 and AS700 deposits were higher (P < 0.001) than those of controls and represented up to 35.6% and 20.2% of total E. coli, respectively. A time-by-treatment interaction (P < 0.001) was observed for the numbers of Tet(r) and Amp(r) E. coli. Except for Amp(r) E. coli in control deposits, all E. coli numbers increased (P < 0.001) in deposits up to day 56. Even after 175 days, high Tet(r) E. coli numbers were detected in A44 and AS700 deposits [5.9 log(10) CFU (g dry matter)(-1) and 5.4 log(10) CFU (g dry matter)(-1), respectively]. E. coli genotypes, as determined by pulsed-field gel electrophoresis, were diverse and were influenced by the antimicrobial growth promoter and the sampling time. Of the determinants screened, bla(TEM1), tetA, tetB, tetC, sul1, and sul2 were frequently detected. Occurrence of determinants was influenced by the feeding of antimicrobials. Fecal deposits remain a source of resistant E. coli even after a considerable period of environmental exposure.

Investigation of public health issues by regional field disease investigation units

The conventional means of delivering animal health services to agricultural animal producers (private veterinary practitioners and state animal disease diagnostic laboratories) leave a gap where important regional disease problems are inefficiently addressed. This gap was successfully targeted by Dr. Clive Gay in the development of the Field Disease Investigation Unit (FDIU) for the northwestern region of the United States. The FDIU has also successfully targeted several zoonotic public health concerns and its success demonstrates the existence of a similar gap in the investigation and control of important public health issues including disseminated Salmonella clones and emergence of antimicrobial resistance.